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Sample records for pathway analysis hydrological

  1. Analysis of Hydrologic Properties Data

    International Nuclear Information System (INIS)

    Liu, H.H.; Ahlers, C.F.

    2001-01-01

    The purpose of this Analysis/Model Report (AMR) is to describe the methods used to determine hydrologic properties based on the available field data from the unsaturated zone at Yucca Mountain, Nevada. This is in accordance with the AMR Development Plan (DP) for U0090 Analysis of Hydrologic Properties Data (CRWMS M and O 1999c). Fracture and matrix properties are developed by compiling and analyzing available survey data from the Exploratory Studies Facility (ESF), Cross Drift of Enhanced Characterization of Repository Block (ECRB), and/or boreholes; air injection testing data from surface boreholes and from boreholes in ESF; in-situ measurements of water potential; and data from laboratory testing of core samples

  2. Network analysis applications in hydrology

    Science.gov (United States)

    Price, Katie

    2017-04-01

    Applied network theory has seen pronounced expansion in recent years, in fields such as epidemiology, computer science, and sociology. Concurrent development of analytical methods and frameworks has increased possibilities and tools available to researchers seeking to apply network theory to a variety of problems. While water and nutrient fluxes through stream systems clearly demonstrate a directional network structure, the hydrological applications of network theory remain under­explored. This presentation covers a review of network applications in hydrology, followed by an overview of promising network analytical tools that potentially offer new insights into conceptual modeling of hydrologic systems, identifying behavioral transition zones in stream networks and thresholds of dynamical system response. Network applications were tested along an urbanization gradient in Atlanta, Georgia, USA. Peachtree Creek and Proctor Creek. Peachtree Creek contains a nest of five long­term USGS streamflow and water quality gages, allowing network application of long­term flow statistics. The watershed spans a range of suburban and heavily urbanized conditions. Summary flow statistics and water quality metrics were analyzed using a suite of network analysis techniques, to test the conceptual modeling and predictive potential of the methodologies. Storm events and low flow dynamics during Summer 2016 were analyzed using multiple network approaches, with an emphasis on tomogravity methods. Results indicate that network theory approaches offer novel perspectives for understanding long­ term and event­based hydrological data. Key future directions for network applications include 1) optimizing data collection, 2) identifying "hotspots" of contaminant and overland flow influx to stream systems, 3) defining process domains, and 4) analyzing dynamic connectivity of various system components, including groundwater­surface water interactions.

  3. HYDROLOGIC ANALYSIS, HONOLULU COUNTY, HI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  4. HYDROLOGIC ANALYSIS, MONO COUNTY, CA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  5. HYDROLOGIC ANALYSIS, EDGEFIELD COUNTY, SC

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  6. Hydrologic Analysis of Fort Leonard Wood, Missouri

    Science.gov (United States)

    2015-08-01

    drainage areas are different, hydrological analysis will be conducted on the two basins individually. The results of the two analyses will be combined to...ER D C TR -1 5- 4 Environmental Quality and Installations Hydrologic Analysis of Fort Leonard Wood, Missouri En gi ne er R es ea rc h...Environmental Quality and Installations ERDC TR-15-4 August 2015 Hydrologic Analysis of Fort Leonard Wood, Missouri Michael L. Follum, Darla C. McVan

  7. Analysis of Hydrologic Properties Data

    Energy Technology Data Exchange (ETDEWEB)

    H. H. Liu

    2003-04-03

    This Model Report describes the methods used to determine hydrologic properties based on the available field data from the unsaturated zone (UZ) at Yucca Mountain, Nevada, and documents validation of the active fracture model (AFM). This work was planned in ''Technical Work Plan (TWP) for: Performance Assessment Unsaturated Zone'' (BSC 2002 [160819], Sections 1.10.2, 1.10.3, and 1.10.8). Fracture and matrix properties are developed by analyzing available survey data from the Exploratory Studies Facility (ESF), Cross Drift for Enhanced Characterization of Repository Block (ECRB), and/or boreholes; air injection testing data from surface boreholes and from boreholes in the ESF; and data from laboratory testing of core samples. The AFM is validated on the basis of experimental observations and theoretical developments. This report is a revision of an Analysis Model Report, under the same title, as a scientific analysis with Document Identifier number ANL-NBS-HS-000002 (BSC 2001 [159725]) that did not document activities to validate the AFM. The principal purpose of this work is to provide representative uncalibrated estimates of fracture and matrix properties for use in the model report ''Calibrated Properties Model'' (BSC 2003 [160240]). The present work also provides fracture geometry properties for generating dual permeability grids as documented in the Scientific Analysis Report, ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (BSC 2003 [160109]). The resulting calibrated property sets and numerical grids from these reports will be used in the Unsaturated Zone Flow and Transport Process Model (UZ Model), and Total System Performance Assessment (TSPA) models. The fracture and matrix properties developed in this Model Report include: (1) Fracture properties (frequency, permeability, van Genuchten a and m parameters, aperture, porosity, and interface area) for each UZ Model layer; (2

  8. Hydrological analysis in R: Topmodel and beyond

    Science.gov (United States)

    Buytaert, W.; Reusser, D.

    2011-12-01

    R is quickly gaining popularity in the hydrological sciences community. The wide range of statistical and mathematical functionality makes it an excellent tool for data analysis, modelling and uncertainty analysis. Topmodel was one of the first hydrological models being implemented as an R package and distributed through R's own distribution network CRAN. This facilitated pre- and postprocessing of data such as parameter sampling, calculation of prediction bounds, and advanced visualisation. However, apart from these basic functionalities, the package did not use many of the more advanced features of the R environment, especially from R's object oriented functionality. With R's increasing expansion in arenas such as high performance computing, big data analysis, and cloud services, we revisit the topmodel package, and use it as an example of how to build and deploy the next generation of hydrological models. R provides a convenient environment and attractive features to build and couple hydrological - and in extension other environmental - models, to develop flexible and effective data assimilation strategies, and to take the model beyond the individual computer by linking into cloud services for both data provision and computing. However, in order to maximise the benefit of these approaches, it will be necessary to adopt standards and ontologies for model interaction and information exchange. Some of those are currently being developed, such as the OGC web processing standards, while other will need to be developed.

  9. Pathway analysis of IMC

    DEFF Research Database (Denmark)

    Skrypnyuk, Nataliya; Nielson, Flemming; Pilegaard, Henrik

    2009-01-01

    We present the ongoing work on the pathway analysis of a stochastic calculus. Firstly we present a particular stochastic calculus that we have chosen for our modeling - the Interactive Markov Chains calculus, IMC for short. After that we specify a few restrictions that we have introduced into the...... into the syntax of IMC in order to make our analysis feasible. Finally we describe the analysis itself together with several theoretical results that we have proved for it.......We present the ongoing work on the pathway analysis of a stochastic calculus. Firstly we present a particular stochastic calculus that we have chosen for our modeling - the Interactive Markov Chains calculus, IMC for short. After that we specify a few restrictions that we have introduced...

  10. Stochastic time series analysis of hydrology data for water resources

    Science.gov (United States)

    Sathish, S.; Khadar Babu, S. K.

    2017-11-01

    The prediction to current publication of stochastic time series analysis in hydrology and seasonal stage. The different statistical tests for predicting the hydrology time series on Thomas-Fiering model. The hydrology time series of flood flow have accept a great deal of consideration worldwide. The concentration of stochastic process areas of time series analysis method are expanding with develop concerns about seasonal periods and global warming. The recent trend by the researchers for testing seasonal periods in the hydrologic flowseries using stochastic process on Thomas-Fiering model. The present article proposed to predict the seasonal periods in hydrology using Thomas-Fiering model.

  11. HYDROLOGIC ANALYSIS, SANTA CRUZ COUNTY, CA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  12. A Bayesian Analysis of the Flood Frequency Hydrology Concept

    Science.gov (United States)

    2016-02-01

    ERDC/CHL CHETN-X-1 February 2016 Approved for public release; distribution is unlimited. A Bayesian Analysis of the Flood Frequency Hydrology ...flood frequency hydrology concept as a formal probabilistic-based means by which to coherently combine and also evaluate the worth of different types...and development. INTRODUCTION: Merz and Blöschl (2008a,b) proposed the concept of flood frequency hydrology , which emphasizes the importance of

  13. Hydrology

    Science.gov (United States)

    Sharp, John M.

    1977-01-01

    Lists many recent research projects in hydrology, including flow in fractured media, improvements in remote-sensing techniques, effects of urbanization on water resources, and developments in drainage basins. (MLH)

  14. Hydrology

    International Nuclear Information System (INIS)

    Obando G, E.

    1989-01-01

    Isotopical techniques are used in hydrology area for exploration, evaluation and exploration of water investigation. These techniques have been used successfully and are often the best or only means for providing certain hydrogeological parameters

  15. Hydrology

    Science.gov (United States)

    Brutsaert, Wilfried

    2005-08-01

    Water in its different forms has always been a source of wonder, curiosity and practical concern for humans everywhere. Hydrology - An Introduction presents a coherent introduction to the fundamental principles of hydrology, based on the course that Wilfried Brutsaert has taught at Cornell University for the last thirty years. Hydrologic phenomena are dealt with at spatial and temporal scales at which they occur in nature. The physics and mathematics necessary to describe these phenomena are introduced and developed, and readers will require a working knowledge of calculus and basic fluid mechanics. The book will be invaluable as a textbook for entry-level courses in hydrology directed at advanced seniors and graduate students in physical science and engineering. In addition, the book will be more broadly of interest to professional scientists and engineers in hydrology, environmental science, meteorology, agronomy, geology, climatology, oceanology, glaciology and other earth sciences. Emphasis on fundamentals Clarification of the underlying physical processes Applications of fluid mechanics in the natural environment

  16. Hydrologi

    DEFF Research Database (Denmark)

    Burcharth, Hans F.

    Hydro1ogi er den videnskab, der omhand1er jordens vand, dets forekomst, cirku1ation og forde1ing, dets kemiske og fysiske egenskaber samt indvirkning på omgivelserne, herunder dets relation ti1 alt liv på jorden. Således lyder en b1andt mange definitioner på begrebet hydrologi, og som man kan se...

  17. Controls on shallow landslide initiation: Diverse hydrologic pathways, 3D failure geometries, and unsaturated soil suctions

    Science.gov (United States)

    Reid, Mark; Iverson, Richard; Brien, Dianne; Iverson, Neal; LaHusen, Richard; Logan, Matthew

    2017-04-01

    Shallow landslides and ensuing debris flows are a common hazard worldwide, yet forecasting their initiation at a specific site is challenging. These challenges arise, in part, from diverse near-surface hydrologic pathways under different wetting conditions, 3D failure geometries, and the effects of suction in partially saturated soils. Simplistic hydrologic models typically used for regional hazard assessment disregard these complexities. As an alterative to field studies where the effects of these governing factors can be difficult to isolate, we used the USGS debris-flow flume to conduct controlled, field-scale landslide initiation experiments. Using overhead sprinklers or groundwater injectors on the flume bed, we triggered failures using three different wetting conditions: groundwater inflow from below, prolonged moderate-intensity precipitation, and bursts of high-intensity precipitation. Failures occurred in 6 m3 (0.65-m thick and 2-m wide) prisms of loamy sand on a 31° slope; these field-scale failures enabled realistic incorporation of nonlinear scale-dependent effects such as soil suction. During the experiments, we monitored soil deformation, variably saturated pore pressures, and moisture changes using ˜50 sensors sampling at 20 Hz. From ancillary laboratory tests, we determined shear strength, saturated hydraulic conductivities, and unsaturated moisture retention characteristics. The three different wetting conditions noted above led to different hydrologic pathways and influenced instrumental responses and failure timing. During groundwater injection, pore-water pressures increased from the bed of the flume upwards into the sediment, whereas prolonged moderate infiltration wet the sediment from the ground surface downward. In both cases, pore pressures acting on the impending failure surface slowly rose until abrupt failure. In contrast, a burst of intense sprinkling caused rapid failure without precursory development of widespread positive pore

  18. Identifying and assessing uncertainty in hydrological pathways: a novel approach to end member mixing in a Scottish agricultural catchment

    Science.gov (United States)

    Soulsby, C.; Petry, J.; Brewer, M. J.; Dunn, S. M.; Ott, B.; Malcolm, I. A.

    2003-04-01

    A hydrograph separation based upon end member mixing was carried out to assess the relative importance of the hydrological pathways providing the main sources of runoff during five storm events in a 14.5 km 2 agricultural catchment in north east Scotland. The method utilised event specific end member chemistries to differentiate three catchment-scale hydrological pathways on the basis of observed Si and NO 3-N concentrations in sampled source waters. These were overland flow (OF) (low Si and intermediate NO 3-N); subsurface storm flow (high Si and high NO 3-N) and groundwater flow (high Si and intermediate NO 3-N). The hydrograph separation explicitly accounted for uncertainty in the spatial and temporal variation in end member chemistry using Bayesian statistical methods which assumed that each end member arose from a bivariate normal distribution whose mean vectors and co-variance matrices could be estimated. Markov Chain-Monte Carlo methods were used to model the average and 95 percentile maximum and minimum contributions that each end member made to stream water samples during storm events. Although there is large uncertainty over the contributions of each end member to specific events, the analysis produced hydrograph separations that were broadly believable on the basis of hydrometric observations in the catchment. Moreover, by using event specific end member compositions, the method appeared sensitive to the unique combination of event characteristics, antecedent conditions and seasonality in terms of producing feasible separations for very different events. It is concluded that OF generally dominates the storm peak and provides the main flow path by which P is transferred to stream channels during storm events, whilst subsurface storm flows usually dominate the storm hydrograph volumetrically and route NO 3-rich soil water into streams. Consequently, nutrient enrichment in such streams is largely mediated by event-based hydrological flow paths, a finding

  19. Multi-model analysis in hydrological prediction

    Science.gov (United States)

    Lanthier, M.; Arsenault, R.; Brissette, F.

    2017-12-01

    Hydrologic modelling, by nature, is a simplification of the real-world hydrologic system. Therefore ensemble hydrological predictions thus obtained do not present the full range of possible streamflow outcomes, thereby producing ensembles which demonstrate errors in variance such as under-dispersion. Past studies show that lumped models used in prediction mode can return satisfactory results, especially when there is not enough information available on the watershed to run a distributed model. But all lumped models greatly simplify the complex processes of the hydrologic cycle. To generate more spread in the hydrologic ensemble predictions, multi-model ensembles have been considered. In this study, the aim is to propose and analyse a method that gives an ensemble streamflow prediction that properly represents the forecast probabilities and reduced ensemble bias. To achieve this, three simple lumped models are used to generate an ensemble. These will also be combined using multi-model averaging techniques, which generally generate a more accurate hydrogram than the best of the individual models in simulation mode. This new predictive combined hydrogram is added to the ensemble, thus creating a large ensemble which may improve the variability while also improving the ensemble mean bias. The quality of the predictions is then assessed on different periods: 2 weeks, 1 month, 3 months and 6 months using a PIT Histogram of the percentiles of the real observation volumes with respect to the volumes of the ensemble members. Initially, the models were run using historical weather data to generate synthetic flows. This worked for individual models, but not for the multi-model and for the large ensemble. Consequently, by performing data assimilation at each prediction period and thus adjusting the initial states of the models, the PIT Histogram could be constructed using the observed flows while allowing the use of the multi-model predictions. The under-dispersion has been

  20. Nonstationary Hydrological Frequency Analysis: Theoretical Methods and Application Challenges

    Science.gov (United States)

    Xiong, L.

    2014-12-01

    Because of its great implications in the design and operation of hydraulic structures under changing environments (either climate change or anthropogenic changes), nonstationary hydrological frequency analysis has become so important and essential. Two important achievements have been made in methods. Without adhering to the consistency assumption in the traditional hydrological frequency analysis, the time-varying probability distribution of any hydrological variable can be established by linking the distribution parameters to some covariates such as time or physical variables with the help of some powerful tools like the Generalized Additive Model of Location, Scale and Shape (GAMLSS). With the help of copulas, the multivariate nonstationary hydrological frequency analysis has also become feasible. However, applications of the nonstationary hydrological frequency formula to the design and operation of hydraulic structures for coping with the impacts of changing environments in practice is still faced with many challenges. First, the nonstationary hydrological frequency formulae with time as covariate could only be extrapolated for a very short time period beyond the latest observation time, because such kind of formulae is not physically constrained and the extrapolated outcomes could be unrealistic. There are two physically reasonable methods that can be used for changing environments, one is to directly link the quantiles or the distribution parameters to some measureable physical factors, and the other is to use the derived probability distributions based on hydrological processes. However, both methods are with a certain degree of uncertainty. For the design and operation of hydraulic structures under changing environments, it is recommended that design results of both stationary and nonstationary methods be presented together and compared with each other, to help us understand the potential risks of each method.

  1. Uncertainty Assessment of Hydrological Frequency Analysis Using Bootstrap Method

    Directory of Open Access Journals (Sweden)

    Yi-Ming Hu

    2013-01-01

    Full Text Available The hydrological frequency analysis (HFA is the foundation for the hydraulic engineering design and water resources management. Hydrological extreme observations or samples are the basis for HFA; the representativeness of a sample series to the population distribution is extremely important for the estimation reliability of the hydrological design value or quantile. However, for most of hydrological extreme data obtained in practical application, the size of the samples is usually small, for example, in China about 40~50 years. Generally, samples with small size cannot completely display the statistical properties of the population distribution, thus leading to uncertainties in the estimation of hydrological design values. In this paper, a new method based on bootstrap is put forward to analyze the impact of sampling uncertainty on the design value. By bootstrap resampling technique, a large number of bootstrap samples are constructed from the original flood extreme observations; the corresponding design value or quantile is estimated for each bootstrap sample, so that the sampling distribution of design value is constructed; based on the sampling distribution, the uncertainty of quantile estimation can be quantified. Compared with the conventional approach, this method provides not only the point estimation of a design value but also quantitative evaluation on uncertainties of the estimation.

  2. A sensitivity analysis of regional and small watershed hydrologic models

    Science.gov (United States)

    Ambaruch, R.; Salomonson, V. V.; Simmons, J. W.

    1975-01-01

    Continuous simulation models of the hydrologic behavior of watersheds are important tools in several practical applications such as hydroelectric power planning, navigation, and flood control. Several recent studies have addressed the feasibility of using remote earth observations as sources of input data for hydrologic models. The objective of the study reported here was to determine how accurately remotely sensed measurements must be to provide inputs to hydrologic models of watersheds, within the tolerances needed for acceptably accurate synthesis of streamflow by the models. The study objective was achieved by performing a series of sensitivity analyses using continuous simulation models of three watersheds. The sensitivity analysis showed quantitatively how variations in each of 46 model inputs and parameters affect simulation accuracy with respect to five different performance indices.

  3. Hydrologic monitoring and analysis in the Sundarbans mangrove ecosystem, Bangladesh

    Science.gov (United States)

    Wahid, Shahriar Md.; Babel, Mukand S.; Bhuiyan, Abdur Rahman

    2007-01-01

    SummaryThe unique habitat of the Sundarbans mangrove ecosystem is dependent upon the hydrological regime. Therefore, a comprehensive study to understand the hydrologic behaviour and the changes that have taken place due to anthropogenic activities in and around the area is fundamental to the management of natural resources and environment. In the past, ad hoc and uncoordinated efforts were made due to the inherent inaccessibility and high cost of data collection. The present article documents the results of the hydrologic monitoring, modelling and analysis in the Sundarbans. The study results show that the annual maximum tidal range has increased by about 0.75 m in the eastern and central parts during the last two decades. About 60% area remains in higher salinity condition (>20 ppt) for at least 1.5 months in a year. Organic pollution in the waterways is within the Environmental Quality Standard (EQS) of Bangladesh with the average Dissolved Oxygen (DO) of 5.99 mg/L. Total Ammonia, Nitrate (NO 3-N) and Phosphate (PO 4-P) level are present in sufficient quantity for the aquatic life to survive and are within EQS limit. Lead and Chromium occasionally exceed EQS limit especially along the large barge routes in the western part. The data and information presented in the paper will serve as a baseline for future hydrological and environmental studies.

  4. An approach to quantum-computational hydrologic inverse analysis.

    Science.gov (United States)

    O'Malley, Daniel

    2018-05-02

    Making predictions about flow and transport in an aquifer requires knowledge of the heterogeneous properties of the aquifer such as permeability. Computational methods for inverse analysis are commonly used to infer these properties from quantities that are more readily observable such as hydraulic head. We present a method for computational inverse analysis that utilizes a type of quantum computer called a quantum annealer. While quantum computing is in an early stage compared to classical computing, we demonstrate that it is sufficiently developed that it can be used to solve certain subsurface flow problems. We utilize a D-Wave 2X quantum annealer to solve 1D and 2D hydrologic inverse problems that, while small by modern standards, are similar in size and sometimes larger than hydrologic inverse problems that were solved with early classical computers. Our results and the rapid progress being made with quantum computing hardware indicate that the era of quantum-computational hydrology may not be too far in the future.

  5. Evaluating Hydrologic Response of an Agricultural Watershed for Watershed Analysis

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Jha

    2011-06-01

    Full Text Available This paper describes the hydrological assessment of an agricultural watershed in the Midwestern United States through the use of a watershed scale hydrologic model. The Soil and Water Assessment Tool (SWAT model was applied to the Maquoketa River watershed, located in northeast Iowa, draining an agriculture intensive area of about 5,000 km2. The inputs to the model were obtained from the Environmental Protection Agency’s geographic information/database system called Better Assessment Science Integrating Point and Nonpoint Sources (BASINS. Meteorological input, including precipitation and temperature from six weather stations located in and around the watershed, and measured streamflow data at the watershed outlet, were used in the simulation. A sensitivity analysis was performed using an influence coefficient method to evaluate surface runoff and baseflow variations in response to changes in model input hydrologic parameters. The curve number, evaporation compensation factor, and soil available water capacity were found to be the most sensitive parameters among eight selected parameters. Model calibration, facilitated by the sensitivity analysis, was performed for the period 1988 through 1993, and validation was performed for 1982 through 1987. The model was found to explain at least 86% and 69% of the variability in the measured streamflow data for calibration and validation periods, respectively. This initial hydrologic assessment will facilitate future modeling applications using SWAT to the Maquoketa River watershed for various watershed analyses, including watershed assessment for water quality management, such as total maximum daily loads, impacts of land use and climate change, and impacts of alternate management practices.

  6. Statistical analysis of hydrologic data for Yucca Mountain

    International Nuclear Information System (INIS)

    Rutherford, B.M.; Hall, I.J.; Peters, R.R.; Easterling, R.G.; Klavetter, E.A.

    1992-02-01

    The geologic formations in the unsaturated zone at Yucca Mountain are currently being studied as the host rock for a potential radioactive waste repository. Data from several drill holes have been collected to provide the preliminary information needed for planning site characterization for the Yucca Mountain Project. Hydrologic properties have been measured on the core samples and the variables analyzed here are thought to be important in the determination of groundwater travel times. This report presents a statistical analysis of four hydrologic variables: saturated-matrix hydraulic conductivity, maximum moisture content, suction head, and calculated groundwater travel time. It is important to modelers to have as much information about the distribution of values of these variables as can be obtained from the data. The approach taken in this investigation is to (1) identify regions at the Yucca Mountain site that, according to the data, are distinctly different; (2) estimate the means and variances within these regions; (3) examine the relationships among the variables; and (4) investigate alternative statistical methods that might be applicable when more data become available. The five different functional stratigraphic units at three different locations are compared and grouped into relatively homogeneous regions. Within these regions, the expected values and variances associated with core samples of different sizes are estimated. The results provide a rough estimate of the distribution of hydrologic variables for small core sections within each region

  7. Primary Metabolic Pathways and Metabolic Flux Analysis

    DEFF Research Database (Denmark)

    Villadsen, John

    2015-01-01

    his chapter introduces the metabolic flux analysis (MFA) or stoichiometry-based MFA, and describes the quantitative basis for MFA. It discusses the catabolic pathways in which free energy is produced to drive the cell-building anabolic pathways. An overview of these primary pathways provides...... the reader who is primarily trained in the engineering sciences with atleast a preliminary introduction to biochemistry and also shows how carbon is drained off the catabolic pathways to provide precursors for cell mass building and sometimes for important industrial products. The primary pathways...... to be examined in the following are: glycolysis, primarily by the EMP pathway, but other glycolytic pathways is also mentioned; fermentative pathways in which the redox generated in the glycolytic reactions are consumed; reactions in the tricarboxylic acid (TCA) cycle, which produce biomass precursors and redox...

  8. Hydrologic classification of rivers based on cluster analysis of dimensionless hydrologic signatures: Applications for environmental instream flows

    Science.gov (United States)

    Praskievicz, S. J.; Luo, C.

    2017-12-01

    Classification of rivers is useful for a variety of purposes, such as generating and testing hypotheses about watershed controls on hydrology, predicting hydrologic variables for ungaged rivers, and setting goals for river management. In this research, we present a bottom-up (based on machine learning) river classification designed to investigate the underlying physical processes governing rivers' hydrologic regimes. The classification was developed for the entire state of Alabama, based on 248 United States Geological Survey (USGS) stream gages that met criteria for length and completeness of records. Five dimensionless hydrologic signatures were derived for each gage: slope of the flow duration curve (indicator of flow variability), baseflow index (ratio of baseflow to average streamflow), rising limb density (number of rising limbs per unit time), runoff ratio (ratio of long-term average streamflow to long-term average precipitation), and streamflow elasticity (sensitivity of streamflow to precipitation). We used a Bayesian clustering algorithm to classify the gages, based on the five hydrologic signatures, into distinct hydrologic regimes. We then used classification and regression trees (CART) to predict each gaged river's membership in different hydrologic regimes based on climatic and watershed variables. Using existing geospatial data, we applied the CART analysis to classify ungaged streams in Alabama, with the National Hydrography Dataset Plus (NHDPlus) catchment (average area 3 km2) as the unit of classification. The results of the classification can be used for meeting management and conservation objectives in Alabama, such as developing statewide standards for environmental instream flows. Such hydrologic classification approaches are promising for contributing to process-based understanding of river systems.

  9. Analysis of Geothermal Pathway in the Metamorphic Area, Northeastern Taiwan

    Science.gov (United States)

    Wang, C.; Wu, M. Y.; Song, S. R.; Lo, W.

    2016-12-01

    A quantitative measure by play fairway analysis in geothermal energy development is an important tool that can present the probability map of potential resources through the uncertainty studies in geology for early phase decision making purpose in the related industries. While source, pathway, and fluid are the three main geologic factors in traditional geothermal systems, identifying the heat paths is critical to reduce drilling cost. Taiwan is in East Asia and the western edge of Pacific Ocean, locating on the convergent boundary of Eurasian Plate and Philippine Sea Plate with many earthquake activities. This study chooses a metamorphic area in the western corner of Yi-Lan plain in northeastern Taiwan with high geothermal potential and several existing exploration sites. Having high subsurface temperature gradient from the mountain belts, and plenty hydrologic systems through thousands of millimeters annual precipitation that would bring up heats closer to the surface, current geothermal conceptual model indicates the importance of pathway distribution which affects the possible concentration of extractable heat location. The study conducts surface lineation analysis using analytic hierarchy process to determine weights among various fracture types for their roles in geothermal pathways, based on the information of remote sensing data, published geologic maps and field work measurements, to produce regional fracture distribution probability map. The results display how the spatial distribution of pathways through various fractures could affect geothermal systems, identify the geothermal plays using statistical data analysis, and compare against the existing drilling data.

  10. HydroClimATe: hydrologic and climatic analysis toolkit

    Science.gov (United States)

    Dickinson, Jesse; Hanson, Randall T.; Predmore, Steven K.

    2014-01-01

    The potential consequences of climate variability and climate change have been identified as major issues for the sustainability and availability of the worldwide water resources. Unlike global climate change, climate variability represents deviations from the long-term state of the climate over periods of a few years to several decades. Currently, rich hydrologic time-series data are available, but the combination of data preparation and statistical methods developed by the U.S. Geological Survey as part of the Groundwater Resources Program is relatively unavailable to hydrologists and engineers who could benefit from estimates of climate variability and its effects on periodic recharge and water-resource availability. This report documents HydroClimATe, a computer program for assessing the relations between variable climatic and hydrologic time-series data. HydroClimATe was developed for a Windows operating system. The software includes statistical tools for (1) time-series preprocessing, (2) spectral analysis, (3) spatial and temporal analysis, (4) correlation analysis, and (5) projections. The time-series preprocessing tools include spline fitting, standardization using a normal or gamma distribution, and transformation by a cumulative departure. The spectral analysis tools include discrete Fourier transform, maximum entropy method, and singular spectrum analysis. The spatial and temporal analysis tool is empirical orthogonal function analysis. The correlation analysis tools are linear regression and lag correlation. The projection tools include autoregressive time-series modeling and generation of many realizations. These tools are demonstrated in four examples that use stream-flow discharge data, groundwater-level records, gridded time series of precipitation data, and the Multivariate ENSO Index.

  11. Identification of hydrologic and geochemical pathways using high frequency sampling, REE aqueous sampling and soil characterization at Koiliaris Critical Zone Observatory, Crete

    Energy Technology Data Exchange (ETDEWEB)

    Moraetis, Daniel, E-mail: moraetis@mred.tuc.gr [Department of Environmental Engineering, Technical University of Crete, 73100 Chania (Greece); Stamati, Fotini; Kotronakis, Manolis; Fragia, Tasoula; Paranychnianakis, Nikolaos; Nikolaidis, Nikolaos P. [Department of Environmental Engineering, Technical University of Crete, 73100 Chania (Greece)

    2011-06-15

    Highlights: > Identification of hydrological and geochemical pathways within a complex watershed. > Water increased N-NO{sub 3} concentration and E.C. values during flash flood events. > Soil degradation and impact on water infiltration within the Koiliaris watershed. > Analysis of Rare Earth Elements in water bodies for identification of karstic water. - Abstract: Koiliaris River watershed is a Critical Zone Observatory that represents severely degraded soils due to intensive agricultural activities and biophysical factors. It has typical Mediterranean soils under the imminent threat of desertification which is expected to intensify due to projected climate change. High frequency hydro-chemical monitoring with targeted sampling for Rare Earth Elements (REE) analysis of different water bodies and geochemical characterization of soils were used for the identification of hydrologic and geochemical pathways. The high frequency monitoring of water chemical data highlighted the chemical alterations of water in Koiliaris River during flash flood events. Soil physical and chemical characterization surveys were used to identify erodibility patterns within the watershed and the influence of soils on surface and ground water chemistry. The methodology presented can be used to identify the impacts of degraded soils to surface and ground water quality as well as in the design of methods to minimize the impacts of land use practices.

  12. Bridging arctic pathways: Integrating hydrology, geomorphology and remote sensing in the north

    Science.gov (United States)

    Trochim, Erin D.

    This work presents improved approaches for integrating patterns and processes within hydrology, geomorphology, ecology and permafrost on Arctic landscapes. Emphasis was placed on addressing fundamental interdisciplinary questions using robust, repeatable methods. Water tracks were examined in the foothills of the Brooks Range to ascertain their role within the range of features that transport water in Arctic regions. Classes of water tracks were developed using multiple factor analysis based on their geomorphic, soil and vegetation characteristics. These classes were validated to verify that they were repeatable. Water tracks represented a broad spectrum of patterns and processes primarily driven by surficial geology. This research demonstrated a new approach to better understanding regional hydrological patterns. The locations of the water track classes were mapped using a combination method where intermediate processing of spectral classifications, texture and topography were fed into random forests to identify the water track classes. Overall, the water track classes were best visualized where they were the most discrete from the background landscape in terms of both shape and content. Issues with overlapping and imbalances between water track classes were the biggest challenges. Resolving the spatial locations of different water tracks represents a significant step forward for understanding periglacial landscape dynamics. Leaf area index (LAI) calculations using the gap-method were optimized using normalized difference vegetation index (NDVI) as input for both WorldView-2 and Landsat-7 imagery. The study design used groups to separate the effects of surficial drainage networks and the relative magnitude of change in NDVI over time. LAI values were higher for the WorldView-2 data and for each sensor and group combination the distribution of LAI values was unique. This study indicated that there are tradeoffs between increased spatial resolution and the ability

  13. Tritium migration at the Gasbuggy site: Evaluation of possible hydrologic pathways

    International Nuclear Information System (INIS)

    Chapman, J.; Mihevc, T.; Lyles, B.

    1996-09-01

    An underground nuclear test named Gasbuggy was conducted in northwestern New Mexico in 1967. Subsequent groundwater monitoring in an overlying aquifer by the U.S. Environmental Protection Agency revealed increasing levels of tritium in monitoring well EPNG 10-36, located 132 m from the test, suggesting migration of contaminants from the nuclear cavity. There are three basic scenarios that could explain the occurrence of tritium in well 10-36: (1) introduction of tritium into the well from the land surface, (2) migration of tritium through the Ojo Alamo Formation, and (3) migration through the Pictured Cliffs Formation. The two subsurface transport scenarios were evaluated with a travel time analysis. In one, transport occurs to the Ojo Alamo sandstone either up the emplacement hole or through fractures created by the blast, and then laterally through the aquifer to the monitoring well. In the other, lateral transport occurs through fractures in the underlying Pictured Cliffs detonation horizon and then migrates up the monitoring well through plugged casing connecting the two formations. The travel time analysis indicates that the hydraulic conductivity measured in the Ojo Alamo Formation is too low for lateral transport to account for the observed arrival of tritium at the monitoring well. This suggests transport either through fractures intersecting the Ojo Alamo close to well EPNG 10-36, or through fractures in the Pictured Cliffs and up through the bottom plug in the well. The transport scenarios were investigated using hydrologic logging techniques and sampling at the monitoring well, with the fieldwork conducted after the removal of a string of 0.05-m-diameter tubing that had previously provided the only monitoring access

  14. Analysis of Hydrological Sensitivity for Flood Risk Assessment

    Directory of Open Access Journals (Sweden)

    Sanjay Kumar Sharma

    2018-02-01

    Full Text Available In order for the Indian government to maximize Integrated Water Resource Management (IWRM, the Brahmaputra River has played an important role in the undertaking of the Pilot Basin Study (PBS due to the Brahmaputra River’s annual regional flooding. The selected Kulsi River—a part of Brahmaputra sub-basin—experienced severe floods in 2007 and 2008. In this study, the Rainfall-Runoff-Inundation (RRI hydrological model was used to simulate the recent historical flood in order to understand and improve the integrated flood risk management plan. The ultimate objective was to evaluate the sensitivity of hydrologic simulation using different Digital Elevation Model (DEM resources, coupled with DEM smoothing techniques, with a particular focus on the comparison of river discharge and flood inundation extent. As a result, the sensitivity analysis showed that, among the input parameters, the RRI model is highly sensitive to Manning’s roughness coefficient values for flood plains, followed by the source of the DEM, and then soil depth. After optimizing its parameters, the simulated inundation extent showed that the smoothing filter was more influential than its simulated discharge at the outlet. Finally, the calibrated and validated RRI model simulations agreed well with the observed discharge and the Moderate Imaging Spectroradiometer (MODIS-detected flood extents.

  15. Hydrologic Futures: Using Scenario Analysis to Evaluate Impacts of Forecasted Land Use Change on Hydrologic Services

    Science.gov (United States)

    Land cover and land use changes can substantially alter hydrologic ecosystem services. Water availability and quality can change with modifications to the type or amount of surface vegetation, the permeability of soil and other surfaces, and the introduction of contaminants throu...

  16. Ensemble Analysis of Variational Assimilation of Hydrologic and Hydrometeorological Data into Distributed Hydrologic Model

    Science.gov (United States)

    Lee, H.; Seo, D.; Koren, V.

    2008-12-01

    A prototype 4DVAR (four-dimensional variational) data assimilator for gridded Sacramento soil-moisture accounting and kinematic-wave routing models in the Hydrology Laboratory's Research Distributed Hydrologic Model (HL-RDHM) has been developed. The prototype assimilates streamflow and in-situ soil moisture data and adjusts gridded precipitation and climatological potential evaporation data to reduce uncertainty in the model initial conditions for improved monitoring and prediction of streamflow and soil moisture at the outlet and interior locations within the catchment. Due to large degrees of freedom involved, data assimilation (DA) into distributed hydrologic models is complex. To understand and assess sensitivity of the performance of DA to uncertainties in the model initial conditions and in the data, two synthetic experiments have been carried out in an ensemble framework. Results from the synthetic experiments shed much light on the potential and limitations with DA into distributed models. For initial real-world assessment, the prototype DA has also been applied to the headwater basin at Eldon near the Oklahoma-Arkansas border. We present these results and describe the next steps.

  17. A strategy for evaluating pathway analysis methods.

    Science.gov (United States)

    Yu, Chenggang; Woo, Hyung Jun; Yu, Xueping; Oyama, Tatsuya; Wallqvist, Anders; Reifman, Jaques

    2017-10-13

    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth

  18. Pathway analysis: State of the art

    Directory of Open Access Journals (Sweden)

    Miguel Angel eGarcía-Campos

    2015-12-01

    Full Text Available Pathway analysis is a set of widely used tools for research in life sciences intended to give meaning to high-throughput biological data. The methodology of these tools settles in the gathering and usage of knowledge that comprise biomolecular functioning, coupled with statistical testing and other algorithms. Despite their wide employment, pathway analysis foundations and overall background may not be fully understood, leading to misinterpretation of analysis results. This review attempts to comprise the fundamental knowledge to take into consideration when using pathway analysis as a hypothesis generation tool. We discuss the key elements that are part of these methodologies, their capabilities and current deficiencies. We also present an overview of current and all-time popular methods, highlighting different classes across them. In doing so, we show the exploding diversity of methods that pathway analysis encompasses, point out commonly overlooked caveats, and direct attention to a potential new class of methods that attempt to zoom the analysis scope to the sample scale.

  19. Simplified analysis for liquid pathway studies

    International Nuclear Information System (INIS)

    Codell, R.B.

    1984-08-01

    The analysis of the potential contamination of surface water via groundwater contamination from severe nuclear accidents is routinely calculated during licensing reviews. This analysis is facilitated by the methods described in this report, which is codified into a BASIC language computer program, SCREENLP. This program performs simplified calculations for groundwater and surface water transport and calculates population doses to potential users for the contaminated water irrespective of possible mitigation methods. The results are then compared to similar analyses performed using data for the generic sites in NUREG-0440, Liquid Pathway Generic Study, to determine if the site being investigated would pose any unusual liquid pathway hazards

  20. Hydrological River Drought Analysis (Case Study: Lake Urmia Basin Rivers

    Directory of Open Access Journals (Sweden)

    Mohammad Nazeri Tahrudi

    2017-02-01

    Full Text Available Introduction: Drought from the hydrological viewpoint is a continuation of the meteorological drought that cause of the lack of surface water such as rivers, lakes, reservoirs and groundwater resources. This analysis, which is generally on the surface streams, reservoirs, lakes and groundwater, takes place as hydrological drought considered and studied. So the data on the quantity of flow of the rivers in this study is of fundamental importance. This data are included, level, flow, river flow is no term (5. Overall the hydrological drought studies are focused on annual discharges, maximum annual discharge or minimum discharge period. The most importance of this analysis is periodically during the course of the analysis remains a certain threshold and subthresholdrunoff volume fraction has created. In situations where water for irrigation or water of a river without any reservoir, is not adequate, the minimum flow analysis, the most important factor to be considered (4. The aim of this study is evaluatingthe statistical distributions of drought volume rivers data from the Urmia Lake’s rivers and its return period. Materials and Methods: Urmia Lake is a biggest and saltiest continued lake in Iran. The Lake Urmia basin is one of the most important basins in Iran region which is located in the North West of Iran. With an extent of 52700 square kilometers and an area equivalent to 3.21% of the total area of the country, This basin is located between the circuit of 35 degrees 40 minutes to 38 degrees 29 minutes north latitude and the meridian of 44 degrees 13 minutes to 47 degrees 53 minutes east longitude. In this study used the daily discharge data (m3s-1 of Urmia Lake Rivers. Extraction of river drought volume The drought durations were extracted from the daily discharge of 13 studied stations. The first mean year was calculated for each 365 days using the Eq 1 (14. (1 (For i=1,2,3,…,365 That Ki is aith mean year, Yijis ith day discharge in jth

  1. Evaluating Hydrologic Response of an Agricultural Watershed for Watershed Analysis

    OpenAIRE

    Manoj Kumar Jha

    2011-01-01

    This paper describes the hydrological assessment of an agricultural watershed in the Midwestern United States through the use of a watershed scale hydrologic model. The Soil and Water Assessment Tool (SWAT) model was applied to the Maquoketa River watershed, located in northeast Iowa, draining an agriculture intensive area of about 5,000 km2. The inputs to the model were obtained from the Environmental Protection Agency’s geographic information/database system called Better Assessment Science...

  2. Hydrological Analysis for Inflow Forecasting into Temengor Dam

    Science.gov (United States)

    Najid, MI; Sidek, LM; Hidayah, B.; Roseli, ZA

    2016-03-01

    These days, natural disaster such as flood is the main concern for hydrologists. One of solutions in understanding the reason of flood is by prediction of the event sooner than normal occurrence. One of the criteria is lead time or travel time that is important in the study of fresh waters and flood events. Therefore, estimation of lead or travel time for flood event can be beneficial primary information. The objective of this study is to estimate the lead time or travel time for outlet of Temengor dam in Malaysia. Tenaga Nasional Berhad (TNB) Sungai Perak dam operation has the main contribution on decision support for early water released and flood warning to authorities and locals resident for in the down streams area. For this study, hydrological analysis carried out will help to determine which years that give more rainfall contribution into the reservoir. Rainfall contribution of reservoir help to understanding rainfall distribution and peak discharge on that period. It also help for calibration of forecasting model system for better accuracy of flood hydrograph. There may be various methods to determine the rainfall contribution of catchment. The result has shown that, the rainfall contribution for Temengor catchment, is more on November in each year which is the monsoon season in Malaysia. TNB dam operational decision support systems can prepare and be more aware at this time for flood control and flood mitigation.

  3. Pathway cross-talk network analysis identifies critical pathways in neonatal sepsis.

    Science.gov (United States)

    Meng, Yu-Xiu; Liu, Quan-Hong; Chen, Deng-Hong; Meng, Ying

    2017-06-01

    Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis. Then, attract method was employed to explore the dysregulated pathways associated with neonatal sepsis. To determine the critical pathways in neonatal sepsis, rank product (RP) algorithm, centrality analysis and impact factor (IF) were introduced sequentially, which synthetically considered the differential expression of genes and pathways, pathways cross-talks and pathway parameters in the network. The dysregulated pathways with the highest IF values as well as RPpathways in neonatal sepsis. By integrating three kinds of data, only 6919 common genes were included to perform the pathway cross-talk analysis. By statistic analysis, a total of 1249 significant pathway cross-talks were selected to construct the pathway cross-talk network. Moreover, 47 dys-regulated pathways were identified via attract method, 20 pathways were identified under RPpathways with the highest IF were also screened from the pathway cross-talk network. Among them, we selected 8 common pathways, i.e. critical pathways. In this study, we systematically tracked 8 critical pathways involved in neonatal sepsis by integrating attract method and pathway cross-talk network. These pathways might be responsible for the host response in infection, and of great value for advancing diagnosis and therapy of neonatal sepsis. Copyright © 2017

  4. Final report on the Pathway Analysis Task

    International Nuclear Information System (INIS)

    Whicker, F.W.; Kirchner, T.B.

    1993-04-01

    The Pathway Analysis Task constituted one of several multi-laboratory efforts to estimate radiation doses to people, considering all important pathways of exposure, from the testing of nuclear devices at the Nevada Test Site (NTS). The primary goal of the Pathway Analysis Task was to predict radionuclide ingestion by residents of Utah, Nevada, and portions of seven other adjoining western states following radioactive fallout deposition from individual events at the NTS. This report provides comprehensive documentation of the activities and accomplishments of Colorado State University's Pathway Analysis Task during the entire period of support (1979--91). The history of the project will be summarized, indicating the principal dates and milestones, personnel involved, subcontractors, and budget information. Accomplishments, both primary and auxiliary, will be summarized with general results rather than technical details being emphasized. This will also serve as a guide to the reports and open literature publications produced, where the methodological details and specific results are documented. Selected examples of results on internal dose estimates are provided in this report because the data have not been published elsewhere

  5. Cleanup standards and pathways analysis methods

    International Nuclear Information System (INIS)

    Devgun, J.S.

    1993-01-01

    Remediation of a radioactively contaminated site requires that certain regulatory criteria be met before the site can be released for unrestricted future use. Since the ultimate objective of remediation is to protect the public health and safety, residual radioactivity levels remaining at a site after cleanup must be below certain preset limits or meet acceptable dose or risk criteria. Release of a decontaminated site requires proof that the radiological data obtained from the site meet the regulatory criteria for such a release. Typically release criteria consist of a composite of acceptance limits that depend on the radionuclides, the media in which they are present, and federal and local regulations. In recent years, the US Department of Energy (DOE) has developed a pathways analysis model to determine site-specific soil activity concentration guidelines for radionuclides that do not have established generic acceptance limits. The DOE pathways analysis computer code (developed by Argonne National Laboratory for the DOE) is called RESRAD (Gilbert et al. 1989). Similar efforts have been initiated by the US Nuclear Regulatory Commission (NRC) to develop and use dose-related criteria based on genetic pathways analyses rather than simplistic numerical limits on residual radioactivity. The focus of this paper is radionuclide contaminated soil. Cleanup standards are reviewed, pathways analysis methods are described, and an example is presented in which RESRAD was used to derive cleanup guidelines

  6. Final report on the Pathway Analysis Task

    Energy Technology Data Exchange (ETDEWEB)

    Whicker, F.W.; Kirchner, T.B. [Colorado State Univ., Fort Collins, CO (United States)

    1993-04-01

    The Pathway Analysis Task constituted one of several multi-laboratory efforts to estimate radiation doses to people, considering all important pathways of exposure, from the testing of nuclear devices at the Nevada Test Site (NTS). The primary goal of the Pathway Analysis Task was to predict radionuclide ingestion by residents of Utah, Nevada, and portions of seven other adjoining western states following radioactive fallout deposition from individual events at the NTS. This report provides comprehensive documentation of the activities and accomplishments of Colorado State University`s Pathway Analysis Task during the entire period of support (1979--91). The history of the project will be summarized, indicating the principal dates and milestones, personnel involved, subcontractors, and budget information. Accomplishments, both primary and auxiliary, will be summarized with general results rather than technical details being emphasized. This will also serve as a guide to the reports and open literature publications produced, where the methodological details and specific results are documented. Selected examples of results on internal dose estimates are provided in this report because the data have not been published elsewhere.

  7. Gridded Surface Subsurface Hydrologic Analysis (GSSHA) User's Manual; Version 1.43 for Watershed Modeling System 6.1

    National Research Council Canada - National Science Library

    Downer, Charles W; Ogden, Fred L

    2006-01-01

    The need to simulate surface water flows in watersheds with diverse runoff production mechanisms has led to the development of the physically-based hydrologic model Gridded Surface Subsurface Hydrologic Analysis (GSSHA...

  8. Environmental-pathways analysis for evaluation of a low-level waste disposal site

    International Nuclear Information System (INIS)

    Lee, D.W.; Ketelle, R.H.; Pin, F.G.; Hill, G.S.

    1983-01-01

    The suitability of a site for the shallow land burial of low-level waste is evaluated by an environmental-pathways analysis. The environmental-pathways analysis considers the probable paths for the transport of contamination to man and models the long-term transport of contamination to determine the resulting dose-to-man. The model of the long-term transport of contamination is developed for a proposed site using data obtained from a comprehensive laboratory and field investigation. The proposed site is located at the US Department of Energy Portsmouth Reservation, Piketon, Ohio and is planned to accept low-level radioactive waste generated by the enrichment of uranium. Laboratory studies were performed to characterize the waste and determine the wastes' leaching and retardation characteristics with site soils and groundwater. Comprehensive drilling, sampling and laboratory investigations were performed to provide the necessary information for interpreting the site's geology and hydrology. Field tests were performed to further quantify the site's hydrology. The pathway of greatest concern is the migration of contaminated groundwater and subsequent consumption by man. This pathway was modeled using a numerical simulation of the long-term transport of contamination. Conservative scenarios were developed for leachate generation and migration through the geohydrologic system. The dose-to-man determined from the pathways analysis formed the basis for evaluating site acceptability and providing recommendations for site design and development

  9. Environmental pathways analysis for evaluation of a low-level waste disposal site

    International Nuclear Information System (INIS)

    Lee, D.W.; Ketelle, R.H.; Pin, F.G.; Hill, G.S.

    1984-01-01

    The suitability of a site for the shallow land burial of low-level waste is evaluated by an environmental pathways analysis. The environmental pathways analysis considers the probable paths for the transport of contamination to man and models the long-term transport of contamination to determine the resulting dose to man. The model of the long-term transport of contamination is developed for a proposed site using data obtained from a comprehensive laboratory and field investigation. The proposed site is located at the US Department of Energy Portsmouth Reservation, Piketon, Ohio, and is planned to accept low-level radioactive waste generated by the enrichment of uranium. Laboratory studies were performed to characterize the waste and determine the wastes' leaching and retardation characteristics with site soils and groundwater. Comprehensive drilling, sampling and laboratory investigations were performed to provide the necessary information for interpreting the site's geology and hydrology. Field tests were performed to further quantify the site's hydrology. The pathway of greatest concern is the migration of contaminated groundwater and subsequent consumption by man. This pathway was modelled using a numerical simulation of the long-term transport of contamination. Conservative scenarios were developed for leachate generation and migration through the geohydrologic system. The dose to man determined from the pathways analysis formed the basis for evaluating site acceptability and providing recommendations for site design and development. (author)

  10. Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes

    Directory of Open Access Journals (Sweden)

    Wufeng Fan

    2017-01-01

    Full Text Available In our study, we aimed to extract dysregulated pathways in human monocytes infected by Listeria monocytogenes (LM based on pathway interaction network (PIN which presented the functional dependency between pathways. After genes were aligned to the pathways, principal component analysis (PCA was used to calculate the pathway activity for each pathway, followed by detecting seed pathway. A PIN was constructed based on gene expression profile, protein-protein interactions (PPIs, and cellular pathways. Identifying dysregulated pathways from the PIN was performed relying on seed pathway and classification accuracy. To evaluate whether the PIN method was feasible or not, we compared the introduced method with standard network centrality measures. The pathway of RNA polymerase II pretranscription events was selected as the seed pathway. Taking this seed pathway as start, one pathway set (9 dysregulated pathways with AUC score of 1.00 was identified. Among the 5 hub pathways obtained using standard network centrality measures, 4 pathways were the common ones between the two methods. RNA polymerase II transcription and DNA replication owned a higher number of pathway genes and DEGs. These dysregulated pathways work together to influence the progression of LM infection, and they will be available as biomarkers to diagnose LM infection.

  11. ERM model analysis for adaptation to hydrological model errors

    Science.gov (United States)

    Baymani-Nezhad, M.; Han, D.

    2018-05-01

    Hydrological conditions are changed continuously and these phenomenons generate errors on flood forecasting models and will lead to get unrealistic results. Therefore, to overcome these difficulties, a concept called model updating is proposed in hydrological studies. Real-time model updating is one of the challenging processes in hydrological sciences and has not been entirely solved due to lack of knowledge about the future state of the catchment under study. Basically, in terms of flood forecasting process, errors propagated from the rainfall-runoff model are enumerated as the main source of uncertainty in the forecasting model. Hence, to dominate the exciting errors, several methods have been proposed by researchers to update the rainfall-runoff models such as parameter updating, model state updating, and correction on input data. The current study focuses on investigations about the ability of rainfall-runoff model parameters to cope with three types of existing errors, timing, shape and volume as the common errors in hydrological modelling. The new lumped model, the ERM model, has been selected for this study to evaluate its parameters for its use in model updating to cope with the stated errors. Investigation about ten events proves that the ERM model parameters can be updated to cope with the errors without the need to recalibrate the model.

  12. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

    Science.gov (United States)

    Zhang, Fan; Drabier, Renee

    2012-01-01

    Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpret and distill such large amounts of data. Extensive pathway and network analysis allow for the discovery of highly significant pathways from a set of disease vs. healthy samples in the NGS and GWAS. Knowledge of activation of these processes will lead to elucidation of the complex biological pathways affected by drug treatment, to patient stratification studies of new and existing drug treatments, and to understanding the underlying anti-cancer drug effects. There are approximately 141 biological human pathway resources as of Jan 2012 according to the Pathguide database. However, most currently available resources do not contain disease, drug or organ specificity information such as disease-pathway, drug-pathway, and organ-pathway associations. Systematically integrating pathway, disease, drug and organ specificity together becomes increasingly crucial for understanding the interrelationships between signaling, metabolic and regulatory pathway, drug action, disease susceptibility, and organ specificity from high-throughput omics data (genomics, transcriptomics, proteomics and metabolomics). We designed the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (IPAD, http://bioinfo.hsc.unt.edu/ipad), defining inter-association between pathway, disease, drug and organ specificity, based on six criteria: 1) comprehensive pathway coverage; 2) gene/protein to pathway/disease/drug/organ association; 3) inter-association between pathway, disease, drug, and organ; 4) multiple and quantitative measurement of enrichment and inter-association; 5) assessment of enrichment and inter-association analysis with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources; and 6) cross-linking of

  13. Ensemble catchment hydrological modelling for climate change impact analysis

    Science.gov (United States)

    Vansteenkiste, Thomas; Ntegeka, Victor; Willems, Patrick

    2014-05-01

    It is vital to investigate how the hydrological model structure affects the climate change impact given that future changes not in the range for which the models were calibrated or validated are likely. Thus an ensemble modelling approach which involves a diversity of models with different structures such as spatial resolutions and process descriptions is crucial. The ensemble modelling approach was applied to a set of models: from the lumped conceptual models NAM, PDM and VHM, an intermediate detailed and distributed model WetSpa, to the highly detailed and fully distributed model MIKE-SHE. Explicit focus was given to the high and low flow extremes. All models were calibrated for sub flows and quick flows derived from rainfall and potential evapotranspiration (ETo) time series. In general, all models were able to produce reliable estimates of the flow regimes under the current climate for extreme peak and low flows. An intercomparison of the low and high flow changes under changed climatic conditions was made using climate scenarios tailored for extremes. Tailoring was important for two reasons. First, since the use of many scenarios was not feasible it was necessary to construct few scenarios that would reasonably represent the range of extreme impacts. Second, scenarios would be more informative as changes in high and low flows would be easily traced to changes of ETo and rainfall; the tailored scenarios are constructed using seasonal changes that are defined using different levels of magnitude (high, mean and low) for rainfall and ETo. After simulation of these climate scenarios in the five hydrological models, close agreement was found among the models. The different models predicted similar range of peak flow changes. For the low flows, however, the differences in the projected impact range by different hydrological models was larger, particularly for the drier scenarios. This suggests that the hydrological model structure is critical in low flow predictions

  14. Uncertainty in projected point precipitation extremes for hydrological impact analysis of climate change

    Science.gov (United States)

    Van Uytven, Els; Willems, Patrick

    2017-04-01

    Current trends in the hydro-meteorological variables indicate the potential impact of climate change on hydrological extremes. Therefore, they trigger an increased importance climate adaptation strategies in water management. The impact of climate change on hydro-meteorological and hydrological extremes is, however, highly uncertain. This is due to uncertainties introduced by the climate models, the internal variability inherent to the climate system, the greenhouse gas scenarios and the statistical downscaling methods. In view of the need to define sustainable climate adaptation strategies, there is a need to assess these uncertainties. This is commonly done by means of ensemble approaches. Because more and more climate models and statistical downscaling methods become available, there is a need to facilitate the climate impact and uncertainty analysis. A Climate Perturbation Tool has been developed for that purpose, which combines a set of statistical downscaling methods including weather typing, weather generator, transfer function and advanced perturbation based approaches. By use of an interactive interface, climate impact modelers can apply these statistical downscaling methods in a semi-automatic way to an ensemble of climate model runs. The tool is applicable to any region, but has been demonstrated so far to cases in Belgium, Suriname, Vietnam and Bangladesh. Time series representing future local-scale precipitation, temperature and potential evapotranspiration (PET) conditions were obtained, starting from time series of historical observations. Uncertainties on the future meteorological conditions are represented in two different ways: through an ensemble of time series, and a reduced set of synthetic scenarios. The both aim to span the full uncertainty range as assessed from the ensemble of climate model runs and downscaling methods. For Belgium, for instance, use was made of 100-year time series of 10-minutes precipitation observations and daily

  15. [Gene method for inconsistent hydrological frequency calculation. 2: Diagnosis system of hydrological genes and method of hydrological moment genes with inconsistent characters].

    Science.gov (United States)

    Xie, Ping; Zhao, Jiang Yan; Wu, Zi Yi; Sang, Yan Fang; Chen, Jie; Li, Bin Bin; Gu, Hai Ting

    2018-04-01

    The analysis of inconsistent hydrological series is one of the major problems that should be solved for engineering hydrological calculation in changing environment. In this study, the diffe-rences of non-consistency and non-stationarity were analyzed from the perspective of composition of hydrological series. The inconsistent hydrological phenomena were generalized into hydrological processes with inheritance, variability and evolution characteristics or regulations. Furthermore, the hydrological genes were identified following the theory of biological genes, while their inheritance bases and variability bases were determined based on composition of hydrological series under diffe-rent time scales. To identify and test the components of hydrological genes, we constructed a diagnosis system of hydrological genes. With the P-3 distribution as an example, we described the process of construction and expression of the moment genes to illustrate the inheritance, variability and evolution principles of hydrological genes. With the annual minimum 1-month runoff series of Yunjinghong station in Lancangjiang River basin as an example, we verified the feasibility and practicability of hydrological gene theory for the calculation of inconsistent hydrological frequency. The results showed that the method could be used to reveal the evolution of inconsistent hydrological series. Therefore, it provided a new research pathway for engineering hydrological calculation in changing environment and an essential reference for the assessment of water security.

  16. Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

    Science.gov (United States)

    Yang, Qian; Wang, Shuyuan; Dai, Enyu; Zhou, Shunheng; Liu, Dianming; Liu, Haizhou; Meng, Qianqian; Jiang, Bin; Jiang, Wei

    2017-08-16

    Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Pathway analysis concepts for radiological impact assessment

    International Nuclear Information System (INIS)

    Moroney, J.R.

    1992-06-01

    The concepts underlying exposure pathways analysis are outlined with reference to the features of the two broad types of radionuclide transport models now in use - dynamic and steady-state - and the methods for constructing and developing them. By way of illustration, representative radiation doses are estimated for the four main exposure pathways likely to be involved in the land application of effluent water from Retention Pond 2 of Ranger Uranium Mines. These include: external irradiation by 226 Ra and natural uranium (Un at) in soil, ingestion of 226 Ra and Un at in food, inhalation of 222 Rn daughter products from 226 Rn in soil, and inhalation of 226 Ra and Un at in airborne dust resuspended from soil. Consideration has been given to local residents pursuing a traditional lifestyle on conclusion of the land application program. Because of the possible importance of the contribution from resuspended dust, currently available data are explored in refining the methodology for the pathway and developing a more appropriate model for it. 37 refs., 9 tabs., 6 figs

  18. Hydrological Response and Complex Impact Pathways of the 2015/2016 El Niño in Eastern and Southern Africa

    Science.gov (United States)

    Siderius, C.; Gannon, K. E.; Ndiyoi, M.; Opere, A.; Batisani, N.; Olago, D.; Pardoe, J.; Conway, D.

    2018-01-01

    The 2015/2016 El Niño has been classified as one of the three most severe on record. El Niño teleconnections are commonly associated with droughts in southern Africa and high precipitation in eastern Africa. Despite their relatively frequent occurrence, evidence for their hydrological effects and impacts beyond agriculture is limited. We examine the hydrological response and impact pathways of the 2015/2016 El Niño in eastern and southern Africa, focusing on Botswana, Kenya, and Zambia. We use in situ and remotely sensed time series of precipitation, river flow, and lake levels complemented by qualitative insights from interviews with key organizations in each country about awareness, impacts, and responses. Our results show that drought conditions prevailed in large parts of southern Africa, reducing runoff and contributing to unusually low lake levels in Botswana and Zambia. Key informants characterized this El Niño through record high temperatures and water supply disruption in Botswana and through hydroelectric load shedding in Zambia. Warnings of flood risk in Kenya were pronounced, but the El Niño teleconnection did not materialize as expected in 2015/2016. Extreme precipitation was limited and caused localized impacts. The hydrological impacts in southern Africa were severe and complex, strongly exacerbated by dry antecedent conditions, recent changes in exposure and sensitivity and management decisions. Improved understanding of hydrological responses and the complexity of differing impact pathways can support design of more adaptive, region-specific management strategies.

  19. A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

    Science.gov (United States)

    Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia

    2015-01-01

    Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI). PMID:25551156

  20. Spatially explicit scenario analysis for hydrologic services in an urbanizing agricultural watershed

    Science.gov (United States)

    Qiu, J.; Booth, E.; Carpenter, S. R.; Turner, M.

    2013-12-01

    freshwater supply and surface water quality were sustained or enhanced overall, these hydrologic services declined in ~60% and 20% of the landscape, respectively. The greatest improvement for most hydrologic services corresponded to areas of restored wetland, forest and perennial crops, which were less vulnerable to future degradation. In the Investment in Innovation scenario, freshwater supply declined in almost the entire watershed; improvement of surface water quality and flood regulation occurred mainly in urban areas, where highly engineered systems made them less vulnerable. Overall, our results indicated that hydrologic services will respond differently to future climate and land-use change, and sustaining one may involve tradeoffs of another. Technological progress can conserve particular services but might not be the panacea for the future. How society reacts in the face of changes can have an important role in determining the pathways to the future and the provision and spatial patterns of ecosystem services.

  1. A physically based catchment partitioning method for hydrological analysis

    Science.gov (United States)

    Menduni, Giovanni; Riboni, Vittoria

    2000-07-01

    We propose a partitioning method for the topographic surface, which is particularly suitable for hydrological distributed modelling and shallow-landslide distributed modelling. The model provides variable mesh size and appears to be a natural evolution of contour-based digital terrain models. The proposed method allows the drainage network to be derived from the contour lines. The single channels are calculated via a search for the steepest downslope lines. Then, for each network node, the contributing area is determined by means of a search for both steepest upslope and downslope lines. This leads to the basin being partitioned into physically based finite elements delimited by irregular polygons. In particular, the distributed computation of local geomorphological parameters (i.e. aspect, average slope and elevation, main stream length, concentration time, etc.) can be performed easily for each single element. The contributing area system, together with the information on the distribution of geomorphological parameters provide a useful tool for distributed hydrological modelling and simulation of environmental processes such as erosion, sediment transport and shallow landslides.

  2. Real-Time Analysis and Forecasting of Multisite River Flow Using a Distributed Hydrological Model

    Directory of Open Access Journals (Sweden)

    Mingdong Sun

    2014-01-01

    Full Text Available A spatial distributed hydrological forecasting system was developed to promote the analysis of river flow dynamic state in a large basin. The research presented the real-time analysis and forecasting of multisite river flow in the Nakdong River Basin using a distributed hydrological model with radar rainfall forecast data. A real-time calibration algorithm of hydrological distributed model was proposed to investigate the particular relationship between the water storage and basin discharge. Demonstrate the approach of simulating multisite river flow using a distributed hydrological model couple with real-time calibration and forecasting of multisite river flow with radar rainfall forecasts data. The hydrographs and results exhibit that calibrated flow simulations are very approximate to the flow observation at all sites and the accuracy of forecasting flow is gradually decreased with lead times extending from 1 hr to 3 hrs. The flow forecasts are lower than the flow observation which is likely caused by the low estimation of radar rainfall forecasts. The research has well demonstrated that the distributed hydrological model is readily applicable for multisite real-time river flow analysis and forecasting in a large basin.

  3. Life cycle analysis of transportation fuel pathways

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-02-24

    The purpose of this work is to improve the understanding of the concept of life cycle analysis (LCA) of transportation fuels and some of its pertinent issues among non-technical people, senior managers, and policy makers. This work should provide some guidance to nations considering LCA-based policies and to people who are affected by existing policies or those being developed. While the concept of employing LCA to evaluate fuel options is simple and straightforward, the act of putting the concept into practice is complex and fraught with issues. Policy makers need to understand the limitations inherent in carrying out LCA work for transportation fuel systems. For many systems, even those that have been employed for a 100 years, there is a lack of sound data on the performance of those systems. Comparisons between systems should ideally be made using the same tool, so that differences caused by system boundaries, allocation processes, and temporal issues can be minimized (although probably not eliminated). Comparing the results for fuel pathway 1 from tool A to those of fuel system 2 from tool B introduces significant uncertainty into the results. There is also the question of the scale of system changes. LCA will give more reliable estimates when it is used to examine small changes in transportation fuel pathways than when used to estimate large scale changes that replace current pathways with completely new pathways. Some LCA tools have been developed recently primarily for regulatory purposes. These tools may deviate from ISO principles in order to facilitate simplicity and ease of use. In a regulatory environment, simplicity and ease of use are worthy objectives and in most cases there is nothing inherently wrong with this approach, particularly for assessing relative performance. However, the results of these tools should not be confused with, or compared to, the results that are obtained from a more complex and rigorous ISO compliant LCA. It should be

  4. Information on Hydrologic Conceptual Models, Parameters, Uncertainty Analysis, and Data Sources for Dose Assessments at Decommissioning Sites

    International Nuclear Information System (INIS)

    Meyer, Philip D.; Gee, Glendon W.; Nicholson, Thomas J.

    1999-01-01

    This report addresses issues related to the analysis of uncertainty in dose assessments conducted as part of decommissioning analyses. The analysis is limited to the hydrologic aspects of the exposure pathway involving infiltration of water at the ground surface, leaching of contaminants, and transport of contaminants through the groundwater to a point of exposure. The basic conceptual models and mathematical implementations of three dose assessment codes are outlined along with the site-specific conditions under which the codes may provide inaccurate, potentially nonconservative results. In addition, the hydrologic parameters of the codes are identified and compared. A methodology for parameter uncertainty assessment is outlined that considers the potential data limitations and modeling needs of decommissioning analyses. This methodology uses generic parameter distributions based on national or regional databases, sensitivity analysis, probabilistic modeling, and Bayesian updating to incorporate site-specific information. Data sources for best-estimate parameter values and parameter uncertainty information are also reviewed. A follow-on report will illustrate the uncertainty assessment methodology using decommissioning test cases

  5. Information on Hydrologic Conceptual Models, Parameters, Uncertainty Analysis, and Data Sources for Dose Assessments at Decommissioning Sites

    International Nuclear Information System (INIS)

    Meyer D, Philip; Gee W, Glendon

    2000-01-01

    This report addresses issues related to the analysis of uncertainty in dose assessments conducted as part of decommissioning analyses. The analysis is limited to the hydrologic aspects of the exposure pathway involving infiltration of water at the ground surface, leaching of contaminants, and transport of contaminants through the groundwater to a point of exposure. The basic conceptual models and mathematical implementations of three dose assessment codes are outlined along with the site-specific conditions under which the codes may provide inaccurate, potentially nonconservative results. In addition, the hydrologic parameters of the codes are identified and compared. A methodology for parameter uncertainty assessment is outlined that considers the potential data limitations and modeling needs of decommissioning analyses. This methodology uses generic parameter distributions based on national or regional databases, sensitivity analysis, probabilistic modeling, and Bayesian updating to incorporate site-specific information. Data sources for best-estimate parameter values and parameter uncertainty information are also reviewed. A follow-on report will illustrate the uncertainty assessment methodology using decommissioning test cases

  6. Uncertainty analysis of hydrological modeling in a tropical area using different algorithms

    Science.gov (United States)

    Rafiei Emam, Ammar; Kappas, Martin; Fassnacht, Steven; Linh, Nguyen Hoang Khanh

    2018-01-01

    Hydrological modeling outputs are subject to uncertainty resulting from different sources of errors (e.g., error in input data, model structure, and model parameters), making quantification of uncertainty in hydrological modeling imperative and meant to improve reliability of modeling results. The uncertainty analysis must solve difficulties in calibration of hydrological models, which further increase in areas with data scarcity. The purpose of this study is to apply four uncertainty analysis algorithms to a semi-distributed hydrological model, quantifying different source of uncertainties (especially parameter uncertainty) and evaluate their performance. In this study, the Soil and Water Assessment Tools (SWAT) eco-hydrological model was implemented for the watershed in the center of Vietnam. The sensitivity of parameters was analyzed, and the model was calibrated. The uncertainty analysis for the hydrological model was conducted based on four algorithms: Generalized Likelihood Uncertainty Estimation (GLUE), Sequential Uncertainty Fitting (SUFI), Parameter Solution method (ParaSol) and Particle Swarm Optimization (PSO). The performance of the algorithms was compared using P-factor and Rfactor, coefficient of determination (R 2), the Nash Sutcliffe coefficient of efficiency (NSE) and Percent Bias (PBIAS). The results showed the high performance of SUFI and PSO with P-factor>0.83, R-factor 0.91, NSE>0.89, and 0.18analysis. Indeed, the uncertainty analysis must be accounted when the outcomes of the model use for policy or management decisions.

  7. Computational Chemical Synthesis Analysis and Pathway Design

    Directory of Open Access Journals (Sweden)

    Fan Feng

    2018-06-01

    Full Text Available With the idea of retrosynthetic analysis, which was raised in the 1960s, chemical synthesis analysis and pathway design have been transformed from a complex problem to a regular process of structural simplification. This review aims to summarize the developments of computer-assisted synthetic analysis and design in recent years, and how machine-learning algorithms contributed to them. LHASA system started the pioneering work of designing semi-empirical reaction modes in computers, with its following rule-based and network-searching work not only expanding the databases, but also building new approaches to indicating reaction rules. Programs like ARChem Route Designer replaced hand-coded reaction modes with automatically-extracted rules, and programs like Chematica changed traditional designing into network searching. Afterward, with the help of machine learning, two-step models which combine reaction rules and statistical methods became the main stream. Recently, fully data-driven learning methods using deep neural networks which even do not require any prior knowledge, were applied into this field. Up to now, however, these methods still cannot replace experienced human organic chemists due to their relatively low accuracies. Future new algorithms with the aid of powerful computational hardware will make this topic promising and with good prospects.

  8. Dysregulated Pathway Identification of Alzheimer's Disease Based on Internal Correlation Analysis of Genes and Pathways.

    Science.gov (United States)

    Kong, Wei; Mou, Xiaoyang; Di, Benteng; Deng, Jin; Zhong, Ruxing; Wang, Shuaiqun

    2017-11-20

    Dysregulated pathway identification is an important task which can gain insight into the underlying biological processes of disease. Current pathway-identification methods focus on a set of co-expression genes and single pathways and ignore the correlation between genes and pathways. The method proposed in this study, takes into account the internal correlations not only between genes but also pathways to identifying dysregulated pathways related to Alzheimer's disease (AD), the most common form of dementia. In order to find the significantly differential genes for AD, mutual information (MI) is used to measure interdependencies between genes other than expression valves. Then, by integrating the topology information from KEGG, the significant pathways involved in the feature genes are identified. Next, the distance correlation (DC) is applied to measure the pairwise pathway crosstalks since DC has the advantage of detecting nonlinear correlations when compared to Pearson correlation. Finally, the pathway pairs with significantly different correlations between normal and AD samples are known as dysregulated pathways. The molecular biology analysis demonstrated that many dysregulated pathways related to AD pathogenesis have been discovered successfully by the internal correlation detection. Furthermore, the insights of the dysregulated pathways in the development and deterioration of AD will help to find new effective target genes and provide important theoretical guidance for drug design. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. The use of distributed hydrological models for the Gard 2002 flash flood event: Analysis of associated hydrological processes

    Science.gov (United States)

    Braud, Isabelle; Roux, Hélène; Anquetin, Sandrine; Maubourguet, Marie-Madeleine; Manus, Claire; Viallet, Pierre; Dartus, Denis

    2010-11-01

    SummaryThis paper presents a detailed analysis of the September 8-9, 2002 flash flood event in the Gard region (southern France) using two distributed hydrological models: CVN built within the LIQUID® hydrological platform and MARINE. The models differ in terms of spatial discretization, infiltration and water redistribution representation, and river flow transfer. MARINE can also account for subsurface lateral flow. Both models are set up using the same available information, namely a DEM and a pedology map. They are forced with high resolution radar rainfall data over a set of 18 sub-catchments ranging from 2.5 to 99 km2 and are run without calibration. To begin with, models simulations are assessed against post field estimates of the time of peak and the maximum peak discharge showing a fair agreement for both models. The results are then discussed in terms of flow dynamics, runoff coefficients and soil saturation dynamics. The contribution of the subsurface lateral flow is also quantified using the MARINE model. This analysis highlights that rainfall remains the first controlling factor of flash flood dynamics. High rainfall peak intensities are very influential of the maximum peak discharge for both models, but especially for the CVN model which has a simplified overland flow transfer. The river bed roughness also influences the peak intensity and time. Soil spatial representation is shown to have a significant role on runoff coefficients and on the spatial variability of saturation dynamics. Simulated soil saturation is found to be strongly related with soil depth and initial storage deficit maps, due to a full saturation of most of the area at the end of the event. When activated, the signature of subsurface lateral flow is also visible in the spatial patterns of soil saturation with higher values concentrating along the river network. However, the data currently available do not allow the assessment of both patterns. The paper concludes with a set of

  10. Hydrological flow analysis at Yucca Mountain, Nevada. Final report

    International Nuclear Information System (INIS)

    1995-01-01

    This final report, prepared by Hydro Geo Chem staff for Los Alamos National Laboratory, summarizes work conducted by the company under Subcontract 52OHHOOI 5-3G, which was terminated by LANL effective 7 February 1995 for practical reasons, in that responsibilities for all tasks in the Statement of Work had been transitioned to LANL employees. The ultimate objective of this work is to characterize the movement of subsurface water in the vicinity of Yucca Mountain, Nevada. Data produced under this contract is to be used by the U.S. Department of Energy in its Yucca Mountain Site Characterization Project (YMP) to help determine hydrologic flows that may affect the performance of a potential nuclear waste,, repository. The data may be used in the licensing proceedings, and certain quality assurance procedures have thus been required. The work has focused on measuring the distribution of environmental tracers- chlorine-36, chlorine, and bromine-and on evaluating the depth to which these conservative solutes have percolated in the unsaturated zone at Yucca Mountain. The period of performance for the original Subcontract was I October 1994 to 31 December 1996. Obviously, we have not completed, nor are we expected to complete, all of the scope of work in the Subcontract. The following discussion summarizes progress made on the tasks outlined in the Statement of Work for this Subcontract Details of this work and all data acquired by Hydro Geo Chem for this Subcontract have, been systematically organized in logbooks and - laboratory notebooks (Appendices A and B). These documents have been structured to make it easy to trace the analytical history of a sample, from time of receipt to the final analytical results. The current status of this work and its relevance for the Yucca Mountain Project are described in a LANL report co-authored by Hydro Geo Chem staff

  11. Multivariate stochastic analysis for Monthly hydrological time series at Cuyahoga River Basin

    Science.gov (United States)

    zhang, L.

    2011-12-01

    Copula has become a very powerful statistic and stochastic methodology in case of the multivariate analysis in Environmental and Water resources Engineering. In recent years, the popular one-parameter Archimedean copulas, e.g. Gumbel-Houggard copula, Cook-Johnson copula, Frank copula, the meta-elliptical copula, e.g. Gaussian Copula, Student-T copula, etc. have been applied in multivariate hydrological analyses, e.g. multivariate rainfall (rainfall intensity, duration and depth), flood (peak discharge, duration and volume), and drought analyses (drought length, mean and minimum SPI values, and drought mean areal extent). Copula has also been applied in the flood frequency analysis at the confluences of river systems by taking into account the dependence among upstream gauge stations rather than by using the hydrological routing technique. In most of the studies above, the annual time series have been considered as stationary signal which the time series have been assumed as independent identically distributed (i.i.d.) random variables. But in reality, hydrological time series, especially the daily and monthly hydrological time series, cannot be considered as i.i.d. random variables due to the periodicity existed in the data structure. Also, the stationary assumption is also under question due to the Climate Change and Land Use and Land Cover (LULC) change in the fast years. To this end, it is necessary to revaluate the classic approach for the study of hydrological time series by relaxing the stationary assumption by the use of nonstationary approach. Also as to the study of the dependence structure for the hydrological time series, the assumption of same type of univariate distribution also needs to be relaxed by adopting the copula theory. In this paper, the univariate monthly hydrological time series will be studied through the nonstationary time series analysis approach. The dependence structure of the multivariate monthly hydrological time series will be

  12. From Site Data to Safety Assessment: Analysis of Present and Future Hydrological Conditions at a Coastal Site in Sweden

    International Nuclear Information System (INIS)

    Berglund, Sten; Bosson, Emma; Sassner, Mona

    2013-01-01

    This paper presents an analysis of present and future hydrological conditions at the Forsmark site in Sweden, which has been proposed as the site for a geological repository for spent nuclear fuel. Forsmark is a coastal site that changes in response to shoreline displacement. In the considered time frame (until year 10 000 ad), the hydrological system will be affected by landscape succession associated with shoreline displacement and changes in vegetation, regolith stratigraphy, and climate. Based on extensive site investigations and modeling of present hydrological conditions, the effects of different processes on future site hydrology are quantified. As expected, shoreline displacement has a strong effect on local hydrology (e.g., groundwater flow) in areas that change from sea to land. The comparison between present and future land areas emphasizes the importance of climate variables relative to other factors for main hydrological features such as water balances

  13. Hydrological Response Unit Analysis Using AVSWAT 2000 for Keuliling Reservoir Watershed, Aceh Province, Indonesia

    Directory of Open Access Journals (Sweden)

    . Azmeri

    2015-04-01

    Full Text Available Sediments deposition derived from the erosion in upstream areas can lead to river siltation or canals downstream irrigation. According to the complexity of erosion problem at Keuliling reservoir, it is essential that topography, hydrology, soil type and land use to be analyzed comprehensively. Software used to analyze is AVSWAT 2000 (Arc View Soil and Water Assessment Tools-2000, one of the additional tool of ArcView program. The results obtained are the watershed delineation map, soil type map to produce soil erodibility factor (K which indicates the resistance of soil particles toward exfoliation, land use map to produce crop management factor (C and soil conservation and its management factors (P. Hydrology analysis includes soil type, land use and utility for the erosion rate analysis through Hydrologic Response Unit (HRU. The biggest HRU value of sub-basin is on area 5 and the lowest one is on area 10. All four HRU in sub-basin area 5 are potentially donating high value for HRU. In short, this area has the longest slope length so that it has a large LS factor. About 50% of the land was covered by bushes which gain higher C factor rather than forest. Moreover, it has contour crop conservation technique with 9-20 % declivity resulting in having dominant factor of P. Soil type is dominated by Meucampli Formation which has soil erodibility factor with high level of vulnerable toward the rainfall kinetic energy. All in all, the vast majority of HRU parameters in this sub-basin area obtain the highest HRU value. Hydrology analysis, soil type, and use-land are useful for land area analysis that is susceptible to erosion which was identified through Hydrologic Response Unit (HRU using GIS. As the matter of fact, spatially studies constructed with GIS can facilitate the agency to determine critical areas which are needed to be aware or fully rehabilitated.

  14. Analysis of thermal-hydrologic-mechanical behavior near an emplacement drift at Yucca Mountain

    International Nuclear Information System (INIS)

    Rutqvist, Jonny; Tsang, Chin-Fu

    2002-01-01

    A coupled thermal, hydrologic and mechanical (THM) analysis is conducted to evaluate the impact of coupled THM processes on the performance of a potential nuclear waste repository at Yucca Mountain, Nevada. The analysis considers changes in rock mass porosity, permeability, and capillary pressure caused by rock deformations during drift excavation, as well as those caused by thermo-mechanically induced rock deformations after emplacement of the heat-generating waste. The analysis consists of a detailed calibration of coupled hydraulic-mechanical rock mass properties against field experiments, followed by a prediction of the coupled thermal, hydrologic, and mechanical behavior around a potential repository drift. For the particular problem studied and parameters used, the analysis indicates that the stress-induced permeability changes will be within one order of magnitude and that these permeability changes do not significantly impact the overall flow pattern around the repository drift

  15. Sensitivity analysis for hydrology and pesticide supply towards the river in SWAT

    Science.gov (United States)

    Holvoet, K.; van Griensven, A.; Seuntjens, P.; Vanrolleghem, P. A.

    The dynamic behaviour of pesticides in river systems strongly depends on varying climatological conditions and agricultural management practices. To describe this behaviour at the river-basin scale, integrated hydrological and water quality models are needed. A crucial step in understanding the various processes determining pesticide fate is to perform a sensitivity analysis. Sensitivity analysis for hydrology and pesticide supply in SWAT (Soil and Water Assessment Tool) will provide useful support for the development of a reliable hydrological model and will give insight in which parameters are most sensitive concerning pesticide supply towards rivers. The study was performed on the Nil catchment in Belgium. In this study we utilised an LH-OAT sensitivity analysis. The LH-OAT method combines the One-factor-At-a-Time (OAT) design and Latin Hypercube (LH) sampling by taking the Latin Hypercube samples as initial points for an OAT design. By means of the LH-OAT sensitivity analysis, the dominant hydrological parameters were determined and a reduction of the number of model parameters was performed. Dominant hydrological parameters were the curve number (CN2), the surface runoff lag (surlag), the recharge to deep aquifer (rchrg_dp) and the threshold depth of water in the shallow aquifer (GWQMN). Next, the selected parameters were estimated by manual calibration. Hereby, the Nash-Sutcliffe coefficient of efficiency improved from an initial value of -22.4 to +0.53. In the second part, sensitivity analyses were performed to provide insight in which parameters or model inputs contribute most to variance in pesticide output. The results of this study show that for the Nil catchment, hydrologic parameters are dominant in controlling pesticide predictions. The other parameter that affects pesticide concentrations in surface water is ‘apfp_pest’, which meaning was changed into a parameter that controls direct losses to the river system (e.g., through the clean up of spray

  16. A coupled stochastic rainfall-evapotranspiration model for hydrological impact analysis

    Science.gov (United States)

    Pham, Minh Tu; Vernieuwe, Hilde; De Baets, Bernard; Verhoest, Niko E. C.

    2018-02-01

    A hydrological impact analysis concerns the study of the consequences of certain scenarios on one or more variables or fluxes in the hydrological cycle. In such an exercise, discharge is often considered, as floods originating from extremely high discharges often cause damage. Investigating the impact of extreme discharges generally requires long time series of precipitation and evapotranspiration to be used to force a rainfall-runoff model. However, such kinds of data may not be available and one should resort to stochastically generated time series, even though the impact of using such data on the overall discharge, and especially on the extreme discharge events, is not well studied. In this paper, stochastically generated rainfall and corresponding evapotranspiration time series, generated by means of vine copulas, are used to force a simple conceptual hydrological model. The results obtained are comparable to the modelled discharge using observed forcing data. Yet, uncertainties in the modelled discharge increase with an increasing number of stochastically generated time series used. Notwithstanding this finding, it can be concluded that using a coupled stochastic rainfall-evapotranspiration model has great potential for hydrological impact analysis.

  17. Parameterization and Uncertainty Analysis of SWAT model in Hydrological Simulation of Chaohe River Basin

    Science.gov (United States)

    Jie, M.; Zhang, J.; Guo, B. B.

    2017-12-01

    As a typical distributed hydrological model, the SWAT model also has a challenge in calibrating parameters and analysis their uncertainty. This paper chooses the Chaohe River Basin China as the study area, through the establishment of the SWAT model, loading the DEM data of the Chaohe river basin, the watershed is automatically divided into several sub-basins. Analyzing the land use, soil and slope which are on the basis of the sub-basins and calculating the hydrological response unit (HRU) of the study area, after running SWAT model, the runoff simulation values in the watershed are obtained. On this basis, using weather data, known daily runoff of three hydrological stations, combined with the SWAT-CUP automatic program and the manual adjustment method are used to analyze the multi-site calibration of the model parameters. Furthermore, the GLUE algorithm is used to analyze the parameters uncertainty of the SWAT model. Through the sensitivity analysis, calibration and uncertainty study of SWAT, the results indicate that the parameterization of the hydrological characteristics of the Chaohe river is successful and feasible which can be used to simulate the Chaohe river basin.

  18. A systems biology approach for pathway level analysis

    OpenAIRE

    Draghici, Sorin; Khatri, Purvesh; Tarca, Adi Laurentiu; Amin, Kashyap; Done, Arina; Voichita, Calin; Georgescu, Constantin; Romero, Roberto

    2007-01-01

    A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By usin...

  19. Separate enrichment analysis of pathways for up- and downregulated genes.

    Science.gov (United States)

    Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

    2014-03-06

    Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

  20. The future use of pathway analysis in IAEA safeguards

    International Nuclear Information System (INIS)

    Budlong Sylvester, Kory; Pilat, J.; Murphy, Chantell

    2013-01-01

    Pathway analysis has the potential to play an important role in the development of a safeguards system that is more information driven, leveraging all the information available to the International Atomic Energy Agency (IAEA). Pathway analysis should be seen as an extension of traditional hypothesis testing used by the Agency in the past. The most attractive pathways based on the assessed capabilities of a given state can be identified and used in the development of state-level safeguards approaches. This ranking of pathways can be revised based on evidence of pathway use, or preparations for use, allowing limited safeguards resources to flow to the areas of highest concern. The possible uses of pathway analysis in the implementation of the IAEA's state-level concept are described along with implementation issues that will likely arise. The paper is followed by the slides of the presentation. (authors)

  1. Genetic variants in two pathways influence serum urate levels and gout risk: a systematic pathway analysis.

    Science.gov (United States)

    Dong, Zheng; Zhou, Jingru; Xu, Xia; Jiang, Shuai; Li, Yuan; Zhao, Dongbao; Yang, Chengde; Ma, Yanyun; Wang, Yi; He, Hongjun; Ji, Hengdong; Zhang, Juan; Yuan, Ziyu; Yang, Yajun; Wang, Xiaofeng; Pang, Yafei; Jin, Li; Zou, Hejian; Wang, Jiucun

    2018-03-01

    The aims of this study were to identify candidate pathways associated with serum urate and to explore the genetic effect of those pathways on the risk of gout. Pathway analysis of the loci identified in genome-wide association studies (GWASs) showed that the ion transmembrane transporter activity pathway (GO: 0015075) and the secondary active transmembrane transporter activity pathway (GO: 0015291) were both associated with serum urate concentrations, with P FDR values of 0.004 and 0.007, respectively. In a Chinese population of 4,332 individuals, the two pathways were also found to be associated with serum urate (P FDR  = 1.88E-05 and 3.44E-04, separately). In addition, these two pathways were further associated with the pathogenesis of gout (P FDR  = 1.08E-08 and 2.66E-03, respectively) in the Chinese population and a novel gout-associated gene, SLC17A2, was identified (OR = 0.83, P FDR  = 0.017). The mRNA expression of candidate genes also showed significant differences among different groups at pathway level. The present study identified two transmembrane transporter activity pathways (GO: 0015075 and GO: 0015291) were associations with serum urate concentrations and the risk of gout. SLC17A2 was identified as a novel gene that influenced the risk of gout.

  2. Hydrology of Bishop Creek, California: An Isotopic Analysis

    Science.gov (United States)

    Michael L. Space; John W. Hess; Stanley D. Smith

    1989-01-01

    Five power generation plants along an eleven kilometer stretch divert Bishop Creek water for hydro-electric power. Stream diversion may be adversely affecting the riparian vegetation. Stable isotopic analysis is employed to determine surface water/ground-water interactions along the creek. surface water originates primarily from three headwater lakes. Discharge into...

  3. Uncertainty, sensitivity analysis and the role of data based mechanistic modeling in hydrology

    Science.gov (United States)

    Ratto, M.; Young, P. C.; Romanowicz, R.; Pappenberger, F.; Saltelli, A.; Pagano, A.

    2007-05-01

    In this paper, we discuss a joint approach to calibration and uncertainty estimation for hydrologic systems that combines a top-down, data-based mechanistic (DBM) modelling methodology; and a bottom-up, reductionist modelling methodology. The combined approach is applied to the modelling of the River Hodder catchment in North-West England. The top-down DBM model provides a well identified, statistically sound yet physically meaningful description of the rainfall-flow data, revealing important characteristics of the catchment-scale response, such as the nature of the effective rainfall nonlinearity and the partitioning of the effective rainfall into different flow pathways. These characteristics are defined inductively from the data without prior assumptions about the model structure, other than it is within the generic class of nonlinear differential-delay equations. The bottom-up modelling is developed using the TOPMODEL, whose structure is assumed a priori and is evaluated by global sensitivity analysis (GSA) in order to specify the most sensitive and important parameters. The subsequent exercises in calibration and validation, performed with Generalized Likelihood Uncertainty Estimation (GLUE), are carried out in the light of the GSA and DBM analyses. This allows for the pre-calibration of the the priors used for GLUE, in order to eliminate dynamical features of the TOPMODEL that have little effect on the model output and would be rejected at the structure identification phase of the DBM modelling analysis. In this way, the elements of meaningful subjectivity in the GLUE approach, which allow the modeler to interact in the modelling process by constraining the model to have a specific form prior to calibration, are combined with other more objective, data-based benchmarks for the final uncertainty estimation. GSA plays a major role in building a bridge between the hypothetico-deductive (bottom-up) and inductive (top-down) approaches and helps to improve the

  4. Bayesian analysis of data and model error in rainfall-runoff hydrological models

    Science.gov (United States)

    Kavetski, D.; Franks, S. W.; Kuczera, G.

    2004-12-01

    A major unresolved issue in the identification and use of conceptual hydrologic models is realistic description of uncertainty in the data and model structure. In particular, hydrologic parameters often cannot be measured directly and must be inferred (calibrated) from observed forcing/response data (typically, rainfall and runoff). However, rainfall varies significantly in space and time, yet is often estimated from sparse gauge networks. Recent work showed that current calibration methods (e.g., standard least squares, multi-objective calibration, generalized likelihood uncertainty estimation) ignore forcing uncertainty and assume that the rainfall is known exactly. Consequently, they can yield strongly biased and misleading parameter estimates. This deficiency confounds attempts to reliably test model hypotheses, to generalize results across catchments (the regionalization problem) and to quantify predictive uncertainty when the hydrologic model is extrapolated. This paper continues the development of a Bayesian total error analysis (BATEA) methodology for the calibration and identification of hydrologic models, which explicitly incorporates the uncertainty in both the forcing and response data, and allows systematic model comparison based on residual model errors and formal Bayesian hypothesis testing (e.g., using Bayes factors). BATEA is based on explicit stochastic models for both forcing and response uncertainty, whereas current techniques focus solely on response errors. Hence, unlike existing methods, the BATEA parameter equations directly reflect the modeler's confidence in all the data. We compare several approaches to approximating the parameter distributions: a) full Markov Chain Monte Carlo methods and b) simplified approaches based on linear approximations. Studies using synthetic and real data from the US and Australia show that BATEA systematically reduces the parameter bias, leads to more meaningful model fits and allows model comparison taking

  5. A spatiotemporal analysis of hydrological patterns based on a wireless sensor network system

    Science.gov (United States)

    Plaza, F.; Slater, T. A.; Zhong, X.; Li, Y.; Liang, Y.; Liang, X.

    2017-12-01

    Understanding complicated spatiotemporal patterns of eco-hydrological variables at a small scale plays a profound role in improving predictability of high resolution distributed hydrological models. However, accurate and continuous monitoring of these complex patterns has become one of the main challenges in the environmental sciences. Wireless sensor networks (WSNs) have emerged as one of the most widespread potential solutions to achieve this. This study presents a spatiotemporal analysis of hydrological patterns (e.g., soil moisture, soil water potential, soil temperature and transpiration) based on observational data collected from a dense multi-hop wireless sensor network (WSN) in a steep-forested testbed located in Southwestern Pennsylvania, USA. At this WSN testbed with an approximate area of 3000 m2, environmental variables are collected from over 240 sensors that are connected to more than 100 heterogeneous motes. The sensors include the soil moisture of EC-5, soil temperature and soil water potential of MPS-1 and MPS-2, and sap flow sensors constructed in house. The motes consist of MICAz, IRIS and TelosB. In addition, several data loggers have been installed along the site to provide a comparative reference to the WSN measurements for the purpose of checking the WSN data quality. The edaphic properties monitored by the WSN sensors show strong agreement with the data logger measurements. Moreover, sap flow measurements, scaled to tree stand transpiration, are found to be reasonable. This study also investigates the feasibility and roles that these sensor measurements play in improving the performance of high-resolution distributed hydrological models. In particular, we explore this using a modified version of the Distributed Hydrological Soil Vegetation Model (DHSVM).

  6. Safety assessment for deep underground disposal vault-pathways analysis

    International Nuclear Information System (INIS)

    Lyon, R.B.; Rosinger, E.L.J.

    1980-01-01

    The concept verification phase of the Canadian programme for the disposal of nuclear fuel waste encompasses a period of about three years before the start of site selection. During this time, the methodology for Environmental and Safety Assessment studies is being developed by focusing on a model site. Pathways analysis is an important component of these studies. It involves the prediction of the rate at which radionuclides might be released from a disposal vault and travel through the geosphere and biosphere to reach man. The pathways analysis studies cover three major topics: geosphere pathways analysis, biosphere pathways analysis and potentially-disruptive-phenomena analysis. Geosphere pathways analysis includes a total systems analysis, using the computer program GARD2, vault analysis, which considers container failure and waste leaching, hydrogeological modelling and geochemical modelling. Biosphere pathways analysis incorporates a compartmental modelling approach using the computer program RAMM, and a food chain analysis using the computer program FOOD II. Potentially-disruptive-phenomena analysis involves the estimation of the probability and consequences of events such as earthquakes which might reduce the effectiveness of the barriers preventing the release of radionuclides. The current stage of development of the required methodology and data is discussed in each of the three areas and preliminary results are presented. (author)

  7. Primer: Using Watershed Modeling System (WMS) for Gridded Surface Subsurface Hydrologic Analysis (GSSHA) Data Development - WMS 6.1 and GSSHA 1.43C

    National Research Council Canada - National Science Library

    Downer, Charles

    2003-01-01

    This document is a primer for use of the Watershed Modeling System (WMS) interface with the physically based, distributed-parameter hydrologic model Gridded Surface Subsurface Hydrologic Analysis (GSSHA...

  8. Water System Adaptation To Hydrological Changes: Module 14, Life Cycle Analysis (LCA) and Prioritization Tools in Water System Adaptation

    Science.gov (United States)

    This course will introduce students to the fundamental principles of water system adaptation to hydrological changes, with emphasis on data analysis and interpretation, technical planning, and computational modeling. Starting with real-world scenarios and adaptation needs, the co...

  9. Pathway Analysis in Attention Deficit Hyperactivity Disorder: An Ensemble Approach

    Science.gov (United States)

    Mooney, Michael A.; McWeeney, Shannon K.; Faraone, Stephen V.; Hinney, Anke; Hebebrand, Johannes; Nigg, Joel T.; Wilmot, Beth

    2016-01-01

    Despite a wealth of evidence for the role of genetics in attention deficit hyperactivity disorder (ADHD), specific and definitive genetic mechanisms have not been identified. Pathway analyses, a subset of gene-set analyses, extend the knowledge gained from genome-wide association studies (GWAS) by providing functional context for genetic associations. However, there are numerous methods for association testing of gene sets and no real consensus regarding the best approach. The present study applied six pathway analysis methods to identify pathways associated with ADHD in two GWAS datasets from the Psychiatric Genomics Consortium. Methods that utilize genotypes to model pathway-level effects identified more replicable pathway associations than methods using summary statistics. In addition, pathways implicated by more than one method were significantly more likely to replicate. A number of brain-relevant pathways, such as RhoA signaling, glycosaminoglycan biosynthesis, fibroblast growth factor receptor activity, and pathways containing potassium channel genes, were nominally significant by multiple methods in both datasets. These results support previous hypotheses about the role of regulation of neurotransmitter release, neurite outgrowth and axon guidance in contributing to the ADHD phenotype and suggest the value of cross-method convergence in evaluating pathway analysis results. PMID:27004716

  10. minepath.org: a free interactive pathway analysis web server.

    Science.gov (United States)

    Koumakis, Lefteris; Roussos, Panos; Potamias, George

    2017-07-03

    ( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Hydrological behaviour and water balance analysis for Xitiaoxi catchment of Taihu Basin

    Directory of Open Access Journals (Sweden)

    Xue Lijuan

    2008-09-01

    Full Text Available With the rapid social and economic development of the Taihu region, Taihu Lake now faces an increasingly severe eutrophication problem. Pollution from surrounding catchments contributes greatly to the eutrophication of water bodies in the region. Investigation of surface flow and associated mass transport for the Xitiaoxi catchment is of a significant degree of importance as the Xitiaoxi catchment is one of the major catchments within the Taihu region. A SWAT-based distributed hydrological model was established for the Xitiaoxi catchment. The model was calibrated and verified using hydrometeorological data from 1988 to 2001. The results indicate that the modeled daily and annual stream flow match the observed data both in the calibration period and the verification period, with a linear regression coefficient R2 and a coefficient e for modeled daily stream flow greater than 0.8 at Hengtangcun and Fanjiacun gauge stations. The results show that the runoff process in the Xitiaoxi catchment is affected both by rainfall and human activities (e.g., reservoirs and polder areas. Moreover, the human activities weaken flood peaks more noticeably during rainstorms. The water balance analysis reveals the percentages of precipitation made up by surface flow, evapotranspiration, groundwater recharge and the change of soil storage, all of which are considered useful to the further understanding of the hydrological processes in the Xitiaoxi catchment. This study provides a good base for further studies in mass transport modeling and comparison of modeling results from similar hydrological models.

  12. Numerical analysis of thermal-hydrological conditions in the single heater test at Yucca Mountain

    International Nuclear Information System (INIS)

    Birkholzer, Jens T.; Tsang, Yvonne W.

    1998-01-01

    The Single Heater Test (SHT) is one of two in-situ thermal tests included in the site characterization program for the potential underground nuclear waste repository at Yucca Mountain. The heating phase of the SHT started in August 1996, and was completed in May 1997 after 9 months of heating. The coupled processes in the unsaturated fractured rock mass around the heater were monitored by numerous sensors for thermal, hydrological, mechanical and chemical data. In addition to passive monitoring, active testing of the rock mass moisture content was performed using geophysical methods and air injection testing. The extensive data set available from this test gives a unique opportunity to improve the understanding of the thermal-hydrological situation in the natural setting of the repository rocks. The present paper focuses on the 3-D numerical simulation of the thermal-hydrological processes in the SHT using TOUGH2. In the comparative analysis, they are particularly interested in the accuracy of different fracture-matrix-interaction concepts such as the Effective Continuum (ECM), the Dual Continuum (DKM), and the Multiple Interacting Continua (MINC) method

  13. Enabling Web-Based Analysis of CUAHSI HIS Hydrologic Data Using R and Web Processing Services

    Science.gov (United States)

    Ames, D. P.; Kadlec, J.; Bayles, M.; Seul, M.; Hooper, R. P.; Cummings, B.

    2015-12-01

    The CUAHSI Hydrologic Information System (CUAHSI HIS) provides open access to a large number of hydrological time series observation and modeled data from many parts of the world. Several software tools have been designed to simplify searching and access to the CUAHSI HIS datasets. These software tools include: Desktop client software (HydroDesktop, HydroExcel), developer libraries (WaterML R Package, OWSLib, ulmo), and the new interactive search website, http://data.cuahsi.org. An issue with using the time series data from CUAHSI HIS for further analysis by hydrologists (for example for verification of hydrological and snowpack models) is the large heterogeneity of the time series data. The time series may be regular or irregular, contain missing data, have different time support, and be recorded in different units. R is a widely used computational environment for statistical analysis of time series and spatio-temporal data that can be used to assess fitness and perform scientific analyses on observation data. R includes the ability to record a data analysis in the form of a reusable script. The R script together with the input time series dataset can be shared with other users, making the analysis more reproducible. The major goal of this study is to examine the use of R as a Web Processing Service for transforming time series data from the CUAHSI HIS and sharing the results on the Internet within HydroShare. HydroShare is an online data repository and social network for sharing large hydrological data sets such as time series, raster datasets, and multi-dimensional data. It can be used as a permanent cloud storage space for saving the time series analysis results. We examine the issues associated with running R scripts online: including code validation, saving of outputs, reporting progress, and provenance management. An explicit goal is that the script which is run locally should produce exactly the same results as the script run on the Internet. Our design can

  14. RIMS: An Integrated Mapping and Analysis System with Applications to Earth Sciences and Hydrology

    Science.gov (United States)

    Proussevitch, A. A.; Glidden, S.; Shiklomanov, A. I.; Lammers, R. B.

    2011-12-01

    A web-based information and computational system for analysis of spatially distributed Earth system, climate, and hydrologic data have been developed. The System allows visualization, data exploration, querying, manipulation and arbitrary calculations with any loaded gridded or vector polygon dataset. The system's acronym, RIMS, stands for its core functionality as a Rapid Integrated Mapping System. The system can be deployed for a Global scale projects as well as for regional hydrology and climatology studies. In particular, the Water Systems Analysis Group of the University of New Hampshire developed the global and regional (Northern Eurasia, pan-Arctic) versions of the system with different map projections and specific data. The system has demonstrated its potential for applications in other fields of Earth sciences and education. The key Web server/client components of the framework include (a) a visualization engine built on Open Source libraries (GDAL, PROJ.4, etc.) that are utilized in a MapServer; (b) multi-level data querying tools built on XML server-client communication protocols that allow downloading map data on-the-fly to a client web browser; and (c) data manipulation and grid cell level calculation tools that mimic desktop GIS software functionality via a web interface. Server side data management of the system is designed around a simple database of dataset metadata facilitating mounting of new data to the system and maintaining existing data in an easy manner. RIMS contains "built-in" river network data that allows for query of upstream areas on-demand which can be used for spatial data aggregation and analysis of sub-basin areas. RIMS is an ongoing effort and currently being used to serve a number of websites hosting a suite of hydrologic, environmental and other GIS data.

  15. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

    Directory of Open Access Journals (Sweden)

    Zhongqi Ge

    2018-04-01

    Full Text Available Summary: Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies. : Ge et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to provide a comprehensive characterization of the ubiquitin pathway. They detect somatic driver candidates in the ubiquitin pathway and identify a cluster of patients with poor survival, highlighting the importance of this pathway in cancer development. Keywords: ubiquitin pathway, pan-cancer analysis, The Cancer Genome Atlas, tumor subtype, cancer prognosis, therapeutic targets, biomarker, FBXW7

  16. Multi-criteria decision analysis using hydrological indicators for decision support - a conceptual framework.

    Science.gov (United States)

    Butchart-Kuhlmann, Daniel; Kralisch, Sven; Meinhardt, Markus; Fleischer, Melanie

    2017-04-01

    Assessing the quantity and quality of water available in water stressed environments under various potential climate and land-use changes is necessary for good water and environmental resources management and governance. Within the region covered by the Southern African Science Service Centre for Climate Change and Adaptive Land Management (SASSCAL) project, such areas are common. One goal of the SASSCAL project is to develop and provide an integrated decision support system (DSS) with which decision makers (DMs) within a given catchment can obtain objective information regarding potential changes in water flow quantity and timing. The SASSCAL DSS builds upon existing data storage and distribution capability, through the SASSCAL Information System (IS), as well as the J2000 hydrological model. Using output from validated J2000 models, the SASSCAL DSS incorporates the calculation of a range of hydrological indicators based upon Indicators of Hydrological Alteration/Environmental Flow Components (IHA/EFC) calculated for a historic time series (pre-impact) and a set of model simulations based upon a selection of possible climate and land-use change scenarios (post-impact). These indicators, obtained using the IHA software package, are then used as input for a multi-criteria decision analysis (MCDA) undertaken using the open source diviz software package. The results of these analyses will provide DMs with an indication as to how various hydrological indicators within a catchment may be altered under different future scenarios, as well providing a ranking of how each scenario is preferred according to different DM preferences. Scenarios are represented through a combination of model input data and parameter settings in J2000, and preferences are represented through criteria weighting in the MCDA. Here, the methodology is presented and applied to the J2000 Luanginga model results using a set of hypothetical decision maker preference values as input for an MCDA based on

  17. Hydrology Analysis and Modelling for Klang River Basin Flood Hazard Map

    Science.gov (United States)

    Sidek, L. M.; Rostam, N. E.; Hidayah, B.; Roseli, ZA; Majid, W. H. A. W. A.; Zahari, N. Z.; Salleh, S. H. M.; Ahmad, R. D. R.; Ahmad, M. N.

    2016-03-01

    Flooding, a common environmental hazard worldwide has in recent times, increased as a result of climate change and urbanization with the effects felt more in developing countries. As a result, the explosive of flooding to Tenaga Nasional Berhad (TNB) substation is increased rapidly due to existing substations are located in flood prone area. By understanding the impact of flood to their substation, TNB has provided the non-structure mitigation with the integration of Flood Hazard Map with their substation. Hydrology analysis is the important part in providing runoff as the input for the hydraulic part.

  18. Hydrological threats to riparian wetlands of international importance – a global quantitative and qualitative analysis

    Directory of Open Access Journals (Sweden)

    C. Schneider

    2017-06-01

    Full Text Available Riparian wetlands have been disappearing at an accelerating rate. Their ecological integrity as well as their vital ecosystem services for humankind depend on regular patterns of inundation and drying provided by natural flow regimes. However, river hydrology has been altered worldwide. Dams cause less variable flow regimes and water abstractions decrease the amount of flow so that ecologically important flood pulses are often reduced. Given growing population pressure and projected climate change, immediate action is required. However, the implementation of counteractive measures is often a complex task. This study develops a screening tool for assessing hydrological threats to riparian wetlands on global scales. The approach is exemplified on 93 Ramsar sites, many of which are located in transboundary basins. First, the WaterGAP3 hydrological modeling framework is used to quantitatively compare current and future modified flow regimes to reference flow conditions. In our simulations current water resource management seriously impairs riparian wetland inundation at 29 % of the analyzed sites. A further 8 % experience significantly reduced flood pulses. In the future, eastern Europe, western Asia, as well as central South America could be hotspots of further flow modifications due to climate change. Second, a qualitative analysis of the 93 sites determined potential impact on overbank flows resulting from planned or proposed dam construction projects. They take place in one-third of the upstream areas and are likely to impair especially wetlands located in South America, Asia, and the Balkan Peninsula. Third, based on the existing legal/institutional framework and water resource availability upstream, further qualitative analysis evaluated the capacity to preserve overbank flows given future streamflow changes due to dam construction and climate change. Results indicate hotspots of vulnerability exist, especially in northern Africa and the

  19. Modelling and Analysis of Biochemical Signalling Pathway Cross-talk

    Directory of Open Access Journals (Sweden)

    Robin Donaldson

    2010-02-01

    Full Text Available Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising parallel composition of instances of generic modules (with internal and external labels. Pathways are then composed by (synchronising parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways.

  20. Pathway analysis for alternate low-level waste disposal methods

    International Nuclear Information System (INIS)

    Rao, R.R.; Kozak, M.W.; McCord, J.T.; Olague, N.E.

    1992-01-01

    The purpose of this paper is to evaluate a complete set of environmental pathways for disposal options and conditions that the Nuclear Regulatory Commission (NRC) may analyze for a low-level radioactive waste (LLW) license application. The regulations pertaining In the past, shallow-land burial has been used for the disposal of low-level radioactive waste. However, with the advent of the State Compact system of LLW disposal, many alternative technologies may be used. The alternative LLW disposal facilities include below- ground vault, tumulus, above-ground vault, shaft, and mine disposal This paper will form the foundation of an update of the previously developed Sandia National Laboratories (SNL)/NRC LLW performance assessment methodology. Based on the pathway assessment for alternative disposal methods, a determination will be made about whether the current methodology can satisfactorily analyze the pathways and phenomena likely to be important for the full range of potential disposal options. We have attempted to be conservative in keeping pathways in the lists that may usually be of marginal importance. In this way we can build confidence that we have spanned the range of cases likely to be encountered at a real site. Results of the pathway assessment indicate that disposal methods can be categorized in groupings based on their depth of disposal. For the deep disposal options of shaft and mine disposal, the key pathways are identical. The shallow disposal options, such as tumulus, shallow-land, and below-ground vault disposal also may be grouped together from a pathway analysis perspective. Above-ground vault disposal cannot be grouped with any of the other disposal options. The pathway analysis shows a definite trend concerning depth of disposal. The above-ground option has the largest number of significant pathways. As the waste becomes more isolated, the number of significant pathways is reduced. Similar to shallow-land burial, it was found that for all

  1. Climate change impacts analysis on hydrological processes in the Weyib River basin in Ethiopia

    Science.gov (United States)

    Serur, Abdulkerim Bedewi; Sarma, Arup Kumar

    2017-12-01

    The study aims to examine the variation of hydrological processes (in terms of mean annual, seasonal, and monthly) under changing climate within the Weyib River basin in Ethiopia at both basin and sub-basin level using ArcSWAT hydrologic model. The climate change impacts on temperature and precipitation characteristics within the basin have been studied using GFDL-ESM2M, CanESM2, and GFDL-ESM2G models for RCP8.5, RCP4.5, and RCP2.6 scenarios from coupled model inter-comparison project 5 (CMIP5) which have been downscaled by SDSM. The results revealed that the mean annual temperature and precipitation reveal a statistically significant (at 5% significant level) increasing trend in the nine ESM-RCP scenarios for all the future time slices. The mean annual actual evapotranspiration, baseflow, soil water content, percolation, and water availability in the stream exhibit a rise for all the ESMs-RCP scenarios in the entire basin and in all the sub-basins. However, surface runoff and potential evapotranspiration show a decreasing trend. The mean annual water availability increases between 9.18 and 27.97% (RCP8.5), 3.98 and 19.61% (RCP4.5), and 11.82 and 17.06% (RCP2.6) in the entire basin. The sub-basin level analysis reveals that the annual, seasonal, and monthly variations of hydrological processes in all the sub-basins are similar regarding direction but different in magnitude as compared to that of the entire basin analysis. In addition, it is observed that there is a larger monthly and seasonal variation in hydrological processes as compared to the variation in annual scale. The net water availability tends to decline in the dry season; this might cause water shortage in the lowland region and greater increases in an intermediate and rainy seasons; this might cause flooding to some flood prone region of the basin. Since the variation of water availability among the sub-basins in upcoming period is high, there is a scope of meeting agriculture water demand through

  2. Statistical analysis of extreme values from insurance, finance, hydrology and other fields

    CERN Document Server

    Reiss, Rolf-Dieter

    1997-01-01

    The statistical analysis of extreme data is important for various disciplines, including hydrology, insurance, finance, engineering and environmental sciences. This book provides a self-contained introduction to the parametric modeling, exploratory analysis and statistical interference for extreme values. The entire text of this third edition has been thoroughly updated and rearranged to meet the new requirements. Additional sections and chapters, elaborated on more than 100 pages, are particularly concerned with topics like dependencies, the conditional analysis and the multivariate modeling of extreme data. Parts I–III about the basic extreme value methodology remain unchanged to some larger extent, yet notable are, e.g., the new sections about "An Overview of Reduced-Bias Estimation" (co-authored by M.I. Gomes), "The Spectral Decomposition Methodology", and "About Tail Independence" (co-authored by M. Frick), and the new chapter about "Extreme Value Statistics of Dependent Random Variables" (co-authored ...

  3. Designing hydrological and financial instruments for small scale farmers in Sub-Saharan Africa: A socio-hydrological analysis

    Science.gov (United States)

    Moshtaghi, M.; Pande, S.; Savenije, H. H. G.; den Besten, N. I.

    2016-12-01

    Eighty percent of the farmland in Sub-Saharan Africa is managed by smallholders and they are often economically stressed; low income as a result of poor crop yields. Indeed, smallholders' well-being is naturally important, which often suffers due to hydro-climatic variability and fluctuations in prices of inputs (seeds, fertilizer) and outputs (crops). Appropriate designed insurances can guarantee their wellbeing and food security in whole continent, if they focus on specified requirement of smallholders in each region. In this research, we apply recently developed socio-hydrologic modelling, which interprets a small scale farm system as a coupled system of 6 variables: soil moisture, solid fertility, capital, livestock, fodder and labor availability. By using datasets of potential evaporation, rainfall, land cover and etc, we want to make a comparison between application of yield index insurance, weather index insurance and biomass Index Insurance to highlight the importance of considering the interplay between fertilizer and water availability in food security and also determine type of regional insurance which works better in a certain land.

  4. Hydrology and Oceanography Analysis Regarding The NPP Site Screening Process at Banten Province

    International Nuclear Information System (INIS)

    Yarianto-S-Budi-Susilo

    2007-01-01

    Regarding the NPP development in the future, it is needed to make inventory of potential site in the Java Island as well as in the outside Java Island. The NPP site inventory availability is to answer the energy demand challenge. Site screening process should be performed in accordance with the IAEA safety standard regarding the site selection, investigating several aspects related to the NPP safety (exclusion, safety and suitability factor) in the large area to obtain potential site candidates. For the site survey stage of hydrology and oceanography aspects, the analysis are more focused on the tidal phenomena along the north coastline, bathymetry, water resource, and hydrology system in the Banten Province. The method used are secondary data collection, field confirmation and internet searching. The result of the study showed that Tanjung Pujut and Tanjung Pasir are suitable based on the bathymetry and water intake facility consideration. Meanwhile Tanjung Kait and Tanjung Pasir more suitable considering tsunami aspects that may be generated by Krakatau Volcano. (author)

  5. A hydrological analysis of the 4 November 2011 event in Genoa

    Directory of Open Access Journals (Sweden)

    F. Silvestro

    2012-09-01

    Full Text Available On the 4 November 2011 a flash flood event hit the area of Genoa with dramatic consequences. Such an event represents, from the meteorological and hydrological perspective, a paradigm of flash floods in the Mediterranean environment.

    The hydro-meteorological probabilistic forecasting system for small and medium size catchments in use at the Civil Protection Centre of Liguria region exhibited excellent performances for the event, by predicting, 24–48 h in advance, the potential level of risk associated with the forecast. It greatly helped the decision makers in issuing a timely and correct alert.

    In this work we present the operational outputs of the system provided during the Liguria events and the post event hydrological modelling analysis that has been carried out accounting also for the crowd sourcing information and data. We discuss the benefit of the implemented probabilistic systems for decision-making under uncertainty, highlighting how, in this case, the multi-catchment approach used for predicting floods in small basins has been crucial.

  6. Sensitivity analysis and parameter estimation for distributed hydrological modeling: potential of variational methods

    Directory of Open Access Journals (Sweden)

    W. Castaings

    2009-04-01

    Full Text Available Variational methods are widely used for the analysis and control of computationally intensive spatially distributed systems. In particular, the adjoint state method enables a very efficient calculation of the derivatives of an objective function (response function to be analysed or cost function to be optimised with respect to model inputs.

    In this contribution, it is shown that the potential of variational methods for distributed catchment scale hydrology should be considered. A distributed flash flood model, coupling kinematic wave overland flow and Green Ampt infiltration, is applied to a small catchment of the Thoré basin and used as a relatively simple (synthetic observations but didactic application case.

    It is shown that forward and adjoint sensitivity analysis provide a local but extensive insight on the relation between the assigned model parameters and the simulated hydrological response. Spatially distributed parameter sensitivities can be obtained for a very modest calculation effort (~6 times the computing time of a single model run and the singular value decomposition (SVD of the Jacobian matrix provides an interesting perspective for the analysis of the rainfall-runoff relation.

    For the estimation of model parameters, adjoint-based derivatives were found exceedingly efficient in driving a bound-constrained quasi-Newton algorithm. The reference parameter set is retrieved independently from the optimization initial condition when the very common dimension reduction strategy (i.e. scalar multipliers is adopted.

    Furthermore, the sensitivity analysis results suggest that most of the variability in this high-dimensional parameter space can be captured with a few orthogonal directions. A parametrization based on the SVD leading singular vectors was found very promising but should be combined with another regularization strategy in order to prevent overfitting.

  7. Forest hydrology

    Science.gov (United States)

    Ge Sun; Devendra Amatya; Steve McNulty

    2016-01-01

    Forest hydrology studies the distribution, storage, movement, and quality of water and the hydrological processes in forest-dominated ecosystems. Forest hydrological science is regarded as the foundation of modern integrated water¬shed management. This chapter provides an overview of the history of forest hydrology and basic principles of this unique branch of...

  8. Hydrological model calibration for derived flood frequency analysis using stochastic rainfall and probability distributions of peak flows

    Science.gov (United States)

    Haberlandt, U.; Radtke, I.

    2014-01-01

    Derived flood frequency analysis allows the estimation of design floods with hydrological modeling for poorly observed basins considering change and taking into account flood protection measures. There are several possible choices regarding precipitation input, discharge output and consequently the calibration of the model. The objective of this study is to compare different calibration strategies for a hydrological model considering various types of rainfall input and runoff output data sets and to propose the most suitable approach. Event based and continuous, observed hourly rainfall data as well as disaggregated daily rainfall and stochastically generated hourly rainfall data are used as input for the model. As output, short hourly and longer daily continuous flow time series as well as probability distributions of annual maximum peak flow series are employed. The performance of the strategies is evaluated using the obtained different model parameter sets for continuous simulation of discharge in an independent validation period and by comparing the model derived flood frequency distributions with the observed one. The investigations are carried out for three mesoscale catchments in northern Germany with the hydrological model HEC-HMS (Hydrologic Engineering Center's Hydrologic Modeling System). The results show that (I) the same type of precipitation input data should be used for calibration and application of the hydrological model, (II) a model calibrated using a small sample of extreme values works quite well for the simulation of continuous time series with moderate length but not vice versa, and (III) the best performance with small uncertainty is obtained when stochastic precipitation data and the observed probability distribution of peak flows are used for model calibration. This outcome suggests to calibrate a hydrological model directly on probability distributions of observed peak flows using stochastic rainfall as input if its purpose is the

  9. Atmospheric Pathway Screening Analysis for Saltstone Disposal Facility Vault 4

    International Nuclear Information System (INIS)

    COOK, JAMES

    2004-01-01

    A sequential screening process using a methodology developed by the National Council on Radiation Protection and Measurements, professional judgment and process knowledge has been used to produce a list of radionuclides requiring detailed analysis to derive disposal limits for the Saltstone Disposal Facility based on the atmospheric pathway

  10. Distributed Evaluation of Local Sensitivity Analysis (DELSA), with application to hydrologic models

    Science.gov (United States)

    Rakovec, O.; Hill, M. C.; Clark, M. P.; Weerts, A. H.; Teuling, A. J.; Uijlenhoet, R.

    2014-01-01

    This paper presents a hybrid local-global sensitivity analysis method termed the Distributed Evaluation of Local Sensitivity Analysis (DELSA), which is used here to identify important and unimportant parameters and evaluate how model parameter importance changes as parameter values change. DELSA uses derivative-based "local" methods to obtain the distribution of parameter sensitivity across the parameter space, which promotes consideration of sensitivity analysis results in the context of simulated dynamics. This work presents DELSA, discusses how it relates to existing methods, and uses two hydrologic test cases to compare its performance with the popular global, variance-based Sobol' method. The first test case is a simple nonlinear reservoir model with two parameters. The second test case involves five alternative "bucket-style" hydrologic models with up to 14 parameters applied to a medium-sized catchment (200 km2) in the Belgian Ardennes. Results show that in both examples, Sobol' and DELSA identify similar important and unimportant parameters, with DELSA enabling more detailed insight at much lower computational cost. For example, in the real-world problem the time delay in runoff is the most important parameter in all models, but DELSA shows that for about 20% of parameter sets it is not important at all and alternative mechanisms and parameters dominate. Moreover, the time delay was identified as important in regions producing poor model fits, whereas other parameters were identified as more important in regions of the parameter space producing better model fits. The ability to understand how parameter importance varies through parameter space is critical to inform decisions about, for example, additional data collection and model development. The ability to perform such analyses with modest computational requirements provides exciting opportunities to evaluate complicated models as well as many alternative models.

  11. [Sensitivity analysis of AnnAGNPS model's hydrology and water quality parameters based on the perturbation analysis method].

    Science.gov (United States)

    Xi, Qing; Li, Zhao-Fu; Luo, Chuan

    2014-05-01

    Sensitivity analysis of hydrology and water quality parameters has a great significance for integrated model's construction and application. Based on AnnAGNPS model's mechanism, terrain, hydrology and meteorology, field management, soil and other four major categories of 31 parameters were selected for the sensitivity analysis in Zhongtian river watershed which is a typical small watershed of hilly region in the Taihu Lake, and then used the perturbation method to evaluate the sensitivity of the parameters to the model's simulation results. The results showed that: in the 11 terrain parameters, LS was sensitive to all the model results, RMN, RS and RVC were generally sensitive and less sensitive to the output of sediment but insensitive to the remaining results. For hydrometeorological parameters, CN was more sensitive to runoff and sediment and relatively sensitive for the rest results. In field management, fertilizer and vegetation parameters, CCC, CRM and RR were less sensitive to sediment and particulate pollutants, the six fertilizer parameters (FR, FD, FID, FOD, FIP, FOP) were particularly sensitive for nitrogen and phosphorus nutrients. For soil parameters, K is quite sensitive to all the results except the runoff, the four parameters of the soil's nitrogen and phosphorus ratio (SONR, SINR, SOPR, SIPR) were less sensitive to the corresponding results. The simulation and verification results of runoff in Zhongtian watershed show a good accuracy with the deviation less than 10% during 2005- 2010. Research results have a direct reference value on AnnAGNPS model's parameter selection and calibration adjustment. The runoff simulation results of the study area also proved that the sensitivity analysis was practicable to the parameter's adjustment and showed the adaptability to the hydrology simulation in the Taihu Lake basin's hilly region and provide reference for the model's promotion in China.

  12. Floods in Serbia in the 1999-2009 period: Hydrological analysis and flood protection measures

    Directory of Open Access Journals (Sweden)

    Milanović Ana

    2010-01-01

    Full Text Available The review on greatest floods recorded in Vojvodina and central Serbia within the period from 1999 to 2009 is given in this paper. For 13 hydrological stations, that recorded the greatest floods for the present period, probability of occurrence of these floods has been accomplished. Based on analysis of time series of discharge and water level maximum, performed by applying probability theory and mathematical statistics, and calculated theoretical probability distribution function of floods, probability of occurrence of flood has been obtained. Most often the best agreement with the empirical distribution function had a Log-Pearson III, Pearson III distribution. These results can be used for dimensioning of hydro-technical objects for flood protection. The most significant causes for floods recorded in this period were melting of snow and intensive rainfall. In this paper the current situation of flood protection and future development of flood protection measures were also presented. .

  13. Pathway analysis of kidney cancer using proteomics and metabolic profiling

    Directory of Open Access Journals (Sweden)

    Fiehn Oliver

    2006-11-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is the sixth leading cause of cancer death and is responsible for 11,000 deaths per year in the US. Approximately one-third of patients present with disease which is already metastatic and for which there is currently no adequate treatment, and no biofluid screening tests exist for RCC. In this study, we have undertaken a comprehensive proteomic analysis and subsequently a pathway and network approach to identify biological processes involved in clear cell RCC (ccRCC. We have used these data to investigate urinary markers of RCC which could be applied to high-risk patients, or to those being followed for recurrence, for early diagnosis and treatment, thereby substantially reducing mortality of this disease. Results Using 2-dimensional electrophoresis and mass spectrometric analysis, we identified 31 proteins which were differentially expressed with a high degree of significance in ccRCC as compared to adjacent non-malignant tissue, and we confirmed some of these by immunoblotting, immunohistochemistry, and comparison to published transcriptomic data. When evaluated by several pathway and biological process analysis programs, these proteins are demonstrated to be involved with a high degree of confidence (p values Conclusion Extensive pathway and network analysis allowed for the discovery of highly significant pathways from a set of clear cell RCC samples. Knowledge of activation of these processes will lead to novel assays identifying their proteomic and/or metabolomic signatures in biofluids of patient at high risk for this disease; we provide pilot data for such a urinary bioassay. Furthermore, we demonstrate how the knowledge of networks, processes, and pathways altered in kidney cancer may be used to influence the choice of optimal therapy.

  14. Sensitivity analysis of machine-learning models of hydrologic time series

    Science.gov (United States)

    O'Reilly, A. M.

    2017-12-01

    Sensitivity analysis traditionally has been applied to assessing model response to perturbations in model parameters, where the parameters are those model input variables adjusted during calibration. Unlike physics-based models where parameters represent real phenomena, the equivalent of parameters for machine-learning models are simply mathematical "knobs" that are automatically adjusted during training/testing/verification procedures. Thus the challenge of extracting knowledge of hydrologic system functionality from machine-learning models lies in their very nature, leading to the label "black box." Sensitivity analysis of the forcing-response behavior of machine-learning models, however, can provide understanding of how the physical phenomena represented by model inputs affect the physical phenomena represented by model outputs.As part of a previous study, hybrid spectral-decomposition artificial neural network (ANN) models were developed to simulate the observed behavior of hydrologic response contained in multidecadal datasets of lake water level, groundwater level, and spring flow. Model inputs used moving window averages (MWA) to represent various frequencies and frequency-band components of time series of rainfall and groundwater use. Using these forcing time series, the MWA-ANN models were trained to predict time series of lake water level, groundwater level, and spring flow at 51 sites in central Florida, USA. A time series of sensitivities for each MWA-ANN model was produced by perturbing forcing time-series and computing the change in response time-series per unit change in perturbation. Variations in forcing-response sensitivities are evident between types (lake, groundwater level, or spring), spatially (among sites of the same type), and temporally. Two generally common characteristics among sites are more uniform sensitivities to rainfall over time and notable increases in sensitivities to groundwater usage during significant drought periods.

  15. A coupled distributed hydrological-stability analysis on a terraced slope of Valtellina (northern Italy)

    Science.gov (United States)

    Camera, C.; Apuani, T.; Masetti, M.

    2013-02-01

    The aim of this work was to understand and reproduce the hydrological dynamics of a slope, which was terraced using dry-stone retaining walls and its response to these processes in terms of stability at the slope scale. The slope studied is located in Valtellina (northern Italy), near the village of Tresenda, and in the last 30 yr has experienced several soil slip/debris flow events. In 1983 alone, such events caused the death of 18 people. Direct observation of the events of 1983 enabled the principal triggering cause of these events to be recognized in the formation of an overpressure at the base of a dry-stone wall, which caused its failure. To perform the analyses it is necessary to include the presence of dry-stone walls, considering the importance they have in influencing hydrological and geotechnical processes at the slope scale. This requires a very high resolution DEM (1 m × 1 m because the walls are from 0.60 m to 1.0 m wide) that has been appositely derived. A hydrogeological raster-based model, which takes into account both the unsaturated and saturated flux components, was applied. This was able to identify preferential infiltration zones and was rather precise in the prediction of maximum groundwater levels, providing valid input for the distributed stability analysis. Results of the hydrogeological model were used for the successive stability analysis. Sections of terrace were identified from the downslope base of a retaining wall to the top of the next downslope retaining wall. Within each section a global method of equilibrium was applied to determine its safety factor. The stability model showed a general tendency to overestimate the amount of unstable areas. An investigation of the causes of this unexpected behavior was, therefore, also performed in order to progressively improve the reliability of the model.

  16. Hydrologic Analysis of Ungauged Catchments For The Supply of Water For Irrigation On Railway Embankment Batters

    Science.gov (United States)

    Gyasi-Agyei, Y.; Nissen, D.

    Water has been identified as a key component to the success of grass establishment on railway embankment batters (side slope) within Central Queensland, Australia, to control erosion. However, the region under study being semi-arid experiences less than 600 mm average annual rainfall occurring on about 60 days of the year. Culverts and bridges are integral part of railway embankments. They are used to cross water courses, be it an ephemeral creek or just a surface runoff path. Surface runoff through an ungauged railway embankment culvert is diverted to a temporary excavated pond located at the downstream side of the hydraulic structure. The temporary excavated pond water is used to feed an automated drip irrigation system, with solar as a source of energy to drive a pump. Railway embankment batter erosion remediation is timed in the wet season when irrigation is used to supplement natural rainfall. Hydrologic analysis of ungauged catchments for sizing the temporary excavated pond is presented. It is based on scenarios of runoff coefficient and curve number, and mass curve (Rippl diagram). Three years of continuous rainfall data (1997/1998 -1999/2000) were used to design a pond. The performance of the designed pond was evaluated in a field experiment during the next wet season (2000/2001). It supplied adequate water for irrigation as predicted by the hydrologic analysis during the grass establishment. This helped to achieve 100% grass cover on the railway embankment batter within 12 weeks. The proposed irrigation system has been demonstrated t o be feasible and cost effective.

  17. Developing Flexible, Integrated Hydrologic Modeling Systems for Multiscale Analysis in the Midwest and Great Lakes Region

    Science.gov (United States)

    Hamlet, A. F.; Chiu, C. M.; Sharma, A.; Byun, K.; Hanson, Z.

    2016-12-01

    Physically based hydrologic modeling of surface and groundwater resources that can be flexibly and efficiently applied to support water resources policy/planning/management decisions at a wide range of spatial and temporal scales are greatly needed in the Midwest, where stakeholder access to such tools is currently a fundamental barrier to basic climate change assessment and adaptation efforts, and also the co-production of useful products to support detailed decision making. Based on earlier pilot studies in the Pacific Northwest Region, we are currently assembling a suite of end-to-end tools and resources to support various kinds of water resources planning and management applications across the region. One of the key aspects of these integrated tools is that the user community can access gridded products at any point along the end-to-end chain of models, looking backwards in time about 100 years (1915-2015), and forwards in time about 85 years using CMIP5 climate model projections. The integrated model is composed of historical and projected future meteorological data based on station observations and statistical and dynamically downscaled climate model output respectively. These gridded meteorological data sets serve as forcing data for the macro-scale VIC hydrologic model implemented over the Midwest at 1/16 degree resolution. High-resolution climate model (4km WRF) output provides inputs for the analyses of urban impacts, hydrologic extremes, agricultural impacts, and impacts to the Great Lakes. Groundwater recharge estimated by the surface water model provides input data for fine-scale and macro-scale groundwater models needed for specific applications. To highlight the multi-scale use of the integrated models in support of co-production of scientific information for decision making, we briefly describe three current case studies addressing different spatial scales of analysis: 1) Effects of climate change on the water balance of the Great Lakes, 2) Future

  18. A framework for improving a seasonal hydrological forecasting system using sensitivity analysis

    Science.gov (United States)

    Arnal, Louise; Pappenberger, Florian; Smith, Paul; Cloke, Hannah

    2017-04-01

    Seasonal streamflow forecasts are of great value for the socio-economic sector, for applications such as navigation, flood and drought mitigation and reservoir management for hydropower generation and water allocation to agriculture and drinking water. However, as we speak, the performance of dynamical seasonal hydrological forecasting systems (systems based on running seasonal meteorological forecasts through a hydrological model to produce seasonal hydrological forecasts) is still limited in space and time. In this context, the ESP (Ensemble Streamflow Prediction) remains an attractive forecasting method for seasonal streamflow forecasting as it relies on forcing a hydrological model (starting from the latest observed or simulated initial hydrological conditions) with historical meteorological observations. This makes it cheaper to run than a standard dynamical seasonal hydrological forecasting system, for which the seasonal meteorological forecasts will first have to be produced, while still producing skilful forecasts. There is thus the need to focus resources and time towards improvements in dynamical seasonal hydrological forecasting systems which will eventually lead to significant improvements in the skill of the streamflow forecasts generated. Sensitivity analyses are a powerful tool that can be used to disentangle the relative contributions of the two main sources of errors in seasonal streamflow forecasts, namely the initial hydrological conditions (IHC; e.g., soil moisture, snow cover, initial streamflow, among others) and the meteorological forcing (MF; i.e., seasonal meteorological forecasts of precipitation and temperature, input to the hydrological model). Sensitivity analyses are however most useful if they inform and change current operational practices. To this end, we propose a method to improve the design of a seasonal hydrological forecasting system. This method is based on sensitivity analyses, informing the forecasters as to which element of

  19. Non-stationary hydrologic frequency analysis using B-spline quantile regression

    Science.gov (United States)

    Nasri, B.; Bouezmarni, T.; St-Hilaire, A.; Ouarda, T. B. M. J.

    2017-11-01

    Hydrologic frequency analysis is commonly used by engineers and hydrologists to provide the basic information on planning, design and management of hydraulic and water resources systems under the assumption of stationarity. However, with increasing evidence of climate change, it is possible that the assumption of stationarity, which is prerequisite for traditional frequency analysis and hence, the results of conventional analysis would become questionable. In this study, we consider a framework for frequency analysis of extremes based on B-Spline quantile regression which allows to model data in the presence of non-stationarity and/or dependence on covariates with linear and non-linear dependence. A Markov Chain Monte Carlo (MCMC) algorithm was used to estimate quantiles and their posterior distributions. A coefficient of determination and Bayesian information criterion (BIC) for quantile regression are used in order to select the best model, i.e. for each quantile, we choose the degree and number of knots of the adequate B-spline quantile regression model. The method is applied to annual maximum and minimum streamflow records in Ontario, Canada. Climate indices are considered to describe the non-stationarity in the variable of interest and to estimate the quantiles in this case. The results show large differences between the non-stationary quantiles and their stationary equivalents for an annual maximum and minimum discharge with high annual non-exceedance probabilities.

  20. CRITICAL RADIONUCLIDE AND PATHWAY ANALYSIS FOR THE SAVANNAH RIVER SITE

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, T.

    2011-08-30

    This report is an update to the analysis, Assessment of SRS Radiological Liquid and Airborne Contaminants and Pathways, that was performed in 1997. An electronic version of this large original report is included in the attached CD to this report. During the operational history (1954 to the present) of the Savannah River Site (SRS), many different radionuclides have been released to the environment from the various production facilities. However, as will be shown by this updated radiological critical contaminant/critical pathway analysis, only a small number of the released radionuclides have been significant contributors to potential doses and risks to offsite people. The analysis covers radiological releases to the atmosphere and to surface waters, the principal media that carry contaminants offsite. These releases potentially result in exposure to offsite people. The groundwater monitoring performed at the site shows that an estimated 5 to 10% of SRS has been contaminated by radionuclides, no evidence exists from the extensive monitoring performed that groundwater contaminated with these constituents has migrated off the site (SRS 2011). Therefore, with the notable exception of radiological source terms originating from shallow surface water migration into site streams, onsite groundwater was not considered as a potential exposure pathway to offsite people. In addition, in response to the Department of Energy's (DOE) Order 435.1, several Performance Assessments (WSRC 2008; LWO 2009; SRR 2010; SRR 2011) and a Comprehensive SRS Composite Analysis (SRNO 2010) have recently been completed at SRS. The critical radionuclides and pathways identified in these extensive reports are discussed and, where applicable, included in this analysis.

  1. Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

    Science.gov (United States)

    Beltrame, Luca; Bianco, Luca; Fontana, Paolo; Cavalieri, Duccio

    2013-07-15

    Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher's test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice. Pathway Processor 2.0 is available as a web service at http://compbiotoolbox.fmach.it/pathwayProcessor/. Sample datasets to test the functionality can be used directly from the application. duccio.cavalieri@fmach.it Supplementary data are available at Bioinformatics online.

  2. Hydrologic models and analysis of water availability in Cuyama Valley, California

    Science.gov (United States)

    Hanson, R.T.; Flint, Lorraine E.; Faunt, Claudia C.; Gibbs, Dennis R.; Schmid, Wolfgang

    2014-01-01

    supplied by groundwater, which is augmented by precipitation during wet winter and spring seasons. In addition, the amount of groundwater used for irrigation varies from year to year in response to climate variation and can increase dramatically in dry years. Model simulation results, however, also indicated that irrigation may have been less efficient during wet years. Agricultural pumpage is a major component to simulated outflow that is often poorly recorded. Therefore, an integrated, coupled farm-process model is used to estimate historical pumpage for water-balance subregions that evolved with the development of groundwater in the Valley from 1949 through 2010. The integrated hydrologic model includes these water-balance subregions and delineates natural, municipal, and agricultural land use; streamflow networks; and groundwater flow systems. The redefinition of the geohydrologic framework (including the internal architecture of the sedimentary units) and incorporation of these units into the simulation of the regional groundwater flow system indicated that faults have compartmentalized the alluvial deposits into subregions, which have responded differently to regional groundwater flow, locations of recharge, and the effects of development. The Cuyama Valley comprises nine subregions grouped into three regional zones, the Main, Ventucopa Uplands, and Sierra Madre Foothills, which are fault bounded, represent different proportions of the three alluvial aquifers, and have different water quality. The CUVHM uses MF-OWHM to simulate and assess the use and movement of water, including the evolution of land use and related water-balance regions. The model is capable of being accurate at annual to interannual time frames and at subregional to valley-wide spatial scales, which allows for analysis of the groundwater hydrologic budget for the water years 1950–2010, as well as potential assessment of the sustainable use of groundwater. Simulated changes in storage over time

  3. Comparative analysis of meteorological and hydrological drought in the Pearl River basin during the period 1960-2012

    Science.gov (United States)

    Xu, K.; Wu, C.; Hu, B.; Niu, J.

    2017-12-01

    Drought is one of the major natural hazards that can have devastating impacts on the regional environment, agriculture, and water resources. Previous studies have conducted the assessment of historic changes in meteorological drought over various regional scales but rarely considered hydrological drought due to limited hydrological observations. Here, we use a long-term (1960-2012) gridded hydro-meteorological data to present a comparative analysis of meteorological and hydrological drought in the Pearl River basin in southern China using the standardized precipitation index (SPI) and the standardized runoff index (SRI). The variation in SPI and SRI at four different timescales (1-, 3-, 6-, and 12-month) is investigated using the Mann-Kendall (M-K) method and continuous wavelet transform (CWT). The results indicate that the correlation between SPI and SRI is strong over the Pearl River basin and tends to be stronger at the longer timescale. Meanwhile, the periodic oscillation pattern of SPI becomes more consistent with that of SRI with the increased timescale. The SPI can be used as a substitute for SRI to represent the hydrological drought at the long-term scale. Overall there is a noticeably wetting trend mainly in the eastern parts and a significant drying trend mainly in the western regions and the downstream area of the Pearl River basin. The variability of meteorological drought is significant mainly in the eastern and western regions, while the variability of hydrological drought tends to be larger mainly in the western region. CWT analysis indicates a period of 0.75-7 years in both meteorological and hydrological droughts during the period 1960-2012 in the study region.

  4. HYDROLOGIC MODEL UNCERTAINTY ASSOCIATED WITH SIMULATING FUTURE LAND-COVER/USE SCENARIOS: A RETROSPECTIVE ANALYSIS

    Science.gov (United States)

    GIS-based hydrologic modeling offers a convenient means of assessing the impacts associated with land-cover/use change for environmental planning efforts. Alternative future scenarios can be used as input to hydrologic models and compared with existing conditions to evaluate pot...

  5. Analysis of Membrane Protein Topology in the Plant Secretory Pathway.

    Science.gov (United States)

    Guo, Jinya; Miao, Yansong; Cai, Yi

    2017-01-01

    Topology of membrane proteins provides important information for the understanding of protein function and intermolecular associations. Integrate membrane proteins are generally transported from endoplasmic reticulum (ER) to Golgi and downstream compartments in the plant secretory pathway. Here, we describe a simple method to study membrane protein topology along the plant secretory pathway by transiently coexpressing a fluorescent protein (XFP)-tagged membrane protein and an ER export inhibitor protein, ARF1 (T31N), in tobacco BY-2 protoplast. By fractionation, microsome isolation, and trypsin digestion, membrane protein topology could be easily detected by either direct confocal microscopy imaging or western-blot analysis using specific XFP antibodies. A similar strategy in determining membrane protein topology could be widely adopted and applied to protein analysis in a broad range of eukaryotic systems, including yeast cells and mammalian cells.

  6. Monetary valuation with impact pathway analysis: Benefits of reducing nitrate leaching in European Catchments

    DEFF Research Database (Denmark)

    Andersen, Mikael Skou; Hansen, Morten Søes; Carstensen, Jacob

    2011-01-01

    Integrated assessment frameworks which can account comprehensively for the benefits related to water quality improvements have not yet been established. The main challenge is to link economic valuation with hydrological data in an appropriate way.We here explore the so-called ‘impact pathway...... approach’ as a novel analytical method in the area ofwater management. It can identify site- and catchment-specific benefits associated with management measures by linking economic and hydrological data through consecutive modelling stages, allowing for monetization of specific end point effects...

  7. Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data.

    Science.gov (United States)

    Lee, Hyeonjeong; Shin, Miyoung

    2017-01-01

    The problem of discovering genetic markers as disease signatures is of great significance for the successful diagnosis, treatment, and prognosis of complex diseases. Even if many earlier studies worked on identifying disease markers from a variety of biological resources, they mostly focused on the markers of genes or gene-sets (i.e., pathways). However, these markers may not be enough to explain biological interactions between genetic variables that are related to diseases. Thus, in this study, our aim is to investigate distinctive associations among active pathways (i.e., pathway-sets) shown each in case and control samples which can be observed from gene expression and/or methylation data. The pathway-sets are obtained by identifying a set of associated pathways that are often active together over a significant number of class samples. For this purpose, gene expression or methylation profiles are first analyzed to identify significant (active) pathways via gene-set enrichment analysis. Then, regarding these active pathways, an association rule mining approach is applied to examine interesting pathway-sets in each class of samples (case or control). By doing so, the sets of associated pathways often working together in activity profiles are finally chosen as our distinctive signature of each class. The identified pathway-sets are aggregated into a pathway activity network (PAN), which facilitates the visualization of differential pathway associations between case and control samples. From our experiments with two publicly available datasets, we could find interesting PAN structures as the distinctive signatures of breast cancer and uterine leiomyoma cancer, respectively. Our pathway-set markers were shown to be superior or very comparable to other genetic markers (such as genes or gene-sets) in disease classification. Furthermore, the PAN structure, which can be constructed from the identified markers of pathway-sets, could provide deeper insights into

  8. Towards validation of the Canadian precipitation analysis (CaPA) for hydrologic modeling applications in the Canadian Prairies

    Science.gov (United States)

    Boluwade, Alaba; Zhao, K.-Y.; Stadnyk, T. A.; Rasmussen, P.

    2018-01-01

    This study presents a three-step validation technique to compare the performance of the Canadian Precipitation Analysis (CaPA) product relative to actual observation as a hydrologic forcing in regional watershed simulation. CaPA is an interpolated (6 h or 24 h accumulation) reanalysis precipitation product in near real time covering all of North America. The analysis procedure involves point-to-point (P2P) and map-to-map (M2M) comparisons, followed by proxy validation using an operational version of the WATFLOOD™ hydrologic model from 2002 to 2005 in the Lake Winnipeg Basin (LWB), Canada. The P2P technique using a Bayesian change point analysis shows that CaPA corresponds with actual observations (Canadian daily climate data, CDCD), on both an annual and seasonal basis. CaPA has the same spatial pattern, dependency and autocorrelation properties as CDCD pixel by pixel (M2M). When used as hydrologic forcing in WATFLOOD™, results indicate that CaPA is a reliable product for water resource modeling and predictions, but that the quality of CaPA data varies annually and seasonally, as does the quality of observations. CaPA proved most beneficial as a hydrologic forcing during winter seasons where observation quality is the lowest. Reanalysis products, such as CaPA, can be a reliable option in sparse network areas, and is beneficial for regional governments when the cost of new weather stations is prohibitive.

  9. 2015 Long-Term Hydrologic Monitoring Program Sampling and Analysis Results at Rio Blanco, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    Findlay, Rick [Nararro Research and Engineering, Oak Ridge, TN (United States); Kautsky, Mark [US Department of Energy, Washington, DC (United States). Office of Legacy Management

    2015-12-01

    The U.S. Department of Energy (DOE) Office of Legacy Management conducted annual sampling at the Rio Blanco, Colorado, Site for the Long-Term Hydrologic Monitoring Program (LTHMP) on May 20–21, 2015. This report documents the analytical results of the Rio Blanco annual monitoring event, the trip report, and the data validation package. The groundwater and surface water monitoring samples were shipped to the GEL Group Inc. laboratories for conventional analysis of tritium and analysis of gamma-emitting radionuclides by high-resolution gamma spectrometry. A subset of water samples collected from wells near the Rio Blanco site was also sent to GEL Group Inc. for enriched tritium analysis. All requested analyses were successfully completed. Samples were collected from a total of four onsite wells, including two that are privately owned. Samples were also collected from two additional private wells at nearby locations and from nine surface water locations. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry, and they were analyzed for tritium using the conventional method with a detection limit on the order of 400 picocuries per liter (pCi/L). Four locations (one well and three surface locations) were analyzed using the enriched tritium method, which has a detection limit on the order of 3 pCi/L. The enriched locations included the well at the Brennan Windmill and surface locations at CER-1, CER-4, and Fawn Creek 500 feet upstream.

  10. The Added Utility of Hydrological Model and Satellite Based Datasets in Agricultural Drought Analysis over Turkey

    Science.gov (United States)

    Bulut, B.; Hüsami Afşar, M.; Yilmaz, M. T.

    2017-12-01

    Analysis of agricultural drought, which causes substantial socioeconomically costs in Turkey and in the world, is critical in terms of understanding this natural disaster's characteristics (intensity, duration, influence area) and research on possible precautions. Soil moisture is one of the most important parameters which is used to observe agricultural drought, can be obtained using different methods. The most common, consistent and reliable soil moisture datasets used for large scale analysis are obtained from hydrologic models and remote sensing retrievals. On the other hand, Normalized difference vegetation index (NDVI) and gauge based precipitation observations are also commonly used for drought analysis. In this study, soil moisture products obtained from different platforms, NDVI and precipitation datasets over several different agricultural regions under various climate conditions in Turkey are obtained in growth season period. These datasets are later used to investigate agricultural drought by the help of annual crop yield data of selected agricultural lands. The type of vegetation over these regions are obtained using CORINE Land Cover (CLC 2012) data. The crop yield data were taken from the record of related district's statistics which is provided by Turkish Statistical Institute (TÜİK). This project is supported by TÜBİTAK project number 114Y676.

  11. Analysis of Stomatal Patterning in Selected Mutants of MAPK Pathways

    KAUST Repository

    Felemban, Abrar

    2016-05-01

    Stomata are cellular valves in plants that play an essential role in the regulation of gas exchange and are distributed in the epidermis of aerial organs. In Arabidopsis thaliana, stomatal production and development are coordinated by the mitogen-activated protein kinase (MAPK) signalling pathway, which modulates a variety of other processes, including cell proliferation, regulation of cytokinesis, programed cell death, and response to abiotic and biotic stress. The environment also plays a role in stomatal development, by influencing the frequency at which stomata develop in leaves. This thesis presents an analysis of stomatal development in Arabidopsis mutants in two MAPK pathways: MEKK1-MKK1/MKK2-MPK4, and MAP3K17/18-MKK3. Obtained results demonstrate the effect of stress conditions on stomatal development and specify the involvement of analysed MAPK in stomatal patterning. First, both analysed pathways modulate stomatal patterning in Arabidopsis cotyledons. Second, plant growth-promoting bacteria tested enhance stomatal density and affect guard cell morphology. Third, the sucrose or mannitol treatment increases defects in stomatal patterning. Finally, salt stress or high temperature can suppress stomatal defects in mutants of the MEKK1-MKK1/MKK2-MPK4 pathway.

  12. Hydrology Project

    International Nuclear Information System (INIS)

    Anon.

    Research carried out in the 'Hydrology Project' of the Centro de Energia Nuclear na Agricultura', Piracicaba, Sao Paulo State, Brazil, are described. Such research comprises: Amazon hydrology and Northeast hydrology. Techniques for the measurement of isotope ratios are used. (M.A.) [pt

  13. Using Formal Concept Analysis to Create Pathways through Museum Collections

    DEFF Research Database (Denmark)

    Wray, Tim; Eklund, Peter

    2014-01-01

    This paper presents A Place for Art - an iPad app that allows users to explore an art collection via semantically linked pathways that are generated using Formal Concept Analysis. The app embraces the information seeking approach of exploration and is based on the idea that showing context...... and relationships among objects in a museum collection augments an interpretive experience. The fundamental interaction metaphor inherent in A Place for Art relies on Formal Concept Analysis so the interface has embedded within it the semantic clustering features of machine learning in artificial intelligence....

  14. Hydrologic analysis for ecological risk assessment of watersheds with abandoned mine lands

    International Nuclear Information System (INIS)

    Gallagher, D.; Babendreier, J.; Cherry, D.

    1999-01-01

    As part of on-going study of acid mine drainage (AMD), a comprehensive ecological risk assessment was conducted in the Leading Creek Watershed in southeast Ohio. The watershed is influenced by agriculture and active and abandoned coal-mining operations. This work presents a broad overview of several quantitative measures of hydrology and hydraulic watershed properties available for in risk assessment and evaluates their relation to metrics of ecology. Data analysis included statistical comparisons of metrics of ecology, ecotoxicology, water quality, and physically based parameters describing land use, geomorphology, flow, velocity, and particle size. A multiple regression analysis indicated that abandoned mining operations dominated impacts upon aquatic ecology. It also indicated low flow velocity measurements and a ratio of maximum velocity to average velocity at low flow where helpful in describing variation in macroinvertebrate Total Taxa scores. Other key parameters also identified strong impact relationships with biodiversity trends and included pH, simple knowledge of any mining upstream, calculated % of the subshed covered by strip mines, and the measured depth of streambed sediments from site to site

  15. Moment-based metrics for global sensitivity analysis of hydrological systems

    Directory of Open Access Journals (Sweden)

    A. Dell'Oca

    2017-12-01

    Full Text Available We propose new metrics to assist global sensitivity analysis, GSA, of hydrological and Earth systems. Our approach allows assessing the impact of uncertain parameters on main features of the probability density function, pdf, of a target model output, y. These include the expected value of y, the spread around the mean and the degree of symmetry and tailedness of the pdf of y. Since reliable assessment of higher-order statistical moments can be computationally demanding, we couple our GSA approach with a surrogate model, approximating the full model response at a reduced computational cost. Here, we consider the generalized polynomial chaos expansion (gPCE, other model reduction techniques being fully compatible with our theoretical framework. We demonstrate our approach through three test cases, including an analytical benchmark, a simplified scenario mimicking pumping in a coastal aquifer and a laboratory-scale conservative transport experiment. Our results allow ascertaining which parameters can impact some moments of the model output pdf while being uninfluential to others. We also investigate the error associated with the evaluation of our sensitivity metrics by replacing the original system model through a gPCE. Our results indicate that the construction of a surrogate model with increasing level of accuracy might be required depending on the statistical moment considered in the GSA. The approach is fully compatible with (and can assist the development of analysis techniques employed in the context of reduction of model complexity, model calibration, design of experiment, uncertainty quantification and risk assessment.

  16. An improved method for analysis of In-EDTA, I- and Br- used as active tracers in hydrological studies

    International Nuclear Information System (INIS)

    Stanescu, S.P.; Spiridon, S.

    1992-01-01

    Neutron activation analysis combined with chemical preconcentration of the elements in water samples can give a high sensitivity in the determination of concentrations for In-EDTA, I - and Br - used as active tracers in hydrological studies. The authors have developed an improved method of analysis which is sensitive, selective and applicable to a wide range of underground and surface water samples including those having a high concentration of manganese ions. (author) 6 refs.; 2 figs.; 1 tab

  17. Watershed hydrology. Chapter 7.

    Science.gov (United States)

    Elons S. Verry; Kenneth N. Brooks; Dale S. Nichols; Dawn R. Ferris; Stephen D. Sebestyen

    2011-01-01

    Watershed hydrology is determined by the local climate, land use, and pathways of water flow. At the Marcell Experimental Forest (MEF), streamflow is dominated by spring runoff events driven by snowmelt and spring rains common to the strongly continental climate of northern Minnesota. Snowmelt and rainfall in early spring saturate both mineral and organic soils and...

  18. Characterizing the Connectivity and Cumulative Effects of Wetlands on Downstream Hydrology: A Modeling Analysis

    Science.gov (United States)

    Geographically isolated wetlands (GIWs) are depressional landscape features entirely surrounded by uplands. While “GIW” may imply functional isolation from other surface waters, these systems exhibit a gradient of hydrologic, biological, and/or chemical connectivity. ...

  19. Flood Simulations and Uncertainty Analysis for the Pearl River Basin Using the Coupled Land Surface and Hydrological Model System

    Directory of Open Access Journals (Sweden)

    Yongnan Zhu

    2017-06-01

    Full Text Available The performances of hydrological simulations for the Pearl River Basin in China were analysed using the Coupled Land Surface and Hydrological Model System (CLHMS. Three datasets, including East Asia (EA, high-resolution gauge satellite-merged China Merged Precipitation Analysis (CMPA-Daily, and the Asian Precipitation Highly-Resolved Observational Data Integration Towards Evaluation (APHRODITE daily precipitation were used to drive the CLHMS model to simulate daily hydrological processes from 1998 to 2006. The results indicate that the precipitation data was the most important source of uncertainty in the hydrological simulation. The simulated streamflow driven by the CMPA-Daily agreed well with observations, with a Pearson correlation coefficient (PMC greater than 0.70 and an index of agreement (IOA similarity coefficient greater than 0.82 at Liuzhou, Shijiao, and Wuzhou Stations. Comparison of the Nash-Sutcliffe efficiency coefficient (NSE shows that the peak flow simulation ability of CLHMS driven with the CMPA-Daily rainfall is relatively superior to that with the EA and APHRODITE datasets. The simulation results for the high-flow periods in 1998 and 2005 indicate that the CLHMS is promising for its future application in the flood simulation and prediction.

  20. 2015 Long-Term Hydrologic Monitoring Program Sampling and Analysis Results Report for Project Rulison, Co

    Energy Technology Data Exchange (ETDEWEB)

    Findlay, Rick [Navarro Research and Engineering, Oak Ridge, TN (United States); Kautsky, Mark [US Department of Energy, Washington, DC (United States). Office of Legacy Management

    2015-12-01

    The U.S. Department of Energy (DOE) Office of Legacy Management conducted annual sampling at the Rulison, Colorado, Site for the Long-Term Hydrologic Monitoring Program (LTHMP) on May 20–22 and 27, 2015. Several of the land owners were not available to allow access to their respective properties, which created the need for several sample collection trips. This report documents the analytical results of the Rulison monitoring event and includes the trip report and the data validation package (Appendix A). The groundwater and surface water monitoring were shipped to the GEL Group Inc. laboratories for analysis. All requested analyses were successfully completed. Samples were analyzed for gamma-emitting radionuclides by high- resolution gamma spectrometry. Tritium was analyzed using two methods, the conventional tritium method, which has a detection limit on the order of 400 picocuries per liter (pCi/L), and the enriched method (for selected samples), which has a detection limit on the order of 3 pCi/L.

  1. Hydrologically complemented deterministic slope stability analysis in part of Indian Lesser Himalaya

    Directory of Open Access Journals (Sweden)

    John Mathew

    2016-09-01

    Full Text Available This study uses a deterministic approach to evaluate the factor of safety (FS of the terrain for different hydrological conditions, in part of Indian Lesser Himalaya. The results indicate sudden increase in the percentage unstable area from 7.5% to 13.8% for rainfall intensity variation from 50 to 100 mm/day. For the rainfall intensity of 15 August 2007 which caused many landslides in the study area, 18.5% of the total area was unstable and it increases to 21.7%, 23.5% and 24.7%, respectively, for rainfall intensities corresponding to 10, 25 and 50 year return periods. This increment stagnates at about 260 mm/day, making about 25% of the area unstable. Higher rainfall intensities make progressively gentler slopes unstable, but limited to 25 degrees of slope in this area. The area underlain by granitic gneiss showed 23.1% of area as unstable for 135 mm/day of rainfall intensity, and was followed by those areas underlain by amphibolite (16%, limestone (13.7% and quartzite (10.4%. Receiver operating characteristic (ROC curve analysis has given 84.2% accuracy for the model. Conversion of FS to failure probability through Z scores enables identification unstable or marginally unstable areas, for planning selective slope stabilization measures.

  2. Hydrologic Evaluation of TRMM Multisatellite Precipitation Analysis for Nanliu River Basin in Humid Southwestern China.

    Science.gov (United States)

    Zhao, Yinjun; Xie, Qiongying; Lu, Yuan; Hu, Baoqing

    2017-06-01

    The accuracy of Tropical Rainfall Measuring Mission (TRMM) multi-satellite precipitation analysis (TMPA) daily accumulated precipitation products (3B42RTV7 and 3B42V7) was evaluated for a small basin (the Nanliu river basin). A direct comparison was performed against gauge observations from a period of 9 years (2000-2009) at temporal and spatial scales. The results show that the temporal-spatial precipitation characteristics of the Nanliu river basin are highly consistent with 3B42V7 relative to 3B42RTV7, with higher correlation coefficient (CC) approximately 0.9 at all temporal scales except for the daily scale and a lower relative bias percentage. 3B42V7 slightly overestimates precipitation at all temporal scales except the yearly scale; it slightly underestimates the precipitation at the daily spatial scale. The results also reveal that the precision of TMPA products increases with longer time-aggregated data, and the detection capability of daily TMPA precipitation products are enhanced by augmentation with daily precipitation rates. In addition, daily TMPA products were input into the Xin'anjiang hydrologic model; the results show that 3B42V7-based simulated outputs were well in line with actual stream flow observations, with a high CC (0.90) and Nash-Sutcliffe efficiency coefficient (NSE, 0.79), and the results adequately captured the pattern of the observed flow curve.

  3. Reliability analysis of hydrologic containment of liquefied petroleum gas within unlined rock caverns.

    Science.gov (United States)

    Gao, X.; Yan, E. C.; Yeh, T. C. J.; Wang, Y.; Liang, Y.; Hao, Y.

    2017-12-01

    Notice that most of the underground liquefied petroleum gas (LPG) storage caverns are constructed in unlined rock caverns (URCs), where the variability of hydraulic properties (in particular, hydraulic conductivity) has significant impacts on hydrologic containment performance. However, it is practically impossible to characterize the spatial distribution of these properties in detail at the site of URCs. This dilemma forces us to cope with uncertainty in our evaluations of gas containment. As a consequence, the uncertainty-based analysis is deemed more appropriate than the traditional deterministic analysis. The objectives of this paper are 1) to introduce a numerical first order method to calculate the gas containment reliability within a heterogeneous, two-dimensional unlined rock caverns, and 2) to suggest a strategy for improving the gas containment reliability. In order to achieve these goals, we first introduced the stochastic continuum representation of saturated hydraulic conductivity (Ks) of fractured rock and analyzed the spatial variability of Ks at a field site. We then conducted deterministic simulations to demonstrate the importance of heterogeneity of Ks in the analysis of gas tightness performance of URCs. Considering the uncertainty of the heterogeneity in the real world situations, we subsequently developed a numerical first order method (NFOM) to determine the gas tightness reliability at crucial locations of URCs. Using the NFOM, the effect of spatial variability of Ks on gas tightness reliability was investigated. Results show that as variance or spatial structure anisotropy of Ks increases, most of the gas tightness reliability at crucial locations reduces. Meanwhile, we compare the results of NFOM with those of Monte Carlo simulation, and we find the accuracy of NFOM is mainly affected by the magnitude of the variance of Ks. At last, for improving gas containment reliability at crucial locations at this study site, we suggest that vertical

  4. Penalized differential pathway analysis of integrative oncogenomics studies.

    Science.gov (United States)

    van Wieringen, Wessel N; van de Wiel, Mark A

    2014-04-01

    Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving cancer patients. The two molecular levels involved are linked through the central dogma of molecular biology. DNA copy number aberrations abound in the cancer cell. Here we investigate how these aberrations affect gene expression levels within a pathway using observational integrative genomics data of cancer patients. In particular, we aim to identify differential edges between regulatory networks of two groups involving these molecular levels. Motivated by the rate equations, the regulatory mechanism between DNA copy number aberrations and gene expression levels within a pathway is modeled by a simultaneous-equations model, for the one- and two-group case. The latter facilitates the identification of differential interactions between the two groups. Model parameters are estimated by penalized least squares using the lasso (L1) penalty to obtain a sparse pathway topology. Simulations show that the inclusion of DNA copy number data benefits the discovery of gene-gene interactions. In addition, the simulations reveal that cis-effects tend to be over-estimated in a univariate (single gene) analysis. In the application to real data from integrative oncogenomic studies we show that inclusion of prior information on the regulatory network architecture benefits the reproducibility of all edges. Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature.

  5. Interleukin-2 signaling pathway analysis by quantitative phosphoproteomics

    DEFF Research Database (Denmark)

    Osinalde, Nerea; Moss, Helle; Arrizabalaga, Onetsine

    2011-01-01

    among which 79 were found with increased abundance in the tyrosine-phosphorylated complexes, including several previously not reported IL-2 downstream effectors. Combinatorial site-specific phosphoproteomic analysis resulted in identification of 99 phosphorylated sites mapping to the identified proteins...... with increased abundance in the tyrosine-phosphorylated complexes, of which 34 were not previously described. In addition, chemical inhibition of the identified IL-2-mediated JAK, PI3K and MAPK signaling pathways, resulted in distinct alteration on the IL-2 dependent proliferation....

  6. Sensitivity and uncertainty analysis of the PATHWAY radionuclide transport model

    International Nuclear Information System (INIS)

    Otis, M.D.

    1983-01-01

    Procedures were developed for the uncertainty and sensitivity analysis of a dynamic model of radionuclide transport through human food chains. Uncertainty in model predictions was estimated by propagation of parameter uncertainties using a Monte Carlo simulation technique. Sensitivity of model predictions to individual parameters was investigated using the partial correlation coefficient of each parameter with model output. Random values produced for the uncertainty analysis were used in the correlation analysis for sensitivity. These procedures were applied to the PATHWAY model which predicts concentrations of radionuclides in foods grown in Nevada and Utah and exposed to fallout during the period of atmospheric nuclear weapons testing in Nevada. Concentrations and time-integrated concentrations of iodine-131, cesium-136, and cesium-137 in milk and other foods were investigated. 9 figs., 13 tabs

  7. Resilience of Socio-Hydrological Systems in Canadian Prairies to Agricultural Drainage: Policy Analysis and Modelling Approach

    Science.gov (United States)

    Wheater, H. S.; Xu, L.; Gober, P.; Pomeroy, J. W.; Wong, J.

    2017-12-01

    Extensive agricultural drainage of lakes and wetlands in the Canadian Prairies has led to benefits for agricultural production, but has had a substantial influence on hydrological regimes and wetland extent. There is need for the potential impacts of current policy in changing the socio-hydrological resilience of prairie wetland basins in response to agricultural drainage to be examined. Whilst wetland drainage can increase agricultural productivity, it can also reduce stocks of natural capital and decrease ecosystem services, such as pollutant retention, habitat for waterfowls, carbon sequestration, and downstream flood attenuation. Effective policies that balance drainage benefits and negative externalities have to consider pricing. This is explored here using the Cold Regions Hydrological Model for hydrological simulations and the Inclusive Wealth approach for modelling in support of cost-benefit analysis. Inclusive wealth aggregates the value of natural, human, and technological assets used to produce social welfare. A shadow price, defined as the marginal change in social value for a marginal change in the current stock quantity, is used to valuate assets that contribute to social welfare. The shadow price of each asset is estimated by taking into account the social and economic benefits and external losses of wetland services caused by wetland drainage. The coupled model was applied to the Smith Creek Research Basin in south-eastern Saskatchewan, Canada where wetland drainage has caused major alterations of the hydrological regime including increased peak flows, discharge volumes and duration of streamflow. Changes in depressional storage in wetlands was used to calculate the corresponding changes of inclusive wealth over a 30-year period under the impacts from the limitation proposed in the Agricultural Water Management Strategy of Saskatchewan. The adjusted societal values of drainage demonstrate the dynamics between changes in hydrological conditions of

  8. HYDROLOGIC AND FEATURE-BASED SURFACE ANALYSIS FOR TOOL MARK INVESTIGATION ON ARCHAEOLOGICAL FINDS

    Directory of Open Access Journals (Sweden)

    K. Kovács

    2012-07-01

    Full Text Available The improvement of detailed surface documentation methods provides unique tool mark-study opportunities in the field of archaeological researches. One of these data collection techniques is short-range laser scanning, which creates a digital copy of the object’s morphological characteristics from high-resolution datasets. The aim of our work was the accurate documentation of a Bronze Age sluice box from Mitterberg, Austria with a spatial resolution of 0.2 mm. Furthermore, the investigation of the entirely preserved tool marks on the surface of this archaeological find was also accomplished by these datasets. The methodology of this tool mark-study can be summarized in the following way: At first, a local hydrologic analysis has been applied to separate the various patterns of tools on the finds’ surface. As a result, the XYZ coordinates of the special points, which represent the edge lines of the sliding tool marks, were calculated by buffer operations in a GIS environment. During the second part of the workflow, these edge points were utilized to manually clip the triangle meshes of these patterns in reverse engineering software. Finally, circle features were generated and analysed to determine the different sections along these sliding tool marks. In conclusion, the movement of the hand tool could be reproduced by the spatial analysis of the created features, since the horizontal and vertical position of the defined circle centre points indicated the various phases of the movements. This research shows an exact workflow to determine the fine morphological structures on the surface of the archaeological find.

  9. Comparative expression pathway analysis of human and canine mammary tumors

    Directory of Open Access Journals (Sweden)

    Marconato Laura

    2009-03-01

    Full Text Available Abstract Background Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Results We analyzed human and dog gene expression data derived from both tumor and normal mammary samples. By analyzing the expression levels of about ten thousand dog/human orthologous genes we observed a significant overlap of genes deregulated in the mammary tumor samples, as compared to their normal counterparts. Pathway analysis of gene expression data revealed a great degree of similarity in the perturbation of many cancer-related pathways, including the 'PI3K/AKT', 'KRAS', 'PTEN', 'WNT-beta catenin' and 'MAPK cascade'. Moreover, we show that the transcriptional relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Conclusion Our data confirm and further strengthen the value of the canine mammary cancer model and open up new perspectives for the evaluation of novel cancer therapeutics and the development of prognostic and diagnostic biomarkers to be used in clinical studies.

  10. Hydrology team

    Science.gov (United States)

    Ragan, R.

    1982-01-01

    General problems faced by hydrologists when using historical records, real time data, statistical analysis, and system simulation in providing quantitative information on the temporal and spatial distribution of water are related to the limitations of these data. Major problem areas requiring multispectral imaging-based research to improve hydrology models involve: evapotranspiration rates and soil moisture dynamics for large areas; the three dimensional characteristics of bodies of water; flooding in wetlands; snow water equivalents; runoff and sediment yield from ungaged watersheds; storm rainfall; fluorescence and polarization of water and its contained substances; discriminating between sediment and chlorophyll in water; role of barrier island dynamics in coastal zone processes; the relationship between remotely measured surface roughness and hydraulic roughness of land surfaces and stream networks; and modeling the runoff process.

  11. Gridded Surface Subsurface Hydrologic Analysis Modeling for Analysis of Flood Design Features at the Picayune Strand Restoration Project

    Science.gov (United States)

    2016-08-01

    restore its predrainage hydrology and ecological function for beneficial effects on flora and fauna in the project area and surrounding public lands. The...partnership with South Florida Water Management District (SFWMD), is constructing these features. Engineering support is required for hydrologic and...simulation accuracy and related resource requirements. Spatial data products such as digital elevation models, surveyed channel cross sections, soil

  12. RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

    Science.gov (United States)

    Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

    2018-02-22

    The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be

  13. Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma.

    Science.gov (United States)

    Li, Chaoxing; Liu, Li; Dinu, Valentin

    2018-01-01

    Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes

  14. PathwaySplice: An R package for unbiased pathway analysis of alternative splicing in RNA-Seq data.

    Science.gov (United States)

    Yan, Aimin; Ban, Yuguang; Gao, Zhen; Chen, Xi; Wang, Lily

    2018-04-24

    Pathway analysis of alternative splicing would be biased without accounting for the different number of exons or junctions associated with each gene, because genes with higher number of exons or junctions are more likely to be included in the "significant" gene list in alternative splicing. We present PathwaySplice, an R package that (1) Performs pathway analysis that explicitly adjusts for the number of exons or junctions associated with each gene; (2) Visualizes selection bias due to different number of exons or junctions for each gene and formally tests for presence of bias using logistic regression; (3) Supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets; (4) Identifies the significant genes driving pathway significance and (5) Organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph. https://bioconductor.org/packages/release/bioc/html/PathwaySplice.html. lily.wangg@gmail.com, xi.steven.chen@gmail.com.

  15. From spatially variable streamflow to distributed hydrological models: Analysis of key modeling decisions

    Science.gov (United States)

    Fenicia, Fabrizio; Kavetski, Dmitri; Savenije, Hubert H. G.; Pfister, Laurent

    2016-02-01

    This paper explores the development and application of distributed hydrological models, focusing on the key decisions of how to discretize the landscape, which model structures to use in each landscape element, and how to link model parameters across multiple landscape elements. The case study considers the Attert catchment in Luxembourg—a 300 km2 mesoscale catchment with 10 nested subcatchments that exhibit clearly different streamflow dynamics. The research questions are investigated using conceptual models applied at hydrologic response unit (HRU) scales (1-4 HRUs) on 6 hourly time steps. Multiple model structures are hypothesized and implemented using the SUPERFLEX framework. Following calibration, space/time model transferability is tested using a split-sample approach, with evaluation criteria including streamflow prediction error metrics and hydrological signatures. Our results suggest that: (1) models using geology-based HRUs are more robust and capture the spatial variability of streamflow time series and signatures better than models using topography-based HRUs; this finding supports the hypothesis that, in the Attert, geology exerts a stronger control than topography on streamflow generation, (2) streamflow dynamics of different HRUs can be represented using distinct and remarkably simple model structures, which can be interpreted in terms of the perceived dominant hydrologic processes in each geology type, and (3) the same maximum root zone storage can be used across the three dominant geological units with no loss in model transferability; this finding suggests that the partitioning of water between streamflow and evaporation in the study area is largely independent of geology and can be used to improve model parsimony. The modeling methodology introduced in this study is general and can be used to advance our broader understanding and prediction of hydrological behavior, including the landscape characteristics that control hydrologic response, the

  16. Human-induced Terrestrial Water Storage Change: A Global Analysis using Hydrological Models and GRACE

    Science.gov (United States)

    Felfelani, F.; Pokhrel, Y. N.

    2016-12-01

    Hydrological models and data derived from the Gravity Recovery and Climate Experiment (GRACE) satellite mission are used to study terrestrial water storage (TWS) change; however, both have disadvantages that necessitate the integrated use of them. While GRACE doesn't disintegrate the vertical storage into its components, most models do not account for human activities. Here we use two Land Surface Models (LSMs), i.e., HiGW-MAT and PCRGLOBWB that fully couple natural and human drivers of changes in water cycle, explicitly simulating the changes in various TWS compartments. We first evaluate the models performance with GRACE observations. Then, we quantify the human footprint over global river basins located in different geographic and climate regions. To quantify human impacts, a new framework is proposed based on the GRACE observations (representing both climate variability and human activities) together with the natural simulation of LSMs using water budget equation (P-ET-R; P for precipitation, ET for evapotranspiration, and R for runoff). Finally, we examine the uncertainty in TWS simulations arising from the uncertainties in forcing data. Results indicate that, in snow-dominated regions, PCRGLOBWB generally fails to reproduce neither the interannual variability of observed TWS nor the seasonal cycle, while HiGW-MAT model shows significantly better results. In basins with human signatures, PCRGLOBWB generally shows better agreement with GRACE compared to HiGW-MAT. It is found that HiGW-MAT tends to overestimate groundwater depletion in basins with human impacts (e.g., Amudarya, Colorado, Euphrates and Indus), which results in larger negative interannual TWS trend compared to GRACE. Euphrates and Ganges river basins experience the highest human-induced TWS deficit rates (2.08 cm/yr and 1.94 cm/yr, respectively) during the simulation period of 2002-2010. Uncertainty analysis of results from the same model but with different forcing data suggests a high standard

  17. A Flexible Nonlinear Modelling Framework for Nonstationary Generalized Extreme Value Analysis in Hydrology and Climatology

    Science.gov (United States)

    Cannon, A. J.

    2009-12-01

    Parameters in a Generalized Extreme Value (GEV) distribution are specified as a function of covariates using a conditional density network (CDN), which is a probabilistic extension of the multilayer perceptron neural network. If the covariate is time, or is dependent on time, then the GEV-CDN model can be used to perform nonlinear, nonstationary GEV analysis of hydrological or climatological time series. Due to the flexibility of the neural network architecture, the model is capable of representing a wide range of nonstationary relationships. Model parameters are estimated by generalized maximum likelihood, an approach that is tailored to the estimation of GEV parameters from geophysical time series. Model complexity is identified using the Bayesian information criterion and the Akaike information criterion with small sample size correction. Monte Carlo simulations are used to validate GEV-CDN performance on four simple synthetic problems. The model is then demonstrated on precipitation data from southern California, a series that exhibits nonstationarity due to interannual/interdecadal climatic variability. A hierarchy of models can be defined by adjusting three aspects of the GEV-CDN model architecture: (i) by specifying either a linear or a nonlinear hidden-layer activation function; (ii) by adjusting the number of hidden-layer nodes; or (iii) by disconnecting weights leading to output-layer nodes. To illustrate, five GEV-CDN models are shown here in order of increasing complexity for the case of a single covariate, which, in this case, is assumed to be time. The shape parameter is assumed to be constant in all models, although this is not a requirement of the GEV-CDN framework.

  18. A Physically Based Distributed Hydrologic Model with a no-conventional terrain analysis

    Science.gov (United States)

    Rulli, M.; Menduni, G.; Rosso, R.

    2003-12-01

    A physically based distributed hydrological model is presented. Starting from a contour-based terrain analysis, the model makes a no-conventional discretization of the terrain. From the maximum slope lines, obtained using the principles of minimum distance and orthogonality, the models obtains a stream tubes structure. The implemented model automatically can find the terrain morphological characteristics, e.g. peaks and saddles, and deal with them respecting the stream flow. Using this type of discretization, the model divides the elements in which the water flows in two classes; the cells, that are mixtilinear polygons where the overland flow is modelled as a sheet flow and channels, obtained by the interception of two or more stream tubes and whenever surface runoff occurs, the surface runoff is channelised. The permanent drainage paths can are calculated using one of the most common methods: threshold area, variable threshold area or curvature. The subsurface flow is modelled using the Simplified Bucket Model. The model considers three type of overland flow, depending on how it is produced:infiltration excess;saturation of superficial layer of the soil and exfiltration of sub-surface flow from upstream. The surface flow and the subsurface flow across a element are routed according with the mono-dimensional equation of the kinematic wave. The also model considers the spatial variability of the channels geometry with the flow. The channels have a rectangular section with length of the base decreasing with the distance from the outlet and depending on a power of the flow. The model was tested on the Rio Gallina and Missiaga catchments and the results showed model good performances.

  19. Analysis on hydrological condition for uranium ore formation in Wuerhe district, Junggar Basin

    International Nuclear Information System (INIS)

    Zhang Quanqing; Zhang Xinke; Ren Manchuan

    2009-01-01

    Wuerhe district is located in the northwestern part of Junggar Basin, Xinjiang. It belongs to a relative quiet area without the obvious tectonic activities and obvious subsequent tectonic activization. Through the regional uranium resources evaluation on this area, the inter-bedded oxidation zone and uranium mineralization are discovered in Cretaceous. The wall rock, the recharge-runoff-discharge mechanism of groundwater, palaeo-hydrological condition, hydrological and hydrogeochemical features of groundwater are introduced briefly, the favorable uranium ore-forming segment is summarized to be located in the fore-mountain area to the west of Ke-Xia fault terrace zone. (authors)

  20. Integrative analysis of RUNX1 downstream pathways and target genes

    Directory of Open Access Journals (Sweden)

    Liu Marjorie

    2008-07-01

    Full Text Available Abstract Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML. The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. Results Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1 cell lines with RUNX1 mutations from FPD-AML patients, 2 over-expression of RUNX1 and CBFβ, and 3 Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFβ. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. Conclusion This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease

  1. GIS environmental information analysis of the Darro River basin as the key for the management and hydrological forest restoration.

    Science.gov (United States)

    Fernandez, Paz; Delgado, Expectación; Lopez-Alonso, Mónica; Poyatos, José Manuel

    2018-02-01

    This article presents analyses of soil and environmental information for the Darro River basin (Granada-Spain) preliminary to its hydrological and forestry restoration. These analyses were carried out using a geographical information system (GIS) and employing a new procedure that adapts hydrological forest-restoration methods. The complete analysis encompasses morphological conditions, soil and climate characteristics as well as vegetation and land use. The study investigates soil erosion in the basin by using Universal Soil Loss Equation (USLE) and by mapping erosion fragility units. The results are presented in a set of maps and their analysis, providing the starting point for river basin management and the hydrological and forestry-restoration project that was approved at the end of 2015. The presence of soft substrates (e.g. gravel and sand) indicates that the area is susceptible to erosion, particularly the areas that are dominated by human activity and have little soil protection. Finally, land use and vegetation cover were identified as key factors in the soil erosion in the basin. According to the results, river authorities have included several measures in the restoration project aimed at reducing the erosion and helping to recover the environmental value of this river basin and to include it in recreation possibilities for the community of Granada. The presented analytical approach, designed by the authors, would be useful as a tool for environmental restoration in other small Mediterranean river basins. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Pathway Analysis of miR-181a in Hypopharyngeal Squamous Cell ...

    African Journals Online (AJOL)

    syakima

    2012-03-15

    Mar 15, 2012 ... Key words: MicroRNA, head and neck cancer, miR-181a, pathway analysis, luciferase assay, FaDu cell line, transfection ..... prostate carcinoma and glioblastoma cells. Nucleic Acids .... WNT pathway in oral cancer: epigenetic.

  3. Pathways of topological rank analysis (PoTRA: a novel method to detect pathways involved in hepatocellular carcinoma

    Directory of Open Access Journals (Sweden)

    Chaoxing Li

    2018-04-01

    Full Text Available Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway’s topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher’s exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several

  4. Wetland Hydrology

    Science.gov (United States)

    This chapter discusses the state of the science in wetland hydrology by touching upon the major hydraulic and hydrologic processes in these complex ecosystems, their measurement/estimation techniques, and modeling methods. It starts with the definition of wetlands, their benefit...

  5. Final Report: Hydrogen Production Pathways Cost Analysis (2013 – 2016)

    Energy Technology Data Exchange (ETDEWEB)

    James, Brian David [Strategic Analysis Inc., Arlington, VA (United States); DeSantis, Daniel Allan [Strategic Analysis Inc., Arlington, VA (United States); Saur, Genevieve [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-09-30

    This report summarizes work conducted under a three year Department of Energy (DOE) funded project to Strategic Analysis, Inc. (SA) to analyze multiple hydrogen (H2) production technologies and project their corresponding levelized production cost of H2. The analysis was conducted using the H2A Hydrogen Analysis Tool developed by the DOE and National Renewable Energy Laboratory (NREL). The project was led by SA but conducted in close collaboration with the NREL and Argonne National Laboratory (ANL). In-depth techno-economic analysis (TEA) of five different H2 production methods was conducted. These TEAs developed projections for capital costs, fuel/feedstock usage, energy usage, indirect capital costs, land usage, labor requirements, and other parameters, for each H2 production pathway, and use the resulting cost and system parameters as inputs into the H2A discounted cash flow model to project the production cost of H2 ($/kgH2). Five technologies were analyzed as part of the project and are summarized in this report: Proton Exchange Membrane technology (PEM), High temperature solid oxide electrolysis cell technology (SOEC), Dark fermentation of biomass for H2 production, H2 production via Monolithic Piston-Type Reactors with rapid swing reforming and regeneration reactions, and Reformer-Electrolyzer-Purifier (REP) technology developed by Fuel Cell Energy, Inc. (FCE).

  6. Uncertainty analysis of hydrology calculations for final repositories for nuclear waste

    International Nuclear Information System (INIS)

    Gustafsson, B.

    1986-01-01

    The technique of using the NAMMU-HYPAC computer code has been transferred from the group of developers to an end user. The package has been found to be flexible and powerful but also quite demanding. The code has been used to investigate certain numerical properties of hydrological models including variations of permeability

  7. Runoff Trends Analysis and Future Projections of Hydrological Patterns in Small Forested Catchments

    Czech Academy of Sciences Publication Activity Database

    Lamačová, Anna; Hruška, Jakub; Krám, Pavel; Stuchlik, E.; Farda, Aleš; Chuman, T.; Fottová, Daniela

    2014-01-01

    Roč. 9, č. 4 (2014), s. 169-181 ISSN 1801-5395 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073 Institutional support: RVO:67179843 Keywords : climate change * flow pattern * headwater catchments * hydrological modelling Subject RIV: EH - Ecology, Behaviour Impact factor: 0.659, year: 2014

  8. A Hydrological Response Analysis Considering Climatic Variability: Case Study of Hunza Catchment

    Directory of Open Access Journals (Sweden)

    A. N. Laghari

    2018-06-01

    Full Text Available The hydrological response of mountainous catchments particularly dependent on melting runoff is very vulnerable to climatic variability. This study is an attempt to assess hydrological response towards climatic variability of the Hunza catchment located in the mountainous chain of greater Hindu Kush-Himalaya (HKH region. The hydrological response is analyzed through changes in snowmelt, ice melt and total runoff simulated through the application of the hydrological modeling system PREVAH under hypothetically developed climate change scenarios. The developed scenarios are based on changes in precipitation (Prp and temperature (Tmp and their combination. Under all the warmer scenarios, the increase in temperature systematically decreases the mean annual snow melt and increases significantly glacier melt volume. Temperature changes from 1°C to 4°C produce a large increase in spring and summer runoff, while no major variation was observed in the winter and autumn runoff. The maximum seasonal changes recorded under the Tmp+4°C, Prp+10% scenario.

  9. Pathway analysis for a contaminated landfill in Middlesex, New Jersey

    International Nuclear Information System (INIS)

    Yu, C.; Merry-Libby, P.; Yang, J.Y.

    1985-01-01

    Under the Formerly Utilized Sites Remedial Action Program, the US Department of Energy began excavating contaminated materials from the Middlesex Municipal landfill in 1984. A total of 16,000 m 3 of landfill materials covering a 0.2-ha area was excavated, of which 11,000 m 3 was contaminated and has been transported to the nearby sampling plant site for interim storage. Based on the pathway analysis for the onsite and near-site resident scenarios, the radiation dose rates and radionuclide concentrations in groundwater would be below the regulatory requirements for both the short-term and long-term scenarios. Hence, the potential health risks to maximally exposed individuals due to radioactive releases from the Middlesex landfill would be insignificant

  10. In silico tools for the analysis of antibiotic biosynthetic pathways

    DEFF Research Database (Denmark)

    Weber, Tilmann

    2014-01-01

    Natural products of bacteria and fungi are the most important source for antimicrobial drug leads. For decades, such compounds were exclusively found by chemical/bioactivity-guided screening approaches. The rapid progress in sequencing technologies only recently allowed the development of novel...... screening methods based on the genome sequences of potential producing organisms. The basic principle of such genome mining approaches is to identify genes, which are involved in the biosynthesis of such molecules, and to predict the products of the identified pathways. Thus, bioinformatics methods...... and tools are crucial for genome mining. In this review, a comprehensive overview is given on programs and databases for the identification and analysis of antibiotic biosynthesis gene clusters in genomic data....

  11. Sensitivity analysis for the coupling of a subglacial hydrology model with a 3D ice-sheet model.

    Science.gov (United States)

    Bertagna, L.; Perego, M.; Gunzburger, M.; Hoffman, M. J.; Price, S. F.

    2017-12-01

    When studying the movement of ice sheets, one of the most important factors that influence the velocity of the ice is the amount of friction against the bedrock. Usually, this is modeled by a friction coefficient that may depend on the bed geometry and other quantities, such as the temperature and/or water pressure at the ice-bedrock interface. These quantities are often assumed to be known (either by indirect measurements or by means of parameter estimation) and constant in time. Here, we present a 3D computational model for the simulation of the ice dynamics which incorporates a 2D model proposed by Hewitt (2011) for the subglacial water pressure. The hydrology model is fully coupled with the Blatter-Pattyn model for the ice sheet flow, as the subglacial water pressure appears in the expression for the ice friction coefficient, and the ice velocity appears as a source term in the hydrology model. We will present results on real geometries, and perform a sensitivity analysis with respect to the hydrology model parameters.

  12. Statistical analysis of hydrological response in urbanising catchments based on adaptive sampling using inter-amount times

    Science.gov (United States)

    ten Veldhuis, Marie-Claire; Schleiss, Marc

    2017-04-01

    Urban catchments are typically characterised by a more flashy nature of the hydrological response compared to natural catchments. Predicting flow changes associated with urbanisation is not straightforward, as they are influenced by interactions between impervious cover, basin size, drainage connectivity and stormwater management infrastructure. In this study, we present an alternative approach to statistical analysis of hydrological response variability and basin flashiness, based on the distribution of inter-amount times. We analyse inter-amount time distributions of high-resolution streamflow time series for 17 (semi-)urbanised basins in North Carolina, USA, ranging from 13 to 238 km2 in size. We show that in the inter-amount-time framework, sampling frequency is tuned to the local variability of the flow pattern, resulting in a different representation and weighting of high and low flow periods in the statistical distribution. This leads to important differences in the way the distribution quantiles, mean, coefficient of variation and skewness vary across scales and results in lower mean intermittency and improved scaling. Moreover, we show that inter-amount-time distributions can be used to detect regulation effects on flow patterns, identify critical sampling scales and characterise flashiness of hydrological response. The possibility to use both the classical approach and the inter-amount-time framework to identify minimum observable scales and analyse flow data opens up interesting areas for future research.

  13. The Cardiopulmonary Effects of Ambient Air Pollution and Mechanistic Pathways: A Comparative Hierarchical Pathway Analysis

    Science.gov (United States)

    Thomas, Duncan C.; Zhang, Junfeng; Kipen, Howard M.; Rich, David Q.; Zhu, Tong; Huang, Wei; Hu, Min; Wang, Guangfa; Wang, Yuedan; Zhu, Ping; Lu, Shou-En; Ohman-Strickland, Pamela; Diehl, Scott R.; Eckel, Sandrah P.

    2014-01-01

    Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001) and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005). These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours) and the hemostasis pathway responds gradually over a 2–3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system. PMID:25502951

  14. The cardiopulmonary effects of ambient air pollution and mechanistic pathways: a comparative hierarchical pathway analysis.

    Directory of Open Access Journals (Sweden)

    Ananya Roy

    Full Text Available Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001 and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005. These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours and the hemostasis pathway responds gradually over a 2-3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system.

  15. Hydrological Response and Complex Impact Pathways of the 2015/2016 El Niño in Eastern and Southern Africa

    NARCIS (Netherlands)

    Siderius, C.; Gannon, K.E.; Ndiyoi, M.; Opere, A.; Batisani, N.; Olago, D.; Pardoe, J.; Conway, D.

    2018-01-01

    The 2015/2016 El Niño has been classified as one of the three most severe on record. El Niño teleconnections are commonly associated with droughts in southern Africa and high precipitation in eastern Africa. Despite their relatively frequent occurrence, evidence for their hydrological effects and

  16. Model structural uncertainty quantification and hydrologic parameter and prediction error analysis using airborne electromagnetic data

    DEFF Research Database (Denmark)

    Minsley, B. J.; Christensen, Nikolaj Kruse; Christensen, Steen

    Model structure, or the spatial arrangement of subsurface lithological units, is fundamental to the hydrological behavior of Earth systems. Knowledge of geological model structure is critically important in order to make informed hydrological predictions and management decisions. Model structure...... is never perfectly known, however, and incorrect assumptions can be a significant source of error when making model predictions. We describe a systematic approach for quantifying model structural uncertainty that is based on the integration of sparse borehole observations and large-scale airborne...... electromagnetic (AEM) data. Our estimates of model structural uncertainty follow a Bayesian framework that accounts for both the uncertainties in geophysical parameter estimates given AEM data, and the uncertainties in the relationship between lithology and geophysical parameters. Using geostatistical sequential...

  17. Rio Blanco, Colorado, Long-Term Hydrologic Monitoring Program Sampling and Analysis Results for 2009

    International Nuclear Information System (INIS)

    2009-01-01

    The U.S. Department of Energy (DOE) Office of Legacy Management conducted annual sampling at the Rio Blanco, Colorado, Site, for the Long-Term Hydrologic Monitoring Program (LTHMP) on May 13 and 14, 2009. Samples were analyzed by the U.S. Environmental Protection Agency (EPA) Radiation&Indoor Environments National Laboratory in Las Vegas, Nevada. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectroscopy and tritium using the conventional and enriched methods.

  18. Technology demonstration: geostatistical and hydrologic analysis of salt areas. Assessment of effectiveness of geologic isolation systems

    International Nuclear Information System (INIS)

    Doctor, P.G.; Oberlander, P.L.; Rice, W.A.; Devary, J.L.; Nelson, R.W.; Tucker, P.E.

    1982-09-01

    The Office of Nuclear Waste Isolation (ONWI) requested Pacific Northwest Laboratory (PNL) to: (1) use geostatistical analyses to evaluate the adequacy of hydrologic data from three salt regions, each of which contains a potential nuclear waste repository site; and (2) demonstrate a methodology that allows quantification of the value of additional data collection. The three regions examined are the Paradox Basin in Utah, the Permian Basin in Texas, and the Mississippi Study Area. Additional and new data became available to ONWI during and following these analyses; therefore, this report must be considered a methodology demonstration here would apply as illustrated had the complete data sets been available. A combination of geostatistical and hydrologic analyses was used for this demonstration. Geostatistical analyses provided an optimal estimate of the potentiometric surface from the available data, a measure of the uncertainty of that estimate, and a means for selecting and evaluating the location of future data. The hydrologic analyses included the calculation of transmissivities, flow paths, travel times, and ground-water flow rates from hypothetical repository sites. Simulation techniques were used to evaluate the effect of optimally located future data on the potentiometric surface, flow lines, travel times, and flow rates. Data availability, quality, quantity, and conformance with model assumptions differed in each of the salt areas. Report highlights for the three locations are given

  19. Radar-raingauge data combination techniques: a revision and analysis of their suitability for urban hydrology.

    Science.gov (United States)

    Wang, Li-Pen; Ochoa-Rodríguez, Susana; Simões, Nuno Eduardo; Onof, Christian; Maksimović, Cedo

    2013-01-01

    The applicability of the operational radar and raingauge networks for urban hydrology is insufficient. Radar rainfall estimates provide a good description of the spatiotemporal variability of rainfall; however, their accuracy is in general insufficient. It is therefore necessary to adjust radar measurements using raingauge data, which provide accurate point rainfall information. Several gauge-based radar rainfall adjustment techniques have been developed and mainly applied at coarser spatial and temporal scales; however, their suitability for small-scale urban hydrology is seldom explored. In this paper a review of gauge-based adjustment techniques is first provided. After that, two techniques, respectively based upon the ideas of mean bias reduction and error variance minimisation, were selected and tested using as case study an urban catchment (∼8.65 km(2)) in North-East London. The radar rainfall estimates of four historical events (2010-2012) were adjusted using in situ raingauge estimates and the adjusted rainfall fields were applied to the hydraulic model of the study area. The results show that both techniques can effectively reduce mean bias; however, the technique based upon error variance minimisation can in general better reproduce the spatial and temporal variability of rainfall, which proved to have a significant impact on the subsequent hydraulic outputs. This suggests that error variance minimisation based methods may be more appropriate for urban-scale hydrological applications.

  20. Hydrological simulation and uncertainty analysis using the improved TOPMODEL in the arid Manas River basin, China.

    Science.gov (United States)

    Xue, Lianqing; Yang, Fan; Yang, Changbing; Wei, Guanghui; Li, Wenqian; He, Xinlin

    2018-01-11

    Understanding the mechanism of complicated hydrological processes is important for sustainable management of water resources in an arid area. This paper carried out the simulations of water movement for the Manas River Basin (MRB) using the improved semi-distributed Topographic hydrologic model (TOPMODEL) with a snowmelt model and topographic index algorithm. A new algorithm is proposed to calculate the curve of topographic index using internal tangent circle on a conical surface. Based on the traditional model, the improved indicator of temperature considered solar radiation is used to calculate the amount of snowmelt. The uncertainty of parameters for the TOPMODEL model was analyzed using the generalized likelihood uncertainty estimation (GLUE) method. The proposed model shows that the distribution of the topographic index is concentrated in high mountains, and the accuracy of runoff simulation has certain enhancement by considering radiation. Our results revealed that the performance of the improved TOPMODEL is acceptable and comparable to runoff simulation in the MRB. The uncertainty of the simulations resulted from the parameters and structures of model, climatic and anthropogenic factors. This study is expected to serve as a valuable complement for widely application of TOPMODEL and identify the mechanism of hydrological processes in arid area.

  1. Hydrological Bulletin

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Historical report (December 1937-April 1948) containing hydrologic information for the United States, divided into ten regions. While hourly precipitation tables...

  2. Landfilling: Hydrology

    DEFF Research Database (Denmark)

    Kjeldsen, Peter; Beaven, R.

    2011-01-01

    Landfill hydrology deals with the presence and movement of water through a landfill. The main objective in landfill hydrology is usually to predict leachate generation, but the presence and movement of water in a landfill also affect the degradation of the waste, the leaching of pollutants...... and the geotechnical stability of the fill. Understanding landfill hydrology is thus important for many aspects of landfill, in particular siting, design and operation. The objective of this chapter is to give a basic understanding of the hydrology of landfills, and to present ways to estimate leachate quantities...... under specific circumstances. Initially a general water balance equation is defined for a typical landfill, and the different parts of the water balance are discussed. A separate section discusses water flow and the hydrogeology of landfilled wastes and considers the impact of water short...

  3. Hydrological character of the soil of a degraded area: comparison of analysis physical, chemical and floristic vegetational

    Science.gov (United States)

    Manfredi, Paolo; Cassinari, Chiara; Giupponi, Luca; Sichel, Giorgio Maria; Trevisan, Marco

    2013-04-01

    This work is an integral part of a project co-financed by the European Union "Environmental recovery of degraded soils and desertified land by a new technology treatment for the recovery of the land" (Life 10 ENV IT 400 "New Life"); this technology is based on a treatment (patented by m.c.m. Ecosistemi) of chemical mechanical processing of degraded soils with an initial process of disgregation of the same followed by their reconstitution incorporating soil matrices, a subsequent polycondensation with humic acids and a final restoration. The area of intervention of the New Life project lies in the municipal territory of Piacenza, where between the years 70 and 80 has been made a landfill for municipal solid waste with subsequent restoration work by placing a layer of soil cover. The first phase of the New Life project was that of a physical and chemical characterization of different cover soils of the area combined with floristic-vegetational analysis. At this stage the present study aims to compare the data related to the analysis of the vegetation with those returned by investigation of hydrological characteristics of soils performed by laboratory methods, together to confront two theoretical calculation methods for determination of hydrological parameters. The comparison of the ecological study of the vegetation with the outcomes obtained by the classical methods regarding the determination of water retention, allows you to have a picture that is as detailed as possible in describing the characteristics of the substrate. The comparison also with the two methods of calculation, which determines the hydrological character conditions in average soil condition, allows you to ascertain the actual disturbance of the soil in the area. In order to delineate the hydrological characteristics of the soils sampled, were quantified by the Maximum Water Concentration, the capacity range, the point of Withering by the method of the Tensiometric box and the Pressure Membrane

  4. Geomorphological Analysis and Hydrological Potential Zone of Baira River Watershed, Churah in Chamba District of Himachal Pradesh, India

    Directory of Open Access Journals (Sweden)

    Kuldeep Pareta

    2017-03-01

    Full Text Available In the present study, an attempt has been made to study the quantitative geomorphological analysis and hydrological characterization of 95 micro-watersheds (MWS of Baira river watershed in Himachal Pradesh, India with an area of 425.25 Km2. First time in the world, total 173 morphometric parameters have been generated in a single watershed using satellite remote sensing data (i.e. IRS-P6 ResourceSAT-1 LISS-III, LandSAT-7 ETM+, and LandSAT-8 PAN & OLI merge data, digital elevation models (i.e. IRS-P5 CartoSAT-1 DEM, ASTER DEM data, and soI topographical maps of 1: 50,000 scale. The ninety-five micro-watersheds (MWS of Baira river watershed have been prioritized through the morphometric analysis of different morphometric parameters (i.e. drainage network, basin geometry, drainage texture analysis, and relief characterizes . The study has concurrently established the importance of geomorphometry as well as the utility of remote sensing and GIS technology for hydrological characterization of the watershed and there for better resource and environmental managements.

  5. A comparative analysis of projected impacts of climate change on river runoff from global and catchment-scale hydrological models

    Science.gov (United States)

    Gosling, S. N.; Taylor, R. G.; Arnell, N. W.; Todd, M. C.

    2011-01-01

    We present a comparative analysis of projected impacts of climate change on river runoff from two types of distributed hydrological model, a global hydrological model (GHM) and catchment-scale hydrological models (CHM). Analyses are conducted for six catchments that are global in coverage and feature strong contrasts in spatial scale as well as climatic and developmental conditions. These include the Liard (Canada), Mekong (SE Asia), Okavango (SW Africa), Rio Grande (Brazil), Xiangxi (China) and Harper's Brook (UK). A single GHM (Mac-PDM.09) is applied to all catchments whilst different CHMs are applied for each catchment. The CHMs include SLURP v. 12.2 (Liard), SLURP v. 12.7 (Mekong), Pitman (Okavango), MGB-IPH (Rio Grande), AV-SWAT-X 2005 (Xiangxi) and Cat-PDM (Harper's Brook). The CHMs typically simulate water resource impacts based on a more explicit representation of catchment water resources than that available from the GHM and the CHMs include river routing, whereas the GHM does not. Simulations of mean annual runoff, mean monthly runoff and high (Q5) and low (Q95) monthly runoff under baseline (1961-1990) and climate change scenarios are presented. We compare the simulated runoff response of each hydrological model to (1) prescribed increases in global-mean air temperature of 1.0, 2.0, 3.0, 4.0, 5.0 and 6.0 °C relative to baseline from the UKMO HadCM3 Global Climate Model (GCM) to explore response to different amounts of climate forcing, and (2) a prescribed increase in global-mean air temperature of 2.0 °C relative to baseline for seven GCMs to explore response to climate model structural uncertainty. We find that the differences in projected changes of mean annual runoff between the two types of hydrological model can be substantial for a given GCM (e.g. an absolute GHM-CHM difference in mean annual runoff percentage change for UKMO HadCM3 2 °C warming of up to 25%), and they are generally larger for indicators of high and low monthly runoff. However

  6. A comparative analysis of projected impacts of climate change on river runoff from global and catchment-scale hydrological models

    Directory of Open Access Journals (Sweden)

    S. N. Gosling

    2011-01-01

    Full Text Available We present a comparative analysis of projected impacts of climate change on river runoff from two types of distributed hydrological model, a global hydrological model (GHM and catchment-scale hydrological models (CHM. Analyses are conducted for six catchments that are global in coverage and feature strong contrasts in spatial scale as well as climatic and developmental conditions. These include the Liard (Canada, Mekong (SE Asia, Okavango (SW Africa, Rio Grande (Brazil, Xiangxi (China and Harper's Brook (UK. A single GHM (Mac-PDM.09 is applied to all catchments whilst different CHMs are applied for each catchment. The CHMs include SLURP v. 12.2 (Liard, SLURP v. 12.7 (Mekong, Pitman (Okavango, MGB-IPH (Rio Grande, AV-SWAT-X 2005 (Xiangxi and Cat-PDM (Harper's Brook. The CHMs typically simulate water resource impacts based on a more explicit representation of catchment water resources than that available from the GHM and the CHMs include river routing, whereas the GHM does not. Simulations of mean annual runoff, mean monthly runoff and high (Q5 and low (Q95 monthly runoff under baseline (1961–1990 and climate change scenarios are presented. We compare the simulated runoff response of each hydrological model to (1 prescribed increases in global-mean air temperature of 1.0, 2.0, 3.0, 4.0, 5.0 and 6.0 °C relative to baseline from the UKMO HadCM3 Global Climate Model (GCM to explore response to different amounts of climate forcing, and (2 a prescribed increase in global-mean air temperature of 2.0 °C relative to baseline for seven GCMs to explore response to climate model structural uncertainty.

    We find that the differences in projected changes of mean annual runoff between the two types of hydrological model can be substantial for a given GCM (e.g. an absolute GHM-CHM difference in mean annual runoff percentage change for UKMO HadCM3 2 °C warming of up to 25%, and they are generally larger for indicators of high and low monthly runoff

  7. Virtual hydrology observatory: an immersive visualization of hydrology modeling

    Science.gov (United States)

    Su, Simon; Cruz-Neira, Carolina; Habib, Emad; Gerndt, Andreas

    2009-02-01

    The Virtual Hydrology Observatory will provide students with the ability to observe the integrated hydrology simulation with an instructional interface by using a desktop based or immersive virtual reality setup. It is the goal of the virtual hydrology observatory application to facilitate the introduction of field experience and observational skills into hydrology courses through innovative virtual techniques that mimic activities during actual field visits. The simulation part of the application is developed from the integrated atmospheric forecast model: Weather Research and Forecasting (WRF), and the hydrology model: Gridded Surface/Subsurface Hydrologic Analysis (GSSHA). Both the output from WRF and GSSHA models are then used to generate the final visualization components of the Virtual Hydrology Observatory. The various visualization data processing techniques provided by VTK are 2D Delaunay triangulation and data optimization. Once all the visualization components are generated, they are integrated into the simulation data using VRFlowVis and VR Juggler software toolkit. VR Juggler is used primarily to provide the Virtual Hydrology Observatory application with fully immersive and real time 3D interaction experience; while VRFlowVis provides the integration framework for the hydrologic simulation data, graphical objects and user interaction. A six-sided CAVETM like system is used to run the Virtual Hydrology Observatory to provide the students with a fully immersive experience.

  8. Chapter 7. Cloning and analysis of natural product pathways.

    Science.gov (United States)

    Gust, Bertolt

    2009-01-01

    The identification of gene clusters of natural products has lead to an enormous wealth of information about their biosynthesis and its regulation, and about self-resistance mechanisms. Well-established routine techniques are now available for the cloning and sequencing of gene clusters. The subsequent functional analysis of the complex biosynthetic machinery requires efficient genetic tools for manipulation. Until recently, techniques for the introduction of defined changes into Streptomyces chromosomes were very time-consuming. In particular, manipulation of large DNA fragments has been challenging due to the absence of suitable restriction sites for restriction- and ligation-based techniques. The homologous recombination approach called recombineering (referred to as Red/ET-mediated recombination in this chapter) has greatly facilitated targeted genetic modifications of complex biosynthetic pathways from actinomycetes by eliminating many of the time-consuming and labor-intensive steps. This chapter describes techniques for the cloning and identification of biosynthetic gene clusters, for the generation of gene replacements within such clusters, for the construction of integrative library clones and their expression in heterologous hosts, and for the assembly of entire biosynthetic gene clusters from the inserts of individual library clones. A systematic approach toward insertional mutation of a complete Streptomyces genome is shown by the use of an in vitro transposon mutagenesis procedure.

  9. Regulatory pathway analysis by high-throughput in situ hybridization.

    Directory of Open Access Journals (Sweden)

    Axel Visel

    2007-10-01

    Full Text Available Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways. Towards this end, an atlas housing approximately 1,000 spatial gene expression patterns of the midgestation mouse embryo was generated. Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This process ordered hundreds of complex expression patterns into a matrix that reflects the embryonic architecture and the relatedness of patterns of expression. Clustering yielded 12 distinct groups of expression patterns. Because of the similarity of expression patterns within a group, members of each group may be components of regulatory cascades. We focused on the group containing Pax6, an evolutionary conserved transcriptional master mediator of development. Seventeen of the 82 genes in this group showed a change of expression in the developing neocortex of Pax6-deficient embryos. Electromobility shift assays were used to test for the presence of Pax6-paired domain binding sites. This led to the identification of 12 genes not previously known as potential targets of Pax6 regulation. These findings suggest that cluster analysis of annotated gene expression patterns obtained by automated in situ hybridization is a novel approach for identifying components of signaling cascades.

  10. Supply Chain Sustainability Analysis of Three Biofuel Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Jacob J. Jacobson; Erin Searcy; Kara Cafferty; Jennifer B. Dunn; Michael Johnson; Zhichao Wang; Michael Wang; Mary Biddy; Abhijit Dutta; Daniel Inman; Eric Tan; Sue Jones; Lesley Snowden-Swan

    2013-11-01

    The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) collaborates with industrial, agricultural, and non-profit partners to develop and deploy biofuels and other biologically-derived products. As part of this effort, BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of technologies to produce biofuels as part state of technology (SOT) analyses. An SOT assesses progress within and across relevant technology areas based on actual experimental results relative to technical targets and cost goals from design cases and includes technical, economic, and environmental criteria as available. Overall assessments of biofuel pathways begin with feedstock production and the logistics of transporting the feedstock from the farm or plantation to the conversion facility or biorefinery. The conversion process itself is modeled in detail as part of the SOT analysis. The teams then develop an estimate of the biofuel minimum selling price (MSP) and assess the cost competitiveness of the biofuel with conventional fuels such as gasoline.

  11. A comparative analysis of 9 multi-model averaging approaches in hydrological continuous streamflow simulation

    Science.gov (United States)

    Arsenault, Richard; Gatien, Philippe; Renaud, Benoit; Brissette, François; Martel, Jean-Luc

    2015-10-01

    This study aims to test whether a weighted combination of several hydrological models can simulate flows more accurately than the models taken individually. In addition, the project attempts to identify the most efficient model averaging method and the optimal number of models to include in the weighting scheme. In order to address the first objective, streamflow was simulated using four lumped hydrological models (HSAMI, HMETS, MOHYSE and GR4J-6), each of which were calibrated with three different objective functions on 429 watersheds. The resulting 12 hydrographs (4 models × 3 metrics) were weighted and combined with the help of 9 averaging methods which are the simple arithmetic mean (SAM), Akaike information criterion (AICA), Bates-Granger (BGA), Bayes information criterion (BICA), Bayesian model averaging (BMA), Granger-Ramanathan average variant A, B and C (GRA, GRB and GRC) and the average by SCE-UA optimization (SCA). The same weights were then applied to the hydrographs in validation mode, and the Nash-Sutcliffe Efficiency metric was measured between the averaged and observed hydrographs. Statistical analyses were performed to compare the accuracy of weighted methods to that of individual models. A Kruskal-Wallis test and a multi-objective optimization algorithm were then used to identify the most efficient weighted method and the optimal number of models to integrate. Results suggest that the GRA, GRB, GRC and SCA weighted methods perform better than the individual members. Model averaging from these four methods were superior to the best of the individual members in 76% of the cases. Optimal combinations on all watersheds included at least one of each of the four hydrological models. None of the optimal combinations included all members of the ensemble of 12 hydrographs. The Granger-Ramanathan average variant C (GRC) is recommended as the best compromise between accuracy, speed of execution, and simplicity.

  12. Gasbuggy, New Mexico, Hydrologic and Natural Gas Sampling and Analysis Results for 2009

    International Nuclear Information System (INIS)

    2009-11-01

    The U.S. Department of Energy (DOE) Office of Legacy Management conducted hydrologic and natural gas sampling for the Gasbuggy, New Mexico, site on June 16, and 17, 2009. Hydrologic sampling consists of collecting water samples from water wells and surface water locations. Natural gas sampling consists of collecting both gas samples and samples of produced water from gas production wells. The water well samples were analyzed for gamma-emitting radionuclides and tritium. Surface water samples were analyzed for tritium. Water samples from gas production wells were analyzed for gamma-emitting radionuclides, gross alpha, gross beta, and tritium. Natural gas samples were analyzed for tritium and carbon-14. Water samples were analyzed by ALS Laboratory Group in Fort Collins, Colorado, and natural gas samples were analyzed by Isotech Laboratories in Champaign, Illinois. Concentrations of tritium and gamma-emitting radionuclides in water samples collected in the vicinity of the Gasbuggy site continue to demonstrate that the sample locations have not been impacted by detonation-related contaminants. Results from the sampling of natural gas from producing wells demonstrate that the gas wells nearest the Gasbuggy site are not currently impacted by detonation-related contaminants. Annual sampling of the gas production wells nearest the Gasbuggy site for gas and produced water will continue for the foreseeable future. The sampling frequency of water wells and surface water sources in the surrounding area will be reduced to once every 5 years. The next hydrologic sampling event at water wells, springs, and ponds will be in 2014.

  13. Multifractal analysis of different hydrological products of X-band radar

    Science.gov (United States)

    Skouri-Plakali, Ilektra; Da Silva Rocha Paz, Igor; Ichiba, Abdellah; Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

    2017-04-01

    Rainfall is widely considered as the hydrological process that triggers all the others. Its accurate measurements are crucial especially when they are used afterwards for the hydrological modeling of urban and peri-urban catchments for decision-making. Rainfall is a complex process and is scale dependent in space and time. Hence a high spatial and temporal resolution of the data is more appropriate for urban modeling. Therefore, a great interest of high-resolution measurements of precipitation in space and time is manifested. Radar technologies have not stopped evolving since their first appearance about the mid-twentieth. Indeed, the turning point work by Marshall-Palmer (1948) has established the Z - R power-law relation that has been widely used, with major scientific efforts being devoted to find "the best choice" of the two associated parameters. Nowadays X-band radars, being provided with dual-polarization and Doppler means, offer more accurate data of higher resolution. The fact that drops are oblate induces a differential phase shift between the two polarizations. The quantity most commonly used for the rainfall rate computation is actually the specific differential phase shift, which is the gradient of the differential phase shift along the radial beam direction. It is even stronger correlated to the rain rate R than reflectivity Z. Hence the rain rate can be computed with a different power-law relation, which again depends on only two parameters. Furthermore, an attenuation correction is needed to adjust the loss of radar energy due to the absorption and scattering as it passes through the atmosphere. Due to natural variations of reflectivity with altitude, vertical profile of reflectivity should be corrected as well. There are some other typical radar data filtering procedures, all resulting in various hydrological products. In this work, we use the Universal Multifractal framework to analyze and to inter-compare different products of X-band radar

  14. Analysis of hydrological features of portions of the Lake Ontario basin using Skylab and aircraft data

    Science.gov (United States)

    Polcyn, F. C. (Principal Investigator); Rebel, D. L.; Colwell, J. E.

    1976-01-01

    The author has identified the following significant results. S190A and S190B photography proved to be useful for mapping large scale geomorophological features, and for assessing water depth and water quality. Available S192 data were affected by low frequency noise caused by diode light. Hydrological features were classified, and upland green herbaceous vegetation was separated into several classes based on percent vegetation cover. A model for estimating surface soil moisture based on red and near infrared reflectance data was developed and subsequently implemented.

  15. HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

    Science.gov (United States)

    Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

    2010-12-01

    A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party

  16. Application of bivariate mapping for hydrological classification and analysis of temporal change and scale effects in Switzerland

    NARCIS (Netherlands)

    Speich, Matthias J.R.; Bernhard, Luzi; Teuling, Ryan; Zappa, Massimiliano

    2015-01-01

    Hydrological classification schemes are important tools for assessing the impacts of a changing climate on the hydrology of a region. In this paper, we present bivariate mapping as a simple means of classifying hydrological data for a quantitative and qualitative assessment of temporal change.

  17. PathNet: a tool for pathway analysis using topological information

    Directory of Open Access Journals (Sweden)

    Dutta Bhaskar

    2012-09-01

    Full Text Available Abstract Background Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental studies. However, most algorithms treat pathways as sets of genes, disregarding any inter- and intra-pathway connectivity information, and do not provide insights beyond identifying lists of pathways. Results We developed an algorithm (PathNet that utilizes the connectivity information in canonical pathway descriptions to help identify study-relevant pathways and characterize non-obvious dependencies and connections among pathways using gene expression data. PathNet considers both the differential expression of genes and their pathway neighbors to strengthen the evidence that a pathway is implicated in the biological conditions characterizing the experiment. As an adjunct to this analysis, PathNet uses the connectivity of the differentially expressed genes among all pathways to score pathway contextual associations and statistically identify biological relations among pathways. In this study, we used PathNet to identify biologically relevant results in two Alzheimer’s disease microarray datasets, and compared its performance with existing methods. Importantly, PathNet identified de-regulation of the ubiquitin-mediated proteolysis pathway as an important component in Alzheimer’s disease progression, despite the absence of this pathway in the standard enrichment analyses. Conclusions PathNet is a novel method for identifying enrichment and association between canonical pathways in the context of gene expression data. It takes into account topological information present in pathways to reveal biological information. PathNet is available as an R workspace image from http://www.bhsai.org/downloads/pathnet/.

  18. Analysis of Stomatal Patterning in Selected Mutants of MAPK Pathways

    KAUST Repository

    Felemban, Abrar

    2016-01-01

    -activated protein kinase (MAPK) signalling pathway, which modulates a variety of other processes, including cell proliferation, regulation of cytokinesis, programed cell death, and response to abiotic and biotic stress. The environment also plays a role in stomatal

  19. Integrated analysis of hydrological system, use and management. Langueyu stream basin, Tandil, Argentina

    International Nuclear Information System (INIS)

    Ruiz de Galarreta, V.A.; Banda Noriega, R.B.; Barranquero, R.S.; Diaz, A.A.; Rodriguez, C.I.; Miguel, R.E.

    2010-01-01

    This work is aim to hydrological and environmental characterization of Langueyu stream basin, where Tandil city is located. This basin is developed on northern hillside of Tandilia system, in Buenos Aires province, and it drains to NE. There are two different hydrogeological units: crystalline rocks and Cenozoic sediments, which correspond with two hydrolithological characters, fissured and clastic porous, respectively. The population is supplied by groundwater sources. Water exploitation and use were analyzed, according to the growing demands from industrial, agricultural and urban uses. The impacts of intense exploitation were evaluated. High levels of nitrate were corroborated in older wells of the city, which nowadays are in use. The hydrodynamic change in a section of the stream, where it converts to influent, was detected. This disturbance of the natural relation could be a potential source of contamination to the aquifer, due to high charges of industrial and urban effluents which the stream receives. Several population sectors, which have neither a drinking water net nor a sewer system, showed microbiological and chemical water contamination. Other water impact is constituted by several abandoned quarries which have historically received wastes, mainly from foundry industries. In conclusion, water management basin does not aim to sustainable development, due to its lack of integration. It demands the knowledge of hydrological system, according with the goal to avoid water quality degradation and to guarantee its protection. (Author).

  20. Coupled analysis on landscape pattern and hydrological processes in Yanhe watershed of China.

    Science.gov (United States)

    Li, J; Zhou, Z X

    2015-02-01

    As a typical experimental Soil and Water Conservation District, Yanhe watershed has long been plagued by soil erosion due to severe human disturbances. Exerting remote sensing (RS) and geographic information system (GIS) technology, this paper firstly analyzed and simulated ecological hydrological process in Yanhe watershed based on SWAT model, constructed a comprehensive landscape indices which was closely related to soil erosion, and reflected the coupling relationship between regional landscape pattern change and soil erosion. The results are as follows: (1) Areas of different land use types remained relatively stable from 1990 to 2000 and then changed drastically from 2000 to 2010, which was characterized by lawn expansion and cultivated land shrinkage. (2) In terms of the spatial heterogeneity of hydrological response unit (HRUs), the correlation coefficient of seven selected landscape indices and runoff was very small, and cannot pass all significant testing. But correlation between the indices and sediment yield except for Total Core Area (TCA) and Interspersion and Juxtaposition Index (IJI) was remarkable. (3) According to 'the source-sink' theory of soil erosion, new landscape index-slope-HRU landscape index (SHLI) was built, and reflected the relationship between landscape pattern and soil erosion processes to a certain extent. (4) Coupling relationship between SHLI in 2010 and annual sediment was very prominent. In the sub-basin scale, SHLI has obvious regional differentiation from annual sediment. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. A hydrologic-economic modeling approach for analysis of urban water supply dynamics in Chennai, India

    Science.gov (United States)

    Srinivasan, Veena; Gorelick, Steven M.; Goulder, Lawrence

    2010-07-01

    In this paper, we discuss a challenging water resources problem in a developing world city, Chennai, India. The goal is to reconstruct past system behavior and diagnose the causes of a major water crisis. In order to do this, we develop a hydrologic-engineering-economic model to address the complexity of urban water supply arising from consumers' dependence on multiple interconnected sources of water. We integrate different components of the urban water system: water flowing into the reservoir system; diversion and distribution by the public water utility; groundwater flow in the aquifer beneath the city; supply, demand, and prices in the informal tanker-truck-based water market; and consumer behavior. Both the economic and physical impacts of consumers' dependence on multiple sources of water are quantified. The model is calibrated over the period 2002-2006 using a range of hydrologic and socio-economic data. The model's results highlight the inadequacy of the reservoir system and the buffering role played by the urban aquifer and consumers' coping investments during multiyear droughts.

  2. Analysis of runoff for the Baltic basin with an integrated Atmospheric-Ocean-Hydrology Model

    Directory of Open Access Journals (Sweden)

    K.-G. Richter

    2006-01-01

    Full Text Available A fully integrated Atmospheric-Ocean-Hydrology Model (BALTIMOS = Baltic Integrated Model System has been developed using existing model components. Experiment and model design has been adapted to the Baltic basin with a catchment area of approximately 1 750 000 km2. A comprehensive model validation has been completed using large meteorological and hydrological measurement database. Comparing the calculated runoff from the integrated and non-integrated model system with measurements for three different representative subbasins and the entire Baltic basin, the effect of the integrated model is described. The results display a good agreement between measured and calculated runoff. The effect of the integrated model is rather negligible looking at computed mean values: There is no significant difference between mean monthly runoff of the integrated and non-integrated model during the year with the exception of spring. There is a delay of one month with regard to peak runoff for the non-integrated model in spring caused by different interactive processes during the melting period.

  3. ALL-PATHWAYS DOSE ANALYSIS FOR THE PORTSMOUTH ON-SITE WASTE DISPOSAL FACILITY

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F.; Phifer, M.

    2014-04-10

    A Portsmouth On-Site Waste Disposal Facility (OSWDF) All-Pathways analysis has been conducted that considers the radiological impacts to a resident farmer. It is assumed that the resident farmer utilizes a farm pond contaminated by the OSWDF to irrigate a garden and pasture and water livestock from which food for the resident farmer is obtained, and that the farmer utilizes groundwater from the Berea sandstone aquifer for domestic purposes (i.e. drinking water and showering). As described by FBP 2014b the Hydrologic Evaluation of Landfill Performance (HELP) model (Schroeder et al. 1994) and the Surface Transport Over Multiple Phases (STOMP) model (White and Oostrom 2000, 2006) were used to model the flow and transport from the OSWDF to the Points of Assessment (POAs) associated with the 680-ft elevation sandstone layer (680 SSL) and the Berea sandstone aquifer. From this modeling the activity concentrations radionuclides were projected over time at the POAs. The activity concentrations were utilized as input to a GoldSimTM (GTG 2010) dose model, described herein, in order to project the dose to a resident farmer over time. A base case and five sensitivity cases were analyzed. The sensitivity cases included an evaluation of the impacts of using a conservative inventory, an uncased well to the Berea sandstone aquifer, a low waste zone uranium distribution coefficient (Kd), different transfer factors, and reference person exposure parameters (i.e. at 95 percentile). The maximum base case dose within the 1,000 year assessment period was projected to be 1.5E-14 mrem/yr, and the maximum base case dose at any time less than 10,000 years was projected to be 0.002 mrem/yr. The maximum projected dose of any sensitivity case was approximately 2.6 mrem/yr associated with the use of an uncased well to the Berea sandstone aquifer. This sensitivity case is considered very unlikely because it assumes leakage from the location of greatest concentration in the 680 SSL in to the

  4. Functional analysis of the MAPK pathways in fungi.

    Science.gov (United States)

    Martínez-Soto, Domingo; Ruiz-Herrera, José

    The Mitogen-Activated Protein Kinase (MAPK) signaling pathways constitute one of the most important and evolutionarily conserved mechanisms for the perception of extracellular information in all the eukaryotic organisms. The MAPK pathways are involved in the transfer to the cell of the information perceived from extracellular stimuli, with the final outcome of activation of different transcription factors that regulate gene expression in response to them. In all species of fungi, the MAPK pathways have important roles in their physiology and development; e.g. cell cycle control, mating, morphogenesis, response to different stresses, resistance to UV radiation and to temperature changes, cell wall assembly and integrity, degradation of cellular organelles, virulence, cell-cell signaling, fungus-plant interaction, and response to damage-associated molecular patterns (DAMPs). Considering the importance of the phylogenetically conserved MAPK pathways in fungi, an updated review of the knowledge on them is discussed in this article. This information reveals their importance, their distribution in fungal species evolutionarily distant and with different lifestyles, their organization and function, and the interactions occurring between different MAPK pathways, and with other signaling pathways, for the regulation of the most complex cellular processes. Copyright © 2017 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

  5. Isotope hydrology

    International Nuclear Information System (INIS)

    Drost, W.

    1978-01-01

    The International Symposium on Isotope Hydrology was jointly organized by the IAEA and UNESCO, in co-operation with the National Committee of the Federal Republic of Germany for the International Hydrological Programme (IHP) and the Gesellschaft fuer Strahlen- und Umweltforschung mbH (GSF). Upon the invitation of the Federal Republic of Germany the Symposium was held from 19-23 June 1978 in Neuherberg on the GSF campus. The Symposium was officially opened by Mr. S. Eklund, Director General of the IAEA. The symposium - the fifth meeting held on isotope hydrology - was attended by over 160 participants from 44 countries and four international organizations and by about 30 observers from the Federal Republic of Germany. Due to the absence of scientists from the USSR five papers were cancelled and therefore only 46 papers of the original programme were presented in ten sessions

  6. Conceptual framework and trend analysis of water-level responses to hydrologic stresses, Pahute Mesa–Oasis Valley groundwater basin, Nevada, 1966-2016

    Science.gov (United States)

    Jackson, Tracie R.; Fenelon, Joseph M.

    2018-05-31

    This report identifies water-level trends in wells and provides a conceptual framework that explains the hydrologic stresses and factors causing the trends in the Pahute Mesa–Oasis Valley (PMOV) groundwater basin, southern Nevada. Water levels in 79 wells were analyzed for trends between 1966 and 2016. The magnitude and duration of water-level responses to hydrologic stresses were analyzed graphically, statistically, and with water-level models.The conceptual framework consists of multiple stress-specific conceptual models to explain water-level responses to the following hydrologic stresses: recharge, evapotranspiration, pumping, nuclear testing, and wellbore equilibration. Dominant hydrologic stresses affecting water-level trends in each well were used to categorize trends as nonstatic, transient, or steady state.The conceptual framework of water-level responses to hydrologic stresses and trend analyses provide a comprehensive understanding of the PMOV basin and vicinity. The trend analysis links water-level fluctuations in wells to hydrologic stresses and potential factors causing the trends. Transient and steady-state trend categorizations can be used to determine the appropriate water-level data for groundwater studies.

  7. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

    International Nuclear Information System (INIS)

    Thomassen, Mads; Tan, Qihua; Kruse, Torben A

    2008-01-01

    Metastasis is believed to progress in several steps including different pathways but the determination and understanding of these mechanisms is still fragmentary. Microarray analysis of gene expression patterns in breast tumors has been used to predict outcome in recent studies. Besides classification of outcome, these global expression patterns may reflect biological mechanisms involved in metastasis of breast cancer. Our purpose has been to investigate pathways and transcription factors involved in metastasis by use of gene expression data sets. We have analyzed 8 publicly available gene expression data sets. A global approach, 'gene set enrichment analysis' as well as an approach focusing on a subset of significantly differently regulated genes, GenMAPP, has been applied to rank pathway gene sets according to differential regulation in metastasizing tumors compared to non-metastasizing tumors. Meta-analysis has been used to determine overrepresentation of pathways and transcription factors targets, concordant deregulated in metastasizing breast tumors, in several data sets. The major findings are up-regulation of cell cycle pathways and a metabolic shift towards glucose metabolism reflected in several pathways in metastasizing tumors. Growth factor pathways seem to play dual roles; EGF and PDGF pathways are decreased, while VEGF and sex-hormone pathways are increased in tumors that metastasize. Furthermore, migration, proteasome, immune system, angiogenesis, DNA repair and several signal transduction pathways are associated to metastasis. Finally several transcription factors e.g. E2F, NFY, and YY1 are identified as being involved in metastasis. By pathway meta-analysis many biological mechanisms beyond major characteristics such as proliferation are identified. Transcription factor analysis identifies a number of key factors that support central pathways. Several previously proposed treatment targets are identified and several new pathways that may

  8. Comparative analysis of programmed cell death pathways in filamentous fungi

    Directory of Open Access Journals (Sweden)

    Wortman Jennifer R

    2005-12-01

    Full Text Available Abstract Background Fungi can undergo autophagic- or apoptotic-type programmed cell death (PCD on exposure to antifungal agents, developmental signals, and stress factors. Filamentous fungi can also exhibit a form of cell death called heterokaryon incompatibility (HI triggered by fusion between two genetically incompatible individuals. With the availability of recently sequenced genomes of Aspergillus fumigatus and several related species, we were able to define putative components of fungi-specific death pathways and the ancestral core apoptotic machinery shared by all fungi and metazoa. Results Phylogenetic profiling of HI-associated proteins from four Aspergilli and seven other fungal species revealed lineage-specific protein families, orphan genes, and core genes conserved across all fungi and metazoa. The Aspergilli-specific domain architectures include NACHT family NTPases, which may function as key integrators of stress and nutrient availability signals. They are often found fused to putative effector domains such as Pfs, SesB/LipA, and a newly identified domain, HET-s/LopB. Many putative HI inducers and mediators are specific to filamentous fungi and not found in unicellular yeasts. In addition to their role in HI, several of them appear to be involved in regulation of cell cycle, development and sexual differentiation. Finally, the Aspergilli possess many putative downstream components of the mammalian apoptotic machinery including several proteins not found in the model yeast, Saccharomyces cerevisiae. Conclusion Our analysis identified more than 100 putative PCD associated genes in the Aspergilli, which may help expand the range of currently available treatments for aspergillosis and other invasive fungal diseases. The list includes species-specific protein families as well as conserved core components of the ancestral PCD machinery shared by fungi and metazoa.

  9. Multifractal analysis of the outputs of a fully distributed model for two case studies in urban hydrology

    Science.gov (United States)

    Gires, Auguste; Giangola-Murzyn, Agathe; Tchiguirinskaia, Ioulia; Schertzer, Daniel; Lovejoy, Shaun

    2013-04-01

    Hydrological fields are known to exhibit extreme variability over wide range of spatio-temporal scales. In this paper, these features are investigated in the specific context of urban hydrology with the help of two case studies. The first one consists in a 144 ha flat urban area located in the Seine-Saint-Denis County (North-East of Paris, France), known for suffering occasional pluvial flooding. The second one is a 250 ha urban area with a significant portion of forest located on a steep hillside of the Bièvre River (Yvelines County, South-West of Paris, France). The catchments behaviour is modelled with the help of Multi-Hydro, a fully distributed physically based model (2D/1D) currently under development at Ecole des Ponts ParisTech. It consists of an interacting core between open source software packages, each of them representing a portion of the water cycle in urban environment. The rainfall data comes from the C-band radar of Trappes operated by Météo-France and located at respectively 45 Km and 13 Km of the studied catchments. The resolution is 1 km in space and 5 min in time. Three rainfall events that occurred in 2010 and 2011 that generated significant surface runoff and some local flooding are analysed. First the uncertainty associated with small scale unmeasured rainfall variability (i.e. below the C-band radar resolution) is investigated. This is done through the analysis of the disparities among an ensemble of hydrological simulations performed with the help of downscaled rainfall fields. The downscaling implemented here simply consists in stochastically continuing the underlying Universal Multifractal cascade process observed on the available range of scales. This uncertainty is significant for both simulated conduit discharge and water depth, and therefore cannot be neglected, indicating the need to develop the use of X-band radars (which provide an hectometric resolution) in urban environment. Second it appears that the outputs (maps of water

  10. Hillslope hydrology and stability

    Science.gov (United States)

    Lu, Ning; Godt, Jonathan

    2012-01-01

    Landslides are caused by a failure of the mechanical balance within hillslopes. This balance is governed by two coupled physical processes: hydrological or subsurface flow and stress. The stabilizing strength of hillslope materials depends on effective stress, which is diminished by rainfall. This book presents a cutting-edge quantitative approach to understanding hydro-mechanical processes across variably saturated hillslope environments and to the study and prediction of rainfall-induced landslides. Topics covered include historic synthesis of hillslope geomorphology and hydrology, total and effective stress distributions, critical reviews of shear strength of hillslope materials and different bases for stability analysis. Exercises and homework problems are provided for students to engage with the theory in practice. This is an invaluable resource for graduate students and researchers in hydrology, geomorphology, engineering geology, geotechnical engineering and geomechanics and for professionals in the fields of civil and environmental engineering and natural hazard analysis.

  11. A novel bi-level meta-analysis approach: applied to biological pathway analysis.

    Science.gov (United States)

    Nguyen, Tin; Tagett, Rebecca; Donato, Michele; Mitrea, Cristina; Draghici, Sorin

    2016-02-01

    The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge in integrating genomic data. One practical drawback of many P-value-based meta-analysis methods, including Fisher's, Stouffer's, minP and maxP, is that they are sensitive to outliers. Another drawback is that, because they perform just one statistical test for each individual experiment, they may not fully exploit the potentially large number of samples within each study. We propose a novel bi-level meta-analysis approach that employs the additive method and the Central Limit Theorem within each individual experiment and also across multiple experiments. We prove that the bi-level framework is robust against bias, less sensitive to outliers than other methods, and more sensitive to small changes in signal. For comparative analysis, we demonstrate that the intra-experiment analysis has more power than the equivalent statistical test performed on a single large experiment. For pathway analysis, we compare the proposed framework versus classical meta-analysis approaches (Fisher's, Stouffer's and the additive method) as well as against a dedicated pathway meta-analysis package (MetaPath), using 1252 samples from 21 datasets related to three human diseases, acute myeloid leukemia (9 datasets), type II diabetes (5 datasets) and Alzheimer's disease (7 datasets). Our framework outperforms its competitors to correctly identify pathways relevant to the phenotypes. The framework is sufficiently general to be applied to any type of statistical meta-analysis. The R scripts are available on demand from the authors. sorin@wayne.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e

  12. Analysis of heterogeneous hydrological properties of a mountainous hillslope using intensive water flow measurements

    Science.gov (United States)

    Masaoka, Naoya; Kosugi, Ken'ichirou; Yamakawa, Yosuke; Mizuyama, Takahisa; Tsutsumi, Daizo

    2013-04-01

    Heterogeneous hydrological properties in a foot slope area of mountainous hillslopes should be assessed to understand hydrological phenomena and their effects on discharge and sediment transport. In this study, we analyzed the high-resolution and three-dimensional water movement data to clarify the hydrological process, including heterogeneous phenomena, in detail. We continuously monitored the soil matric pressure head, psi, using 111 tensiometers installed at grid intervals of approximately 1 meter within the soil mantle at the study hillslope. Under a no-rainfall condition, the existence of perennial groundwater seepage flow was detected by exfiltration flux and temporal psi waveforms, which showed delayed responses, only to heavy storm events, and gradual recession limbs. The seepage water spread in the downslope direction and supplied water constantly to the lower section of the slope. At some points in the center of the slope, a perched saturated area was detected in the middle of soil layer, while psi exhibited negative values above the bedrock surface. These phenomena could be inferred partly from the bedrock topography and the distribution of soil hydraulic conductivity assumed from the result of penetration test. At the peak of a rainfall event, on the other hand, continuous high pressure zones (i.e., psi > 50 cmH2O) were generated in the right and left sections of the slope. Both of these high pressure zones converged at the lower region, showing a sharp psi spike up to 100 cmH2O. Along the high pressure zones, flux vectors showed large values and water exfiltration, indicating the occurrence of preferential flow. Moreover, the preferential flow occurred within the area beneath the perched water, indicating the existence of a weathered bedrock layer. This layer had low permeability, which prevented the vertical infiltration of water in the upper part of the layer, but had high permeability as a result of the fractures distributed heterogeneously inside

  13. Analysis of hydrologic variation under climate change environment in southern Taiwan

    Science.gov (United States)

    Chen, Yung-Chau; Chen, Yu-Chin; Chen, Wen-Fu

    2014-05-01

    Impact and adaptation is an important issue in response to climate change. We need to know the affections of climate change on hydrologic characteristics before estimating the impacts and making adaptation strategies of concerned area. The wet and dry seasons of southern Taiwan are significant. In addition, the amount of average annual rainfall is about 2,100mm in southern Taiwan. Most of rainfalls happen in wet season and are caused by cyclones (typhoons) or thunderstorms in wet season. It implies that both quantity and intensity of rainfall are large in wet season, while they are small in dry season. Corresponding to the phenomena, the possibility of flood in wet season and draught in dry season is high. This means significant hydrologic variations may cause disasters. The purpose of this study is to analyze hydrologic variation due to recent climate changes in southern Taiwan, and provide decision makers some information to understand possible impacts and make adaptation strategies. Before typhoon Morakot hit Taiwan, southern Taiwan was suffering from aridity. As usual, people were expecting the rainfall accompanied with typhoons will resolve the drought in this area. However, it fell down huge amount of water within a short period of time and the rain became a big disaster in this area. The rainfall is an over 200-year event, a record breaker. The data used in this research is based on the records of Taiwan Central Weather Bureau at Chiayi, Tainan, Kaohsiung, and Hengchun station, respectively. The trends of temperature, amount of rainfall, and number of rainy days are examined. Both Mann-Kendall trend test and linear regression method are chosen as the means to do trend examination.The results show that annual mean temperatures at Chiayi, Tainan, Kaohsiung, and Hengchun have raised 0.5~0.9°C during past decades under the impact of global warming. The amount of annual rainfall does not appear statistically significant trend. However, the number of annual rainy

  14. Analysis of Phenomenels with Hydrologic Large Risk in the Hydrographic Basin of the Trotuş River

    Directory of Open Access Journals (Sweden)

    Avram Mihaela

    2017-10-01

    Full Text Available The paper presents an analysis of the high hydrological risk phenomena formed in the hydrographic basin of the Trotuş River in the last period of time. The Trotuş River and the tributaries are monitored by 21 hydrometric stations. Precipitation volume processing indicated a number of risk factors that have prevailed over the last 20 years. The hydrological data processing revealed the presence of several flood flows in the same year. The effects of the floods have materialized through the excessive degradation of river bedside regulation and shore defence works. The floods of the past 25 years have resulted in the destruction of a large number of economic and social objectives in the Trotuş River area, as well as human losses. Parameters of hydroclimatic risk highlighted by research are represented by torrential precipitations, floods with high probability, high frequency of high-flow flows, formation of high erosion velocities of the bed, etc. Parameters of hydroclimatic risk impose special conditions for the design of river regularization and shore defence.

  15. Climate and Hydrological Data Analysis for hydrological and solute transport modelling purposes in the Muriaé River basin, Atlantic Forest Biome, SE Brazil

    Science.gov (United States)

    Santos, Juliana; Künne, Annika; Kralisch, Sven; Fink, Manfred; Brenning, Alexander

    2016-04-01

    The Muriaé River basin in SE Brazil has been experiencing an increasing pressure on water resources, due to the population growth of the Rio de Janeiro urban area connected with the growth of the industrial and agricultural sector. This leads to water scarcity, riverine forest degradation, soil erosion and water quality problems among other impacts. Additionally the region has been suffering with seasonal precipitation variations leading to extreme events such as droughts, floods and landslides. Climate projections for the near future indicate a high inter-annual variability of rainfall with an increase in the frequency and intensity of heavy rainfall events combined with a statistically significant increase in the duration of dry periods and a reduced duration of wet periods. This may lead to increased soil erosion during the wet season, while the longer dry periods may reduce the vegetation cover, leaving the soil even more exposed and vulnerable to soil erosion. In consequence, it is crucial to understand how climate affects the interaction between the timing of extreme rainfall events, hydrological processes, vegetation growth, soil cover and soil erosion. In this context, physically-based hydrological modelling can contribute to a better understanding of spatial-temporal process dynamics in the Earth's system and support Integrated Water Resourses Management (IWRM) and adaptation strategies. The study area is the Muriaé river basin which has an area of approx. 8000 km² in Minas Gerais and Rio de Janeiro States. The basin is representative of a region of domain of hillslopes areas with the predominancy of pasture for livestock production. This study will present some of the relevant analyses which have been carried out on data (climate and streamflow) prior to using them for hydrological modelling, including consistency checks, homogeneity, pattern and statistical analyses, or annual and seasonal trends detection. Several inconsistencies on the raw data were

  16. Spatial analysis of geologic and hydrologic features relating to sinkhole occurrence in Jefferson County, West Virginia

    Science.gov (United States)

    Doctor, Daniel H.; Doctor, Katarina Z.

    2012-01-01

    In this study the influence of geologic features related to sinkhole susceptibility was analyzed and the results were mapped for the region of Jefferson County, West Virginia. A model of sinkhole density was constructed using Geographically Weighted Regression (GWR) that estimated the relations among discrete geologic or hydrologic features and sinkhole density at each sinkhole location. Nine conditioning factors on sinkhole occurrence were considered as independent variables: distance to faults, fold axes, fracture traces oriented along bedrock strike, fracture traces oriented across bedrock strike, ponds, streams, springs, quarries, and interpolated depth to groundwater. GWR model parameter estimates for each variable were evaluated for significance, and the results were mapped. The results provide visual insight into the influence of these variables on localized sinkhole density, and can be used to provide an objective means of weighting conditioning factors in models of sinkhole susceptibility or hazard risk.

  17. Sensitivity of hydrological performance assessment analysis to variations in material properties, conceptual models, and ventilation models

    Energy Technology Data Exchange (ETDEWEB)

    Sobolik, S.R.; Ho, C.K.; Dunn, E. [Sandia National Labs., Albuquerque, NM (United States); Robey, T.H. [Spectra Research Inst., Albuquerque, NM (United States); Cruz, W.T. [Univ. del Turabo, Gurabo (Puerto Rico)

    1996-07-01

    The Yucca Mountain Site Characterization Project is studying Yucca Mountain in southwestern Nevada as a potential site for a high-level nuclear waste repository. Site characterization includes surface- based and underground testing. Analyses have been performed to support the design of an Exploratory Studies Facility (ESF) and the design of the tests performed as part of the characterization process, in order to ascertain that they have minimal impact on the natural ability of the site to isolate waste. The information in this report pertains to sensitivity studies evaluating previous hydrological performance assessment analyses to variation in the material properties, conceptual models, and ventilation models, and the implications of this sensitivity on previous recommendations supporting ESF design. This document contains information that has been used in preparing recommendations for Appendix I of the Exploratory Studies Facility Design Requirements document.

  18. Sensitivity of hydrological performance assessment analysis to variations in material properties, conceptual models, and ventilation models

    International Nuclear Information System (INIS)

    Sobolik, S.R.; Ho, C.K.; Dunn, E.; Robey, T.H.; Cruz, W.T.

    1996-07-01

    The Yucca Mountain Site Characterization Project is studying Yucca Mountain in southwestern Nevada as a potential site for a high-level nuclear waste repository. Site characterization includes surface- based and underground testing. Analyses have been performed to support the design of an Exploratory Studies Facility (ESF) and the design of the tests performed as part of the characterization process, in order to ascertain that they have minimal impact on the natural ability of the site to isolate waste. The information in this report pertains to sensitivity studies evaluating previous hydrological performance assessment analyses to variation in the material properties, conceptual models, and ventilation models, and the implications of this sensitivity on previous recommendations supporting ESF design. This document contains information that has been used in preparing recommendations for Appendix I of the Exploratory Studies Facility Design Requirements document

  19. Scoping analysis of in situ thermal-hydrological testing at Yucca Mountain

    International Nuclear Information System (INIS)

    Buscheck, T.A.; Nitao, J.J.

    1996-01-01

    In situ thermal tests, which are to be conducted in the Exploratory Studies Facility (ESF) in the unsaturated zone (UZ) at Yucca Mountain, are required to test coupled thermal-hydrological-geomechanical-geochemical (T-H-M-C) process models that support total system performance assessment. The ESF thermal tests must provide an understanding of coupled T-H-M-C processes that are relevant to expected repository conditions. Current planning includes the possibility of two large-scale tests: (1) the first ESF (drift-scale) thermal test, which will be conducted under an accelerated heatup and cooldown schedule, and (2) a second ESF (multi-drift) test, which will be larger-scale, longer-duration test, conducted under a less accelerated heatup and cooldown schedule. With the V-TOUGH (vectorized transport of unsaturated groundwater and heat) code, the authors modeled and evaluated a range of heater test sizes, heating rates, and heating durations under a range of plausible hydrological conditions to develop a test design that provides sufficient (and timely) information to determine the following: the dominant mode(s) of heat flow; the major T-H regime(s) and the T-H-M-C processes that determine the magnitude and direction of vapor and condensate flow; and the influence of heterogeneous conditions on the flow of heat, vapor, and condensate. A major purpose of the ESF thermal tests is to determine which major decay-heat-driven T-H flow regime(s) will govern the magnitude and direction of vapor and condensate flow in the UZ. Another major purpose of the thermal tests is to determine the degree of vapor diffusion enhancement

  20. Goodness-of-Fit Tests for Generalized Normal Distribution for Use in Hydrological Frequency Analysis

    Science.gov (United States)

    Das, Samiran

    2018-04-01

    The use of three-parameter generalized normal (GNO) as a hydrological frequency distribution is well recognized, but its application is limited due to unavailability of popular goodness-of-fit (GOF) test statistics. This study develops popular empirical distribution function (EDF)-based test statistics to investigate the goodness-of-fit of the GNO distribution. The focus is on the case most relevant to the hydrologist, namely, that in which the parameter values are unidentified and estimated from a sample using the method of L-moments. The widely used EDF tests such as Kolmogorov-Smirnov, Cramer von Mises, and Anderson-Darling (AD) are considered in this study. A modified version of AD, namely, the Modified Anderson-Darling (MAD) test, is also considered and its performance is assessed against other EDF tests using a power study that incorporates six specific Wakeby distributions (WA-1, WA-2, WA-3, WA-4, WA-5, and WA-6) as the alternative distributions. The critical values of the proposed test statistics are approximated using Monte Carlo techniques and are summarized in chart and regression equation form to show the dependence of shape parameter and sample size. The performance results obtained from the power study suggest that the AD and a variant of the MAD (MAD-L) are the most powerful tests. Finally, the study performs case studies involving annual maximum flow data of selected gauged sites from Irish and US catchments to show the application of the derived critical values and recommends further assessments to be carried out on flow data sets of rivers with various hydrological regimes.

  1. A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

    Directory of Open Access Journals (Sweden)

    Elisa Cirillo

    2017-11-01

    Full Text Available Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field. Tool evaluation was performed using a computational epistatic dataset of gene–gene interactions for obesity risk. Next, we report the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data, expressly aiming to define features for more comprehensive pathway-based analysis tools. We conclude by recognizing that pathway analysis of genetic variations data requires a sophisticated combination of the most useful and informative visual aspects of the various tools evaluated.

  2. Hydrological evolution of Atlantis basin, Sirenum Terrae, Mars. Preliminar analysis of MOC and THEMIS images.

    Science.gov (United States)

    de Pablo, M. A.; Márquez, A.; Centeno, J. D.

    The Atlantis basin is one of the martian highlands areas where there was proposed the existence of an ancient lake during the early geological history of Mars [1] [2] [3] [4]. The existence of some morphological features inside the basin and in the surrounding area, allow to check the existence of liquid water in the past of the planet. On the other hand, other morphological features indicate the existence of snow and liquid groundwater in recent times. The detailed study of the geomorphologic features allows to make an approach to the hydrological evolution of the Atlantis basin. The study of the geomorphology of this region has been carried out by means of the analysis of MOC high resolution images obtained by the Mars Global Surveyor mission and the THEMIS images, in the visible spectrum, sent by Mars Odyssey spacecrafts. The most clearly morphological feature indicative of the existence of water in the surface of Mars in the past are the numerous channels that end into Atlantis basin from the highest terrains. In addiction to these fluvial channels, the existence of mass flow deposits is also indicative of the existence of water in the area. Some of these slumps are in the internal slopes of impact craters, but others cover huge extensions around the chaotic terrains of the studied area. The lobated ejecta deposits observed in the Atlantis basin region are indicative of the existence of groundwater (solid or liquid) [5]. Serrated reliefs and tables in the borders of the basins are indicative of the existence of a water sheet. Beneath this water sheet some deposits was formed which was eroded, due to the gradual desiccation of the basin, forming the tables and serrated reliefs. The existence of different chaotic terrains in the area implies the existence of huge amounts of water under the surface according to the different models of chaotic terrain formation [6] [7]. The existence of groundwater could be decided by the existence of collapses in the near to the

  3. Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA.

    Science.gov (United States)

    Yang, Xian; Han, Rui; Guo, Yike; Bradley, Jeremy; Cox, Benita; Dickinson, Robert; Kitney, Richard

    2012-01-01

    Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series of hospital challenges. To date, conventional research lacks a mathematical model to describe clinical pathways. Existing vague descriptions cannot fully capture the complexities accurately in clinical pathways and hinders the effective management and further optimization of clinical pathways. Given this motivation, this paper presents a clinical pathway management platform, the Imperial Clinical Pathway Analyzer (ICPA). By extending the stochastic model performance evaluation process algebra (PEPA), ICPA introduces a clinical-pathway-specific model: clinical pathway PEPA (CPP). ICPA can simulate stochastic behaviours of a clinical pathway by extracting information from public clinical databases and other related documents using CPP. Thus, the performance of this clinical pathway, including its throughput, resource utilisation and passage time can be quantitatively analysed. A typical clinical pathway on stroke extracted from a UK hospital is used to illustrate the effectiveness of ICPA. Three application scenarios are tested using ICPA: 1) redundant resources are identified and removed, thus the number of patients being served is maintained with less cost; 2) the patient passage time is estimated, providing the likelihood that patients can leave hospital within a specific period; 3) the maximum number of input patients are found, helping hospitals to decide whether they can serve more patients with the existing resource allocation. ICPA is an effective platform for clinical pathway management: 1) ICPA can describe a variety of components (state, activity, resource and constraints) in a clinical pathway, thus facilitating the proper understanding of complexities involved in it; 2) ICPA supports the performance analysis of clinical pathway, thereby assisting

  4. Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

    Directory of Open Access Journals (Sweden)

    Wu Xiaogang

    2012-06-01

    Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

  5. Analysis of Chlorogenic Acid Oxidation Pathway in Simulated ...

    African Journals Online (AJOL)

    Purpose: To investigate the pathways involved in the oxidation of chlorogenic acid (CA) and phenol metabolism in honeysuckle buds. Methods: A model that mimics CA oxidation by honeysuckle polyphenol oxidase (PPO) by controlling the reaction temperature or reaction duration was employed, and the resulting products ...

  6. Pathway analysis for identification of potential biomarkers in severe ...

    African Journals Online (AJOL)

    It was found by geneMANIA database search that majority of these genes were coexpressed yielding 84.63 % co-expression. It was found that ten genes were in Physical interactions comprising almost 14.33 %. There were < 1 % pathway and genetic interactions with values of 0.97 and 0.06 %, respectively. Final analyses ...

  7. Analysis of Chlorogenic Acid Oxidation Pathway in Simulated ...

    African Journals Online (AJOL)

    Keywords: Honeysuckle, Chlorogenic acid, Enzymatic browning, Mimic system, Oxidation pathway, ... enzymatic oxidation of CA is the major cause of ..... to the concentration of catechol, o-quinone and current at PPO-modified microcylinder biosensor for diffusion- kinetic model. J Electroanal Chem 2011; 660: 200-208.

  8. Sensitive analysis of low-flow parameters using the hourly hydrological model for two mountainous basins in Japan

    Science.gov (United States)

    Fujimura, Kazumasa; Iseri, Yoshihiko; Kanae, Shinjiro; Murakami, Masahiro

    2014-05-01

    Accurate estimation of low flow can contribute to better water resources management and also lead to more reliable evaluation of climate change impacts on water resources. In the early study, the nonlinearity of low flow related to the storage in the basin was suggested by Horton (1937) as the exponential function of Q=KSN, where Q is the discharge, S is the storage, K is a constant and N is the exponent value. In the recent study by Ding (2011) showed the general storage-discharge equation of Q = KNSN. Since the constant K is defined as the fractional recession constant and symbolized as Au by Ando et al. (1983), in this study, we rewrite this equation as Qg=AuNSgN, where Qg is the groundwater runoff and Sg is the groundwater storage. Although this equation was applied to a short-term runoff event of less than 14 hours using the unit hydrograph method by Ding, it was not yet applied for a long-term runoff event including low flow more than 10 years. This study performed a sensitive analysis of two parameters of the constant Au and exponent value N by using the hourly hydrological model for two mountainous basins in Japan. The hourly hydrological model used in this study was presented by Fujimura et al. (2012), which comprise the Diskin-Nazimov infiltration model, groundwater recharge and groundwater runoff calculations, and a direct runoff component. The study basins are the Sameura Dam basin (SAME basin) (472 km2) located in the western Japan which has variability of rainfall, and the Shirakawa Dam basin (SIRA basin) (205km2) located in a region of heavy snowfall in the eastern Japan, that are different conditions of climate and geology. The period of available hourly data for the SAME basin is 20 years from 1 January 1991 to 31 December 2010, and for the SIRA basin is 10 years from 1 October 2003 to 30 September 2013. In the sensitive analysis, we prepared 19900 sets of the two parameters of Au and N, the Au value ranges from 0.0001 to 0.0100 in steps of 0

  9. Pan-cancer analysis of TCGA data reveals notable signaling pathways

    International Nuclear Information System (INIS)

    Neapolitan, Richard; Horvath, Curt M.; Jiang, Xia

    2015-01-01

    A signal transduction pathway (STP) is a network of intercellular information flow initiated when extracellular signaling molecules bind to cell-surface receptors. Many aberrant STPs have been associated with various cancers. To develop optimal treatments for cancer patients, it is important to discover which STPs are implicated in a cancer or cancer-subtype. The Cancer Genome Atlas (TCGA) makes available gene expression level data on cases and controls in ten different types of cancer including breast cancer, colon adenocarcinoma, glioblastoma, kidney renal papillary cell carcinoma, low grade glioma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian carcinoma, rectum adenocarcinoma, and uterine corpus endometriod carcinoma. Signaling Pathway Impact Analysis (SPIA) is a software package that analyzes gene expression data to identify whether a pathway is relevant in a given condition. We present the results of a study that uses SPIA to investigate all 157 signaling pathways in the KEGG PATHWAY database. We analyzed each of the ten cancer types mentioned above separately, and we perform a pan-cancer analysis by grouping the data for all the cancer types. In each analysis several pathways were found to be markedly more significant than all the other pathways. We call them notable. Research has already established a connection between many of these pathways and the corresponding cancer type. However, some of our discovered pathways appear to be new findings. Altogether there were 37 notable findings in the separate analyses, 26 of them occurred in 7 pathways. These 7 pathways included the 4 notable pathways discovered in the pan-cancer analysis. So, our results suggest that these 7 pathways account for much of the mechanisms of cancer. Furthermore, by looking at the overlap among pathways, we identified possible regions on the pathways where the aberrant activity is occurring. We obtained 37 notable findings concerning 18 pathways. Some of them appear to be

  10. Annual compilation and analysis of hydrologic data for Escondido Creek, San Antonio River basin, Texas

    Science.gov (United States)

    Reddy, D.R.

    1971-01-01

    IntroductionHistory of Small Watershed Projects in TexasThe U.S. Soil Conservation Service is actively engaged in the installation of flood and soil erosion reducing measures in Texas under the authority of the "Flood Control Act of 1936 and 1944" and "Watershed Protection and Flood Prevention Act" (Public Law 566), as amended. The Soil Conservation Service has found a total of approximately 3,500 floodwater-retarding structures to be physically and economically feasible in Texas. As of September 30, 1970, 1,439 of these structures had been built.This watershed-development program will have varying but important effects on the surface and ground-water resources of river basins, especially where a large number of the floodwater-retarding structures are built. Basic hydrologic data under natural and developed conditions are needed to appraise the effects of the structures on the yield and mode of occurrence of runoff.Hydrologic investigations of these small watersheds were begun by the Geological Survey in 1951 and are now being made in 12 study areas (fig. 1). These investigations are being made in cooperation with the Texas Water Development Board, the Soil Conservation Service, the San Antonio River Authority, the city of Dallas, and the Tarrant County Water Control and Improvement District No. 1. The 12 study areas were chosen to sample watershed having different rainfall, topography, geology, and soils. In five of the study areas, (North, Little Elm, Mukewater, little Pond-North Elm, and Pin Oak Creeks), streamflow and rainfall records were collected prior to construction of the floodwater-retarding structures, thus affording the opportunity for analyses of the conditions "before and after" development. A summary of the development of the floodwater-retarding structures in each study areas of September 30, 1970, is shown in table 1.Objectives of the Texas Small Watersheds ProjectThe purpose of these investigations is to collect sufficient data to meeting the

  11. Hydrology and soil erosion

    Science.gov (United States)

    Leonard J. Lane; Mary R. Kidwell

    2003-01-01

    We review research on surface water hydrology and soil erosion at the Santa Rita Experimental Range (SRER). Almost all of the research was associated with eight small experimental watersheds established from 1974 to 1975 and operated until the present. Analysis of climatic features of the SRER supports extending research findings from the SRER to broad areas of the...

  12. ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts

    Directory of Open Access Journals (Sweden)

    Kim Sun

    2008-03-01

    Full Text Available Abstract Background Once a new genome is sequenced, one of the important questions is to determine the presence and absence of biological pathways. Analysis of biological pathways in a genome is a complicated task since a number of biological entities are involved in pathways and biological pathways in different organisms are not identical. Computational pathway identification and analysis thus involves a number of computational tools and databases and typically done in comparison with pathways in other organisms. This computational requirement is much beyond the capability of biologists, so information systems for reconstructing, annotating, and analyzing biological pathways are much needed. We introduce a new comparative pathway analysis workbench, ComPath, which integrates various resources and computational tools using an interactive spreadsheet-style web interface for reliable pathway analyses. Results ComPath allows users to compare biological pathways in multiple genomes using a spreadsheet style web interface where various sequence-based analysis can be performed either to compare enzymes (e.g. sequence clustering and pathways (e.g. pathway hole identification, to search a genome for de novo prediction of enzymes, or to annotate a genome in comparison with reference genomes of choice. To fill in pathway holes or make de novo enzyme predictions, multiple computational methods such as FASTA, Whole-HMM, CSR-HMM (a method of our own introduced in this paper, and PDB-domain search are integrated in ComPath. Our experiments show that FASTA and CSR-HMM search methods generally outperform Whole-HMM and PDB-domain search methods in terms of sensitivity, but FASTA search performs poorly in terms of specificity, detecting more false positive as E-value cutoff increases. Overall, CSR-HMM search method performs best in terms of both sensitivity and specificity. Gene neighborhood and pathway neighborhood (global network visualization tools can be used

  13. Thermal-Hydrologic Sensitivity Analysis of Engineered Barrier System Design Options

    International Nuclear Information System (INIS)

    Dunlap, B.

    2000-01-01

    This sensitivity study presents the effects that changing the ventilation time and initial linear power loading can have on specific thermal-hydrologic response parameters, such as waste package peak temperatures. Results show that an approximate 55 C drop in waste package peak temperature can be expected from the reference case design if the initial line loading is reduced to 0.90 kW/m or if the ventilation time is increased to 125 years. Increasing the waste package to waste package spacing in order to reduce the linear load to 0.90 kW/m requires additional emplacement drifts and an expansion of the area that the repository occupies. Increasing the ventilation duration requires that the repository remains open and is maintained for long periods of time. The effectiveness and expense of each design alternative must be weighed in determining the best way to achieve a particular thermal goal. Also, this sensitivity study shows that certain thermal goals may not be reached if only using ventilation, sometimes only the reduction of the linear load or a combination of linear loading and ventilation can reduce the thermal response to lower temperature specifications, if considered. As an example, Figure 1 shows that waste package peak temperatures below 96 C would require both a reduction in the linear load and an increase in ventilation duration

  14. An analysis of historic and projected climate scenarios in the Western United States using hydrologic landscape classification.

    Science.gov (United States)

    : Identifying areas of similar hydrology within the United States and its regions (hydrologic landscapes - HLs) is an active area of research. HLs are being used to construct spatially distributed assessments of variability in streamflow and climatic response in Oregon, Alaska, a...

  15. Linked Analysis of East Asia Emission Reduction Pathways

    Science.gov (United States)

    Kim, Y.; Woo, J. H.; Bu, C.; Lee, Y.; Kim, J.; Jang, Y.; Park, M.

    2017-12-01

    Air pollution and its impacts over the Northeast Asia are very severe because of the massive pollutant emissions and high population. Korea has been trying to improve air quality with the enhanced environmental legislation. The air quality over Korea, however, does not entirely dependent on its local emissions. Transboundary air pollution from China highly affects Korean atmosphere. The purpose of this research is to understand role of local and transbounday efforts to improve air quality changes over Korea. In this research, we have tried to set up the multiple emission scenario pathways for Korea and China using IIASA's GAINS (Greenhouse gas - Air pollution Interactions aNd Synergies) modeling framework. More up-to-date growth factors and control policy packets were made using regional socio-economic data and control policy information from local governments and international statistics. Four major scenario pathways, 1) Base (Baseline: current legislation), 2) OTB/OTB(On the book/On the way : existing control measure/planed control measure), 3) BOTW_GHG(Beyond on the way : OTW with GHG reduction plan), 4) BOTW_NH3 (OTW with additional NH3 reduction measure) were developed to represent air quality improvement pathways in consideration of both Korean and Chinese efforts. Strict ambient PM2.5 standards from Seoul metropolitan Air quality Improvement Plan(SAIP) seems too enthusiastic without linking air quality control efforts of China. Step-by-step emission controls and following air quality, control cost, health impact from each scenario will be presented at the conference. This subject is supported by Korea Ministry of Environment as "Climate Change Correspondence Program". And This work was supported under the framework of national strategy project on fine particulate matters by Ministry of Science, ICT and Future Planning.

  16. Gene prediction validation and functional analysis of redundant pathways

    DEFF Research Database (Denmark)

    Sønderkær, Mads

    2011-01-01

    have employed a large mRNA-seq data set to improve and validate ab initio predicted gene models. This direct experimental evidence also provides reliable determinations of UTR regions and polyadenylation sites, which are not easily predicted in plants. Furthermore, once an annotated genome sequence...... is available, gene expression by mRNA-Seq enables acquisition of a more complete overview of gene isoform usage in complex enzymatic pathways enabling the identification of key genes. Metabolism in potatoes This information is useful e.g. for crop improvement based on manipulation of agronomically important...

  17. Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

    Directory of Open Access Journals (Sweden)

    Qingzhu Hua

    2016-09-01

    Full Text Available Red dragon fruit or red pitaya (Hylocereus polyrhizus is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing functional food. Currently, the biosynthetic and regulatory pathways for betalain production remain to be fully deciphered. In this study, isobaric tags for relative and absolute quantitation (iTRAQ-based proteomic analyses were used to reveal the molecular mechanism of betalain biosynthesis in H. polyrhizus fruits at white and red pulp stages, respectively. A total of 1946 proteins were identified as the differentially expressed between the two samples, and 936 of them were significantly highly expressed at the red pulp stage of H. polyrhizus. RNA-seq and iTRAQ analyses showed that some transcripts and proteins were positively correlated; they belonged to “phenylpropanoid biosynthesis”, “tyrosine metabolism”, “flavonoid biosynthesis”, “ascorbate and aldarate metabolism”, “betalains biosynthesis” and “anthocyanin biosynthesis”. In betalains biosynthesis pathway, several proteins/enzymes such as polyphenol oxidase, CYP76AD3 and 4,5-dihydroxy-phenylalanine (DOPA dioxygenase extradiol-like protein were identified. The present study provides a new insight into the molecular mechanism of the betalain biosynthesis at the posttranscriptional level.

  18. Multivariate hydrological frequency analysis for extreme events using Archimedean copula. Case study: Lower Tunjuelo River basin (Colombia)

    Science.gov (United States)

    Gómez, Wilmar

    2017-04-01

    By analyzing the spatial and temporal variability of extreme precipitation events we can prevent or reduce the threat and risk. Many water resources projects require joint probability distributions of random variables such as precipitation intensity and duration, which can not be independent with each other. The problem of defining a probability model for observations of several dependent variables is greatly simplified by the joint distribution in terms of their marginal by taking copulas. This document presents a general framework set frequency analysis bivariate and multivariate using Archimedean copulas for extreme events of hydroclimatological nature such as severe storms. This analysis was conducted in the lower Tunjuelo River basin in Colombia for precipitation events. The results obtained show that for a joint study of the intensity-duration-frequency, IDF curves can be obtained through copulas and thus establish more accurate and reliable information from design storms and associated risks. It shows how the use of copulas greatly simplifies the study of multivariate distributions that introduce the concept of joint return period used to represent the needs of hydrological designs properly in frequency analysis.

  19. Critical Radionuclide and Pathway Analysis for the Savannah River Site, 2016 Update

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, Tim [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hartman, Larry [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-09-08

    During the operational history of Savannah River Site, many different radionuclides have been released from site facilities. However, as shown in this analysis, only a relatively small number of the released radionuclides have been significant contributors to doses to the offsite public. This report is an update to the 2011 analysis, Critical Radionuclide and Pathway Analysis for the Savannah River Site. SRS-based Performance Assessments for E-Area, Saltstone, F-Tank Farm, H-Tank Farm, and a Comprehensive SRS Composite Analysis have been completed. The critical radionuclides and pathways identified in those extensive reports are also detailed and included in this analysis.

  20. A cross-study gene set enrichment analysis identifies critical pathways in endometriosis

    Directory of Open Access Journals (Sweden)

    Bai Chunyan

    2009-09-01

    Full Text Available Abstract Background Endometriosis is an enigmatic disease. Gene expression profiling of endometriosis has been used in several studies, but few studies went further to classify subtypes of endometriosis based on expression patterns and to identify possible pathways involved in endometriosis. Some of the observed pathways are more inconsistent between the studies, and these candidate pathways presumably only represent a fraction of the pathways involved in endometriosis. Methods We applied a standardised microarray preprocessing and gene set enrichment analysis to six independent studies, and demonstrated increased concordance between these gene datasets. Results We find 16 up-regulated and 19 down-regulated pathways common in ovarian endometriosis data sets, 22 up-regulated and one down-regulated pathway common in peritoneal endometriosis data sets. Among them, 12 up-regulated and 1 down-regulated were found consistent between ovarian and peritoneal endometriosis. The main canonical pathways identified are related to immunological and inflammatory disease. Early secretory phase has the most over-represented pathways in the three uterine cycle phases. There are no overlapping significant pathways between the dataset from human endometrial endothelial cells and the datasets from ovarian endometriosis which used whole tissues. Conclusion The study of complex diseases through pathway analysis is able to highlight genes weakly connected to the phenotype which may be difficult to detect by using classical univariate statistics. By standardised microarray preprocessing and GSEA, we have increased the concordance in identifying many biological mechanisms involved in endometriosis. The identified gene pathways will shed light on the understanding of endometriosis and promote the development of novel therapies.

  1. Hydrological analysis relevant to surface water storage at Jabiluka. Supervising Scientist report 142

    International Nuclear Information System (INIS)

    Chiew, F.H.S.; Wang, Q.J.

    1999-01-01

    The report is prepared for the Supervising Scientist at Jabiru. It describes part of an investigation into hydrological issues relating to the water management system proposed for the Jabiluka project. Specifically, the objective is to estimate the water storage capacity required to store surface runoff and other water within the total containment zone (TCZ) of the Jabiluka project. The water storage volume is calculated for a range of probabilities up to 0.002% that the pond design volume would be exceeded over a 30-year mine life. In this study, 50 000 sets of 30 years of daily rainfall and monthly pan evaporation data are stochastically generated to simulate the storage water balance. The approach used by Kinhill and Energy Resources of Australia (ERA) is reviewed and the pond design compared with the estimates derived here. The Kinhill-ERA approach is described in the Jabiluka Mill Alternative Public Environment Report and the Jabiluka Mill Alternative Public Environment Report Technical Appendices (hereon referred to as Jabiluka PER Appendices) (1998). The two reports also provide background to many other issues. The structural design of the storage and other features of the mine site are not considered here. This study also assumes that the bunds and other drainage diversion structures will prevent all water outside the TCZ from entering the TCZ and vice versa. The storage water balance components are discussed in section 2. Some of the water inflows into the storage and losses from the storage are discussed in detail, while elsewhere, the values used by Kinhill-ERA are adopted. Section 3 describes the selection of the climate stations used here, the rainfall and pan evaporation characteristics in the area and the stochastic generation of 1.5 million years of daily rainfall and monthly pan evaporation data. Section 4 describes the approach used to estimate the storage capacity, and presents the storage capacity estimates for various probabilities of

  2. GenMAPP 2: new features and resources for pathway analysis

    Directory of Open Access Journals (Sweden)

    Dahlquist Kam D

    2007-06-01

    Full Text Available Abstract Background Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses. Results To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP, a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP, and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. Conclusion GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.

  3. Identifying novel glioma associated pathways based on systems biology level meta-analysis.

    Science.gov (United States)

    Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

    2013-01-01

    With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

  4. Research on Multi Hydrological Models Applicability and Modelling Data Uncertainty Analysis for Flash Flood Simulation in Hilly Area

    Science.gov (United States)

    Ye, L.; Wu, J.; Wang, L.; Song, T.; Ji, R.

    2017-12-01

    Flooding in small-scale watershed in hilly area is characterized by short time periods and rapid rise and recession due to the complex underlying surfaces, various climate type and strong effect of human activities. It is almost impossible for a single hydrological model to describe the variation of flooding in both time and space accurately for all the catchments in hilly area because the hydrological characteristics can vary significantly among different catchments. In this study, we compare the performance of 5 hydrological models with varying degrees of complexity for simulation of flash flood for 14 small-scale watershed in China in order to find the relationship between the applicability of the hydrological models and the catchments characteristics. Meanwhile, given the fact that the hydrological data is sparse in hilly area, the effect of precipitation data, DEM resolution and their interference on the uncertainty of flood simulation is also illustrated. In general, the results showed that the distributed hydrological model (HEC-HMS in this study) performed better than the lumped hydrological models. Xinajiang and API models had good simulation for the humid catchments when long-term and continuous rainfall data is provided. Dahuofang model can simulate the flood peak well while the runoff generation module is relatively poor. In addition, the effect of diverse modelling data on the simulations is not simply superposed, and there is a complex interaction effect among different modelling data. Overall, both the catchment hydrological characteristics and modelling data situation should be taken into consideration in order to choose the suitable hydrological model for flood simulation for small-scale catchment in hilly area.

  5. Triple phase boundary specific pathway analysis for quantitative characterization of solid oxide cell electrode microstructure

    DEFF Research Database (Denmark)

    Jørgensen, Peter Stanley; Ebbehøj, Søren Lyng; Hauch, Anne

    2015-01-01

    of the pathways through which they can be reached. New methods for performing TPB specific pathway analysis on 3D image data are introduced, analyzing the pathway properties of each TPB site in the electrode structure. The methods seek to provide additional information beyond whether the TPB sites are percolating......The density and percolation of Triple phase boundary sites are important quantities in analyzing microstructures of solid oxide fuel cell electrodes from tomography data. However, these measures do not provide descriptions of the quality of the TPB sites in terms of the length and radius...... or not by also analyzing the pathway length to the TPB sites and the bottleneck radius of the pathway. We show how these methods can be utilized in quantifying and relating the TPB specific results to cell test data of an electrode reduction protocol study for Ni/Scandia-and-Yttria-doped-Zirconia (Ni...

  6. A two-stage method of quantitative flood risk analysis for reservoir real-time operation using ensemble-based hydrologic forecasts

    Science.gov (United States)

    Liu, P.

    2013-12-01

    Quantitative analysis of the risk for reservoir real-time operation is a hard task owing to the difficulty of accurate description of inflow uncertainties. The ensemble-based hydrologic forecasts directly depict the inflows not only the marginal distributions but also their persistence via scenarios. This motivates us to analyze the reservoir real-time operating risk with ensemble-based hydrologic forecasts as inputs. A method is developed by using the forecast horizon point to divide the future time into two stages, the forecast lead-time and the unpredicted time. The risk within the forecast lead-time is computed based on counting the failure number of forecast scenarios, and the risk in the unpredicted time is estimated using reservoir routing with the design floods and the reservoir water levels of forecast horizon point. As a result, a two-stage risk analysis method is set up to quantify the entire flood risks by defining the ratio of the number of scenarios that excessive the critical value to the total number of scenarios. The China's Three Gorges Reservoir (TGR) is selected as a case study, where the parameter and precipitation uncertainties are implemented to produce ensemble-based hydrologic forecasts. The Bayesian inference, Markov Chain Monte Carlo, is used to account for the parameter uncertainty. Two reservoir operation schemes, the real operated and scenario optimization, are evaluated for the flood risks and hydropower profits analysis. With the 2010 flood, it is found that the improvement of the hydrologic forecast accuracy is unnecessary to decrease the reservoir real-time operation risk, and most risks are from the forecast lead-time. It is therefore valuable to decrease the avarice of ensemble-based hydrologic forecasts with less bias for a reservoir operational purpose.

  7. POSEIDON: An integrated system for analysis and forecast of hydrological, meteorological and surface marine fields in the Mediterranean area

    Science.gov (United States)

    Speranza, A.; Accadia, C.; Casaioli, M.; Mariani, S.; Monacelli, G.; Inghilesi, R.; Tartaglione, N.; Ruti, P. M.; Carillo, A.; Bargagli, A.; Pisacane, G.; Valentinotti, F.; Lavagnini, A.

    2004-07-01

    The Mediterranean area is characterized by relevant hydrological, meteorological and marine processes developing at horizontal space-scales of the order of 1-100 km. In the recent past, several international programs have been addressed (ALPEX, POEM, MAP, etc.) to "resolving" the dynamics of such motions. Other projects (INTERREG-Flooding, MEDEX, etc.) are at present being developed with special emphasis on catastrophic events with major impact on human society that are, quite often, characterized in their manifestation by processes with the above-mentioned scales of motion. In the dynamical evolution of such events, however, equally important is the dynamics of interaction of the local (and sometimes very damaging) processes with others developing at larger scales of motion. In fact, some of the most catastrophic events in the history of Mediterranean countries are associated with dynamical processes covering all the range of space-time scales from planetary to local. The Prevision Operational System for the mEditerranean basIn and the Defence of the lagOon of veNice (POSEIDON) is an integrated system for the analysis and forecast of hydrological, meteorological, oceanic fields specifically designed and set up in order to bridge the gap between global and local scales of motion, by modeling explicitly the above referred to dynamical processes in the range of scales from Mediterranean to local. The core of POSEIDON consists of a "cascade" of numerical models that, starting from global scale numerical analysis-forecast, goes all the way to very local phenomena, like tidal propagation in Venice Lagoon. The large computational load imposed by such operational design requires necessarily parallel computing technology: the first model in the cascade is a parallelised version of BOlogna Limited Area Model (BOLAM) running on a Quadrics 128 processors computer (also known as QBOLAM). POSEIDON, developed in the context of a co-operation between the Italian Agency for New

  8. Artificial radioisotopes in hydrological investigation

    International Nuclear Information System (INIS)

    Plata-Bedmar, A.

    1988-01-01

    Radioisotope techniques have an important part in hydrological investigations. Sealed radiation sources have been used for measurements of sediments transported by river water, of thickness and density of sediment layers. X-ray fluorescence analysis and well-logging are widely applied in hydrological research. Tracer techniques have been useful in flow rate and river dynamics research, sediments tracing, irrigation and ground water problems, infiltration rate evaluation etc. The IAEA is supporting several projects involving the use of radioactive tracers in hydrological investigations p.e. in Guatemala, Romania, South East Asia, Brazil, Chile and Nicaragua

  9. Development of an open platform system for environmental pathway analysis

    International Nuclear Information System (INIS)

    LePoire, D. J.; Arnish, J. J.; Gnanapragasam, E.; Chen, S. Y.

    2001-01-01

    Most existing computer codes for environmental pathway modeling have been developed to satisfy a specific objective (e.g., perform analyses to demonstrate regulatory compliance). These codes were written in various computer languages and software environments over time and often are not mutually compatible. In recent years, largely driven by advancements in industrial software development, a new concept based on ''modularization'' has emerged. This approach entails the development of common ''modules,'' or components, that can be shared by and used in different applications that have certain common needs. For instance, an air dispersion model can be written as a common component to be shared by several different applications, each with the need to model air dispersion of some material release. When this concept is fully developed, modeling applications would become an exercise of selecting, integrating, and applying a consistent combination of appropriate pre-existing modules for a specific problem. Although modularization holds promising advantages over the traditional approach, a number of issues do exist. These issues must be fully addressed and resolved before the approach can be accepted as a new paradigm for environmental modeling. This paper discusses these issues and provides recommendations and a course of actions for future development

  10. Identification of temporal patterns of long-term hydrological signals in Lower Mississippi River Basin using wavelet analysis

    Science.gov (United States)

    Ying Ouyang

    2016-01-01

    Estimates of surface hydrological characteristics in watershed ecosystems are essential to climate change assessment, water supply planning, water quality protection, ecological restoration, and water resources management.

  11. Effects of clinical pathways in the joint replacement: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Faggiano F

    2009-07-01

    Full Text Available Abstract Background A meta-analysis was performed to evaluate the use of clinical pathways for hip and knee joint replacements when compared with standard medical care. The impact of clinical pathways was evaluated assessing the major outcomes of in-hospital hip and knee joint replacement processes: postoperative complications, number of patients discharged at home, length of in-hospital stay and direct costs. Methods Medline, Cinahl, Embase and the Cochrane Central Register of Controlled Trials were searched. The search was performed from 1975 to 2007. Each study was assessed independently by two reviewers. The assessment of methodological quality of the included studies was based on the Jadad methodological approach and on the New Castle Ottawa Scale. Data analysis abided by the guidelines set out by The Cochrane Collaboration regarding statistical methods. Meta-analyses were performed using RevMan software, version 4.2. Results Twenty-two studies met the study inclusion criteria and were included in the meta-analysis for a total sample of 6,316 patients. The aggregate overall results showed significantly fewer patients suffering postoperative complications in the clinical pathways group when compared with the standard care group. A shorter length of stay in the clinical pathway group was also observed and lower costs during hospital stay were associated with the use of the clinical pathways. No significant differences were found in the rates of discharge to home. Conclusion The results of this meta-analysis show that clinical pathways can significantly improve the quality of care even if it is not possible to conclude that the implementation of clinical pathways is a cost-effective process, because none of the included studies analysed the cost of the development and implementation of the pathways. Based on the results we assume that pathways have impact on the organisation of care if the care process is structured in a standardised way

  12. Network Analysis Tools: from biological networks to clusters and pathways.

    Science.gov (United States)

    Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

    2008-01-01

    Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

  13. An ensemble approach to assess hydrological models' contribution to uncertainties in the analysis of climate change impact on water resources

    Science.gov (United States)

    Velázquez, J. A.; Schmid, J.; Ricard, S.; Muerth, M. J.; Gauvin St-Denis, B.; Minville, M.; Chaumont, D.; Caya, D.; Ludwig, R.; Turcotte, R.

    2012-06-01

    Over the recent years, several research efforts investigated the impact of climate change on water resources for different regions of the world. The projection of future river flows is affected by different sources of uncertainty in the hydro-climatic modelling chain. One of the aims of the QBic3 project (Québec-Bavarian International Collaboration on Climate Change) is to assess the contribution to uncertainty of hydrological models by using an ensemble of hydrological models presenting a diversity of structural complexity (i.e. lumped, semi distributed and distributed models). The study investigates two humid, mid-latitude catchments with natural flow conditions; one located in Southern Québec (Canada) and one in Southern Bavaria (Germany). Daily flow is simulated with four different hydrological models, forced by outputs from regional climate models driven by a given number of GCMs' members over a reference (1971-2000) and a future (2041-2070) periods. The results show that the choice of the hydrological model does strongly affect the climate change response of selected hydrological indicators, especially those related to low flows. Indicators related to high flows seem less sensitive on the choice of the hydrological model. Therefore, the computationally less demanding models (usually simple, lumped and conceptual) give a significant level of trust for high and overall mean flows.

  14. 2020s scenario analysis of nutrient load in the Mekong River Basin using a distributed hydrological model.

    Science.gov (United States)

    Yoshimura, Chihiro; Zhou, Maichun; Kiem, Anthony S; Fukami, Kazuhiko; Prasantha, Hapuarachchi H A; Ishidaira, Hiroshi; Takeuchi, Kuniyoshi

    2009-10-01

    A distributed hydrological model, YHyM, was integrated with the export coefficient concept and applied to simulate the nutrient load in the Mekong River Basin. In the validation period (1992-1999), Nash-Sutcliffe efficiency was 76.4% for discharge, 65.9% for total nitrogen, and 45.3% for total phosphorus at Khong Chiam. Using the model, scenario analysis was then performed for the 2020s taking into account major anthropogenic factors: climate change, population, land cover, fertilizer use, and industrial waste water. The results show that the load at Kompong Cham in 2020s is 6.3 x 10(4)tN a(-1) (+13.0% compared to 1990s) and 4.3 x 10(3)tP a(-1) (+24.7%). Overall, the noticeable nutrient sources are cropland in the middle region and urban load in the lower region. The installation of waste water treatment plants in urban areas possibly cut 60.6%N and 19.9%P of the estimated increase in the case without any treatment.

  15. Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies

    Science.gov (United States)

    Manitz, Juliane; Burger, Patricia; Amos, Christopher I.; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike

    2017-01-01

    The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility. PMID:28785300

  16. Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies.

    Science.gov (United States)

    Friedrichs, Stefanie; Manitz, Juliane; Burger, Patricia; Amos, Christopher I; Risch, Angela; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike; Hofner, Benjamin

    2017-01-01

    The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility.

  17. A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

    Directory of Open Access Journals (Sweden)

    Jordi Leno-Colorado

    2017-07-01

    Full Text Available Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst and linkage disequilibrium (nSL statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value 10 significant pathways (in terms of Fst, comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis, a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other

  18. A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.

    Science.gov (United States)

    Leno-Colorado, Jordi; Hudson, Nick J; Reverter, Antonio; Pérez-Enciso, Miguel

    2017-07-05

    Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig ( Sus scrofa ) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q -value 10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological

  19. A functional genomics approach using metabolomics and in silico pathway analysis

    DEFF Research Database (Denmark)

    Förster, Jochen; Gombert, Andreas Karoly; Nielsen, Jens

    2002-01-01

    analysis techniques and changes in the genotype will in many cases lead to different metabolite profiles. Here, a theoretical framework that may be applied to identify the function of orphan genes is presented. The approach is based on a combination of metabolome analysis combined with in silico pathway...

  20. Metabolic pathway analysis using a nash equilibrium approach

    NARCIS (Netherlands)

    Lucia, Angelo; DiMaggio, Peter A.; Alonso-Martinez, Diego

    2018-01-01

    A novel approach to metabolic network analysis using a Nash Equilibrium (NE) formulation is proposed in which enzymes are considered players in a multi-player game. Each player has its own payoff function with the objective of minimizing the Gibbs free energy associated with the biochemical

  1. Pathways to Medical Home Recognition: A Qualitative Comparative Analysis of the PCMH Transformation Process.

    Science.gov (United States)

    Mendel, Peter; Chen, Emily K; Green, Harold D; Armstrong, Courtney; Timbie, Justin W; Kress, Amii M; Friedberg, Mark W; Kahn, Katherine L

    2017-12-15

    To understand the process of practice transformation by identifying pathways for attaining patient-centered medical home (PCMH) recognition. The CMS Federally Qualified Health Center (FQHC) Advanced Primary Care Practice Demonstration was designed to help FQHCs achieve NCQA Level 3 PCMH recognition and improve patient outcomes. We used a stratified random sample of 20 (out of 503) participating sites for this analysis. We developed a conceptual model of structural, cultural, and implementation factors affecting PCMH transformation based on literature and initial qualitative interview themes. We then used conventional cross-case analysis, followed by qualitative comparative analysis (QCA), a cross-case method based on Boolean logic algorithms, to systematically identify pathways (i.e., combinations of factors) associated with attaining-or not attaining-Level 3 recognition. Site-level indicators were derived from semistructured interviews with site leaders at two points in time (mid- and late-implementation) and administrative data collected prior to and during the demonstration period. The QCA results identified five distinct pathways to attaining PCMH recognition and four distinct pathways to not attaining recognition by the end of the demonstration. Across these pathways, one condition (change leader capacity) was common to all pathways for attaining recognition, and another (previous improvement or recognition experience) was absent in all pathways for not attaining recognition. In general, sites could compensate for deficiencies in one factor with capacity in others, but they needed a threshold of strengths in cultural and implementation factors to attain PCMH recognition. Future efforts at primary care transformation should take into account multiple pathways sites may pursue. Sites should be assessed on key cultural and implementation factors, in addition to structural components, in order to differentiate interventions and technical assistance. © Health

  2. 2003 hydrological drought - natural disaster

    International Nuclear Information System (INIS)

    Trninic, Dusan; Bosnjak, Tomislava

    2004-01-01

    An exceptionally dry and warm period from February to early October 2003 resulted in hydrological drought with attributes of a natural disaster in most of the Croatian regions. The paper presents hydrological analysis of the Sava River near Zupanja for the period 1945-2003 (N=59 years). In defining maximum annual volumes of isolated waves below the reference discharges, the following reference discharges were used:Q 30,95% = 202m 3 s -1 - minimum mean 30-day discharge, 95 % probability, Q 30,80% = 254m 3 s -1 - minimum mean 30-day discharge, 80 % probability, Q 95% = 297m 3 s -1 - (H = -17cm minimum navigation level = 95 % of water level duration from average duration curve). The analysis results have shown that the hydrological drought recorded during the current year belongs to the most thoroughly studied droughts in 59 years. For example, hydrological analysis of the reference discharge of 297m 3 s -1 has shown that this year drought comes second, immediately after the driest year 1946. However, this year hydrological drought hit the record duration of 103 days, unlike the one from 1946, which lasted 98 days. It is interesting that the hydrological droughts affect the Sava River usually in autumn and summer, rarely in winter, and it has never been recorded in spring (referring to the analysed 1945-2003 period). In conclusion, some recommendations are given for increase in low streamflows and on possible impacts of climate changes on these flows.(Author)

  3. Adaption to Extreme Rainfall with Open Urban Drainage System: An Integrated Hydrological Cost-Benefit Analysis

    DEFF Research Database (Denmark)

    Zhou, Qianqian; Panduro, Toke Emil; Thorsen, Bo Jellesmark

    2013-01-01

    with extreme rainfalls is evaluated using a quantitative flood risk approach based on urban inundation modeling and socio-economic analysis of corresponding costs and benefits. A hedonic valuation model is applied to capture the local economic gains or losses from more water bodies in green areas....... The framework was applied to the northern part of the city of Aarhus, Denmark. We investigated four adaptation strategies that encompassed laissez-faire, larger sewer pipes, local infiltration units, and open drainage system in the urban green structure. We found that when taking into account environmental...

  4. PyPathway: Python Package for Biological Network Analysis and Visualization.

    Science.gov (United States)

    Xu, Yang; Luo, Xiao-Chun

    2018-05-01

    Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

  5. Screening key candidate genes and pathways involved in insulinoma by microarray analysis.

    Science.gov (United States)

    Zhou, Wuhua; Gong, Li; Li, Xuefeng; Wan, Yunyan; Wang, Xiangfei; Li, Huili; Jiang, Bin

    2018-06-01

    Insulinoma is a rare type tumor and its genetic features remain largely unknown. This study aimed to search for potential key genes and relevant enriched pathways of insulinoma.The gene expression data from GSE73338 were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified between insulinoma tissues and normal pancreas tissues, followed by pathway enrichment analysis, protein-protein interaction (PPI) network construction, and module analysis. The expressions of candidate key genes were validated by quantitative real-time polymerase chain reaction (RT-PCR) in insulinoma tissues.A total of 1632 DEGs were obtained, including 1117 upregulated genes and 514 downregulated genes. Pathway enrichment results showed that upregulated DEGs were significantly implicated in insulin secretion, and downregulated DEGs were mainly enriched in pancreatic secretion. PPI network analysis revealed 7 hub genes with degrees more than 10, including GCG (glucagon), GCGR (glucagon receptor), PLCB1 (phospholipase C, beta 1), CASR (calcium sensing receptor), F2R (coagulation factor II thrombin receptor), GRM1 (glutamate metabotropic receptor 1), and GRM5 (glutamate metabotropic receptor 5). DEGs involved in the significant modules were enriched in calcium signaling pathway, protein ubiquitination, and platelet degranulation. Quantitative RT-PCR data confirmed that the expression trends of these hub genes were similar to the results of bioinformatic analysis.The present study demonstrated that candidate DEGs and enriched pathways were the potential critical molecule events involved in the development of insulinoma, and these findings were useful for better understanding of insulinoma genesis.

  6. Biomarker Identification and Pathway Analysis by Serum Metabolomics of Lung Cancer

    Directory of Open Access Journals (Sweden)

    Yingrong Chen

    2015-01-01

    Full Text Available Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top altered pathways for analysis and visualization. We constructed a diagnostic model using potential serum biomarkers from patients with lung cancer. We assessed their specificity and sensitivity according to the area under the curve of the receiver operator characteristic (ROC curves, which could be used to distinguish patients with lung cancer from normal subjects. The pathway analysis indicated that sphingolipid metabolism was the top altered pathway in lung cancer. ROC curve analysis indicated that glycerophospho-N-arachidonoyl ethanolamine (GpAEA and sphingosine were potential sensitive and specific biomarkers for lung cancer diagnosis and prognosis. Compared with the traditional lung cancer diagnostic biomarkers carcinoembryonic antigen and cytokeratin 19 fragment, GpAEA and sphingosine were as good or more appropriate for detecting lung cancer. We report our identification of potential metabolic diagnostic and prognostic biomarkers of lung cancer and clarify the metabolic alterations in lung cancer.

  7. Hydrologic Engineering Center River Analysis System (HEC-RAS) Water Temperature Models Developed for the Missouri River Recovery Management Plan and Environmental Impact Statement

    Science.gov (United States)

    2017-09-18

    ER D C/ EL T R- 17 -1 8 Missouri River Recovery Program (MRRP) Hydrologic Engineering Center-River Analysis System (HEC-RAS) Water...Zhonglong Zhang and Billy E. Johnson September 2017 Approved for public release; distribution is unlimited. The U.S. Army Engineer Research...and Development Center (ERDC) solves the nation’s toughest engineering and environmental challenges. ERDC develops innovative solutions in civil and

  8. Genome wide expression analysis in HPV16 Cervical Cancer: identification of altered metabolic pathways

    Directory of Open Access Journals (Sweden)

    Salcedo Mauricio

    2007-09-01

    Full Text Available Abstract Background Cervical carcinoma (CC is a leading cause of death among women worldwide. Human papilloma virus (HPV is a major etiological factor in CC and HPV 16 is the more frequent viral type present. Our aim was to characterize metabolic pathways altered in HPV 16 tumor samples by means of transcriptome wide analysis and bioinformatics tools for visualizing expression data in the context of KEGG biological pathways. Results We found 2,067 genes significantly up or down-modulated (at least 2-fold in tumor clinical samples compared to normal tissues, representing ~3.7% of analyzed genes. Cervical carcinoma was associated with an important up-regulation of Wnt signaling pathway, which was validated by in situ hybridization in clinical samples. Other up-regulated pathways were those of calcium signaling and MAPK signaling, as well as cell cycle-related genes. There was down-regulation of focal adhesion, TGF-β signaling, among other metabolic pathways. Conclusion This analysis of HPV 16 tumors transcriptome could be useful for the identification of genes and molecular pathways involved in the pathogenesis of cervical carcinoma. Understanding the possible role of these proteins in the pathogenesis of CC deserves further studies.

  9. Energy pathway analysis - a hydrogen fuel cycle framework for system studies

    International Nuclear Information System (INIS)

    Badin, J.S.; Tagore, S.

    1997-01-01

    An analytical framework has been developed that can be used to estimate a range of life-cycle costs and impacts that result from the incremental production, storage, transport, and use of different fuels or energy carriers, such as hydrogen, electricity, natural gas, and gasoline. This information is used in a comparative analysis of energy pathways. The pathways provide the U.S. Department of Energy (DOE) with an indication of near-, mid-, and long-term technologies that have the greatest potential for advancement and can meet the cost goals. The methodology and conceptual issues are discussed. Also presented are results for selected pathways from the E3 (Energy, Economics, Emissions) Pathway Analysis Model. This model will be expanded to consider networks of pathways and to be compatible with a linear programming optimization processor. Scenarios and sets of constraints (energy demands, sources, emissions) will be defined so the effects on energy transformation activities included in the solution and on the total optimized system cost can be investigated. This evaluation will be used as a guide to eliminate technically feasible pathways if they are not cost effective or do not meet the threshold requirements for the market acceptance. (Author)

  10. Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

    Science.gov (United States)

    Yang, Oneyeol; Kim, Hye Lim; Weon, Jong-Il; Seo, Young Rok

    2015-01-01

    Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors. PMID:25853100

  11. AGU hydrology publication outlets

    Science.gov (United States)

    Freeze, R. Allan

    In recent months I have been approached on several occasions by members of the hydrology community who asked me which of the various AGU journals and publishing outlets would be most suitable for a particular paper or article that they have prepared.Water Resources Research (WRR) is the primary AGU outlet for research papers in hydrology. It is an interdisciplinary journal that integrates research in the social and natural sciences of water. The editors of WRR invite original contributions in the physical, chemical and biological sciences and also in the social and policy sciences, including economics, systems analysis, sociology, and law. The editor for the physical sciences side of the journal is Donald R. Nielson, LAWR Veihmeyer Hall, University of California Davis, Davis, CA 95616. The editor for the policy sciences side of the journal is Ronald G. Cummings, Department of Economics, University of New Mexico, Albuquerque, NM 87131

  12. Hydrologic analysis of data from the Lower Lost Lake Aquifer at recovery well RWM-12

    International Nuclear Information System (INIS)

    Hiergesell, R.A.

    1994-04-01

    This report presents an analysis of water level responses that were monitored in wells near recovery well RWM-12 when it was brought online on March 23, 1992 as part of the system of wells used to pump and treat a groundwater contaminant plume of trichloroethylene (TCE) beneath the A/M Areas of the Savannah River Site. The series of wells, all similar to RWM-12, pump groundwater and deliver it to air strippers that effectively separate and remove the TCE. Water level responses to pumping at RWM-12 were monitored using both pressure transducers/data loggers, and electric tapes. The purpose of obtaining measurements of water level responses was to obtain the data that is needed to make a quantitative estimate of hydraulic conductivity in the pumped horizon, and to assess the hydraulic connection between adjacent layers

  13. Static analysis of a Model of the LDL degradation pathway

    DEFF Research Database (Denmark)

    Pilegaard, Henrik; Nielson, Flemming; Nielson, Hanne Riis

    2005-01-01

    BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behavior of modelled systems. We use these tools ...... to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases....

  14. Annual compilation and analysis of hydrologic data for urban studies in the Bryan, Texas, metropolitan area, 1969

    Science.gov (United States)

    Robbins, W.D.

    1972-01-01

    Hydrologic investigations of urban areas in Texas were begun by the U.S. Geological Survey in 1954. These studies are now in progress in Austin, Houston, Dallas, Dallas County, Fort Worth, San Antonio, and Bryan. Hydrologic investigations of urban areas in Texas were begun by the U.S. Geological Survey in 1954. These studies are now in progress in Austin, Houston, Dallas, Dallas County, Fort Worth, San Antonio, and Bryan. 1. To determine, on the basis of historical data and hydrologic analyses, the magnitude and frequency of floods. 2. To document and define the areal extent of floods of greater than ordinary magnitude. 3. To determine the effect of urban development on flood peaks and volume. 4. To provide applied research facilities for studies at Texas A & M University at College Stations. This report, the first in a series of reports to be published annually, is primarily applicable to objectives 2, 3, and 4. The report presents the basic hydrologic data collected in two study areas during the 1969 water year (October 1, 1968, to September 30, 1969) and basic hydrologic data collected during part of the 1968 water year (April 5, 1968, to September 30, 1968). The locations of the two basins within the study area, Burton Creek and Hudson Creek, are shown on figure 1.

  15. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    Liu, Stephen V; Lenkiewicz, Elizabeth; Evers, Lisa; Holley, Tara; Kiefer, Jeffrey; Demeure, Michael J; Ramanathan, Ramesh K; Von Hoff, Daniel D; Barrett, Michael T; Ruiz, Christian; Glatz, Katharina; Bubendorf, Lukas; Eng, Cathy

    2012-01-01

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  16. A techno-economic analysis of EU renewable electricity policy pathways in 2030

    International Nuclear Information System (INIS)

    Río, Pablo del; Resch, Gustav; Ortner, Andre; Liebmann, Lukas; Busch, Sebastian; Panzer, Christian

    2017-01-01

    The aim of this paper is to assess several pathways of a harmonised European policy framework for supporting renewable electricity (RES-E) in a 2030 horizon according to different criteria. The pathways combine two main dimensions: degrees of harmonisation and instruments and design elements. A quantitative model-based analysis with the Green-X model is provided. The results of the simulations show that there are small differences between the evaluated cases regarding effectiveness. All the policy pathways score similarly with respect to RES-E deployment, i.e., with different degrees of harmonisation and whether using a feed-in tariff, a feed-in premium, a quota system with banding or a quota without banding scheme. In contrast, the policy costs clearly differ across the pathways, but the differences can mostly be attributed to the instruments rather than to the degrees of harmonisation. This is also the case with other criteria (static and dynamic efficiency and the socioeconomic and environmental benefits in terms of CO2 emissions and fossil fuels avoided). Both the degree of harmonisation and the choice of instrument influence the distribution of support costs across countries. Finally, our findings suggest that keeping strengthened national support leads to similar results to other policy pathways. - Highlights: • Pathways of a harmonised European policy framework for renewable electricity in 2030. • Two main dimensions: degrees of harmonisation and instruments. • A quantitative model-based analysis based on the Green-X model. • Small differences between the pathways regarding the effectiveness criterion. • Important differences between pathways regarding other assessment criteria.

  17. Effect of curcumin on aged Drosophila melanogaster: a pathway prediction analysis.

    Science.gov (United States)

    Zhang, Zhi-guo; Niu, Xu-yan; Lu, Ai-ping; Xiao, Gary Guishan

    2015-02-01

    To re-analyze the data published in order to explore plausible biological pathways that can be used to explain the anti-aging effect of curcumin. Microarray data generated from other study aiming to investigate effect of curcumin on extending lifespan of Drosophila melanogaster were further used for pathway prediction analysis. The differentially expressed genes were identified by using GeneSpring GX with a criterion of 3.0-fold change. Two Cytoscape plugins including BisoGenet and molecular complex detection (MCODE) were used to establish the protein-protein interaction (PPI) network based upon differential genes in order to detect highly connected regions. The function annotation clustering tool of Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for pathway analysis. A total of 87 genes expressed differentially in D. melanogaster melanogaster treated with curcumin were identified, among which 50 were up-regulated significantly and 37 were remarkably down-regulated in D. melanogaster melanogaster treated with curcumin. Based upon these differential genes, PPI network was constructed with 1,082 nodes and 2,412 edges. Five highly connected regions in PPI networks were detected by MCODE algorithm, suggesting anti-aging effect of curcumin may be underlined through five different pathways including Notch signaling pathway, basal transcription factors, cell cycle regulation, ribosome, Wnt signaling pathway, and p53 pathway. Genes and their associated pathways in D. melanogaster melanogaster treated with anti-aging agent curcumin were identified using PPI network and MCODE algorithm, suggesting that curcumin may be developed as an alternative therapeutic medicine for treating aging-associated diseases.

  18. Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

    Directory of Open Access Journals (Sweden)

    Michael Volpers

    Full Text Available The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase-pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly

  19. Groundwater recharge in irrigated semi-arid areas: quantitative hydrological modelling and sensitivity analysis

    Science.gov (United States)

    Jiménez-Martínez, Joaquín; Candela, Lucila; Molinero, Jorge; Tamoh, Karim

    2010-12-01

    For semi-arid regions, methods of assessing aquifer recharge usually consider the potential evapotranspiration. Actual evapotranspiration rates can be below potential rates for long periods of time, even in irrigated systems. Accurate estimations of aquifer recharge in semi-arid areas under irrigated agriculture are essential for sustainable water-resources management. A method to estimate aquifer recharge from irrigated farmland has been tested. The water-balance-modelling approach was based on VisualBALAN v. 2.0, a computer code that simulates water balance in the soil, vadose zone and aquifer. The study was carried out in the Campo de Cartagena (SE Spain) in the period 1999-2008 for three different groups of crops: annual row crops (lettuce and melon), perennial vegetables (artichoke) and fruit trees (citrus). Computed mean-annual-recharge values (from irrigation+precipitation) during the study period were 397 mm for annual row crops, 201 mm for perennial vegetables and 194 mm for fruit trees: 31.4, 20.7 and 20.5% of the total applied water, respectively. The effects of rainfall events on the final recharge were clearly observed, due to the continuously high water content in soil which facilitated the infiltration process. A sensitivity analysis to assess the reliability and uncertainty of recharge estimations was carried out.

  20. Adaption to extreme rainfall with open urban drainage system: an integrated hydrological cost-benefit analysis.

    Science.gov (United States)

    Zhou, Qianqian; Panduro, Toke Emil; Thorsen, Bo Jellesmark; Arnbjerg-Nielsen, Karsten

    2013-03-01

    This paper presents a cross-disciplinary framework for assessment of climate change adaptation to increased precipitation extremes considering pluvial flood risk as well as additional environmental services provided by some of the adaptation options. The ability of adaptation alternatives to cope with extreme rainfalls is evaluated using a quantitative flood risk approach based on urban inundation modeling and socio-economic analysis of corresponding costs and benefits. A hedonic valuation model is applied to capture the local economic gains or losses from more water bodies in green areas. The framework was applied to the northern part of the city of Aarhus, Denmark. We investigated four adaptation strategies that encompassed laissez-faire, larger sewer pipes, local infiltration units, and open drainage system in the urban green structure. We found that when taking into account environmental amenity effects, an integration of open drainage basins in urban recreational areas is likely the best adaptation strategy, followed by pipe enlargement and local infiltration strategies. All three were improvements compared to the fourth strategy of no measures taken.

  1. Study on uncertainty evaluation methodology related to hydrological parameter of regional groundwater flow analysis model

    International Nuclear Information System (INIS)

    Sakai, Ryutaro; Munakata, Masahiro; Ohoka, Masao; Kameya, Hiroshi

    2009-11-01

    In the safety assessment for a geological disposal of radioactive waste, it is important to develop a methodology for long-term estimation of regional groundwater flow from data acquisition to numerical analyses. In the uncertainties associated with estimation of regional groundwater flow, there are the one that concerns parameters and the one that concerns the hydrologeological evolution. The uncertainties of parameters include measurement errors and their heterogeneity. The authors discussed the uncertainties of hydraulic conductivity as a significant parameter for regional groundwater flow analysis. This study suggests that hydraulic conductivities of rock mass are controlled by rock characteristics such as fractures, porosity and test conditions such as hydraulic gradient, water quality, water temperature and that there exists variations more than ten times in hydraulic conductivity by difference due to test conditions such as hydraulic gradient or due to rock type variations such as rock fractures, porosity. In addition this study demonstrated that confining pressure change caused by uplift and subsidence and change of hydraulic gradient under the long-term evolution of hydrogeological environment could possibly produce variations more than ten times of magnitude in hydraulic conductivity. It was also shown that the effect of water quality change on hydraulic conductivity was not negligible and that the replacement of fresh water and saline water caused by sea level change could induce 0.6 times in current hydraulic conductivities in case of Horonobe site. (author)

  2. Global analysis of the sporulation pathway of Clostridium difficile.

    Science.gov (United States)

    Fimlaid, Kelly A; Bond, Jeffrey P; Schutz, Kristin C; Putnam, Emily E; Leung, Jacqueline M; Lawley, Trevor D; Shen, Aimee

    2013-01-01

    The Gram-positive, spore-forming pathogen Clostridium difficile is the leading definable cause of healthcare-associated diarrhea worldwide. C. difficile infections are difficult to treat because of their frequent recurrence, which can cause life-threatening complications such as pseudomembranous colitis. The spores of C. difficile are responsible for these high rates of recurrence, since they are the major transmissive form of the organism and resistant to antibiotics and many disinfectants. Despite the importance of spores to the pathogenesis of C. difficile, little is known about their composition or formation. Based on studies in Bacillus subtilis and other Clostridium spp., the sigma factors σ(F), σ(E), σ(G), and σ(K) are predicted to control the transcription of genes required for sporulation, although their specific functions vary depending on the organism. In order to determine the roles of σ(F), σ(E), σ(G), and σ(K) in regulating C. difficile sporulation, we generated loss-of-function mutations in genes encoding these sporulation sigma factors and performed RNA-Sequencing to identify specific sigma factor-dependent genes. This analysis identified 224 genes whose expression was collectively activated by sporulation sigma factors: 183 were σ(F)-dependent, 169 were σ(E)-dependent, 34 were σ(G)-dependent, and 31 were σ(K)-dependent. In contrast with B. subtilis, C. difficile σ(E) was dispensable for σ(G) activation, σ(G) was dispensable for σ(K) activation, and σ(F) was required for post-translationally activating σ(G). Collectively, these results provide the first genome-wide transcriptional analysis of genes induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes.

  3. Isotope hydrology: A historical overview of achievements

    International Nuclear Information System (INIS)

    1997-01-01

    The IAEA's efforts in the water sector cover all aspects of the three main categories of isotope methodologies, such as the use of radioactive isotopes as tracers for site-specific investigations related to water movement; the use of sealed radioactive sources for in-situ measurement of hydrological field parameters; and the use of naturally occurring isotopic species for the assessment and study of water occurrence, genesis and flow pathways/dynamics at regional-scale hydrological systems

  4. Continuous hydrologic simulation and flood-frequency, hydraulic, and flood-hazard analysis of the Blackberry Creek watershed, Kane County, Illinois

    Science.gov (United States)

    Soong, David T.; Straub, Timothy D.; Murphy, Elizabeth A.

    2006-01-01

    Results of hydrologic model, flood-frequency, hydraulic model, and flood-hazard analysis of the Blackberry Creek watershed in Kane County, Illinois, indicate that the 100-year and 500-year flood plains range from approximately 25 acres in the tributary F watershed (a headwater subbasin at the northeastern corner of the watershed) to almost 1,800 acres in Blackberry Creek main stem. Based on 1996 land-cover data, most of the land in the 100-year and 500-year flood plains was cropland, forested and wooded land, and grassland. A relatively small percentage of urban land was in the flood plains. The Blackberry Creek watershed has undergone rapid urbanization in recent decades. The population and urbanized lands in the watershed are projected to double from the 1990 condition by 2020. Recently, flood-induced damage has occurred more frequently in urbanized areas of the watershed. There are concerns about the effect of urbanization on flood peaks and volumes, future flood-mitigation plans, and potential effects on the water quality and stream habitats. This report describes the procedures used in developing the hydrologic models, estimating the flood-peak discharge magnitudes and recurrence intervals for flood-hazard analysis, developing the hydraulic model, and the results of the analysis in graphical and tabular form. The hydrologic model, Hydrological Simulation Program-FORTRAN (HSPF), was used to perform the simulation of continuous water movements through various patterns of land uses in the watershed. Flood-frequency analysis was applied to an annual maximum series to determine flood quantiles in subbasins for flood-hazard analysis. The Hydrologic Engineering Center-River Analysis System (HEC-RAS) hydraulic model was used to determine the 100-year and 500-year flood elevations, and to determine the 100-year floodway. The hydraulic model was calibrated and verified using high water marks and observed inundation maps for the July 17-18, 1996, flood event. Digital

  5. Documentation and hydrologic analysis of Hurricane Sandy in New Jersey, October 29–30, 2012

    Science.gov (United States)

    Suro, Thomas P.; Deetz, Anna; Hearn, Paul

    2016-11-17

    higher than the previously recorded period-of-record maximum. A comparison of peak storm-tide elevations to preliminary FEMA Coastal Flood Insurance Study flood elevations indicated that these areas experienced the highest recurrence intervals along the coast of New Jersey. Analysis showed peak storm-tide elevations exceeded the 100-year FEMA flood elevations in many parts of Middlesex, Union, Essex, Hudson, and Bergen Counties, and peak storm-tide elevations at many locations in Monmouth County exceeded the 500-year recurrence interval.A level 1 HAZUS (HAZards United States) analysis was done for the counties in New Jersey affected by flooding to estimate total building stock losses. The aggregated total building stock losses estimated by HAZUS for New Jersey, on the basis of the final inundation verified by USGS high-water marks, was almost $19 billion. A comparison of Hurricane Sandy with historic coastal storms showed that peak storm-tide elevations associated with Hurricane Sandy exceeded most of the previously documented elevations associated with the storms of December 1992, March 1962, September 1960, and September 1944 at many coastal communities in New Jersey. This scientific investigation report was prepared in cooperation with FEMA to document flood processes and flood damages resulting from this storm and to assist in future flood mitigation actions in New Jersey.

  6. Seasonal Hydrological Loading in Southern Tibet Detected by Joint Analysis of GPS and GRACE.

    Science.gov (United States)

    Zou, Rong; Wang, Qi; Freymueller, Jeffrey T; Poutanen, Markku; Cao, Xuelian; Zhang, Caihong; Yang, Shaomin; He, Ping

    2015-12-04

    In southern Tibet, ongoing vertical and horizontal motions due to the collision between India and Eurasia are monitored by large numbers of global positioning system (GPS) continuous and campaign sites installed in the past decade. Displacements measured by GPS usually include tectonic deformation as well as non-tectonic, time-dependent signals. To estimate the regional long-term tectonic deformation using GPS more precisely, seasonal elastic deformation signals associated with surface loading must be removed from the observations. In this study, we focus on seasonal variation in vertical and horizontal motions of southern Tibet by performing a joint analysis of GRACE (Gravity Recovery and Climate Experiment) and GPS data, not only using continuous sites but also GPS campaign-mode sites. We found that the GPS-observed and GRACE-modeled seasonal oscillations are in good agreements, and a seasonal displacement model demonstrates that the main reason for seasonal variations in southern Tibet is from the summer monsoon and its precipitation. The biggest loading appears from July to August in the summer season. Vertical deformations observed by GPS and modeled by GRACE are two to three times larger than horizontal oscillations, and the north components demonstrate larger amplitudes than the east components. We corrected the GPS position time series using the GRACE-modeled seasonal variations, which gives significant reductions in the misfit and weighted root-mean-squares (WRMS). Misfit (χ2 divided by degree of freedom) reductions for campaign sites range between 20% and 56% for the vertical component, and are much smaller for the horizontal components. Moreover, time series of continuous GPS (cGPS) sites near the 2015 Nepal earthquakes must be corrected using appropriate models of seasonal loading for analyzing postseismic deformation to avoid biasing estimates of the postseismic relaxation.

  7. Utilizing dimensional analysis with observed data to determine the significance of hydrodynamic solutions in coastal hydrology

    Science.gov (United States)

    Swain, Eric D.; Decker, Jeremy D.; Hughes, Joseph D.

    2014-01-01

    In this paper, the authors present an analysis of the magnitude of the temporal and spatial acceleration (inertial) terms in the surface-water flow equations and determine the conditions under which these inertial terms have sufficient magnitude to be required in the computations. Data from two South Florida field sites are examined and the relative magnitudes of temporal acceleration, spatial acceleration, and the gravity and friction terms are compared. Parameters are derived by using dimensionless numbers and applied to quantify the significance of the hydrodynamic effects. The time series of the ratio of the inertial and gravity terms from field sites are presented and compared with both a simplified indicator parameter and a more complex parameter called the Hydrodynamic Significance Number (HSN). Two test-case models were developed by using the SWIFT2D hydrodynamic simulator to examine flow behavior with and without the inertial terms and compute the HSN. The first model represented one of the previously-mentioned field sites during gate operations of a structure-managed coastal canal. The second model was a synthetic test case illustrating the drainage of water down a sloped surface from an initial stage while under constant flow. The analyses indicate that the times of substantial hydrodynamic effects are sporadic but significant. The simplified indicator parameter correlates much better with the hydrodynamic effect magnitude for a constant width channel such as Miami Canal than at the non-uniform North River. Higher HSN values indicate flow situations where the inertial terms are large and need to be taken into account.

  8. Life Cycle Greenhouse Gas Analysis of Multiple Vehicle Fuel Pathways in China

    Directory of Open Access Journals (Sweden)

    Tianduo Peng

    2017-11-01

    Full Text Available The Tsinghua University Life Cycle Analysis Model (TLCAM is applied to calculate the life cycle fossil energy consumption and greenhouse gas (GHG emissions for more than 20 vehicle fuel pathways in China. In addition to conventional gasoline and diesel, these include coal- and gas-based vehicle fuels, and electric vehicle (EV pathways. The results indicate the following. (1 China’s current dependence on coal and relative low-efficiency processes limits the potential for most alternative fuel pathways to decrease energy consumption and emissions; (2 Future low-carbon electricity pathways offer more obvious advantages, with coal-based pathways needing to adopt carbon dioxide capture and storage technology to compete; (3 A well-to-wheels analysis of the fossil energy consumption of vehicles fueled by compressed natural gas and liquefied natural gas (LNG showed that they are comparable to conventional gasoline vehicles. However, importing rather than domestically producing LNG for vehicle use can decrease domestic GHG emissions by 35% and 31% compared with those of conventional gasoline and diesel vehicles, respectively; (4 The manufacturing and recovery of battery and vehicle in the EV analysis has significant impact on the overall ability of EVs to decrease fossil energy consumption and GHG emissions from ICEVs.

  9. Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.

    Science.gov (United States)

    Cava, Claudia; Bertoli, Gloria; Colaprico, Antonio; Olsen, Catharina; Bontempi, Gianluca; Castiglioni, Isabella

    2018-01-06

    Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functional genomic studies. However, few methods consider the functional non-equal roles of genes in pathways and the complex gene-gene interactions in a network. We present a novel method in pan-cancer analysis that identifies de-regulated genes with a functional role by integrating pathway and network data. A pan-cancer analysis of 7158 tumour/normal samples from 16 cancer types identified 895 genes with a central role in pathways and de-regulated in cancer. Comparing our approach with 15 current tools that identify cancer driver genes, we found that 35.6% of the 895 genes identified by our method have been found as cancer driver genes with at least 2/15 tools. Finally, we applied a machine learning algorithm on 16 independent GEO cancer datasets to validate the diagnostic role of cancer driver genes for each cancer. We obtained a list of the top-ten cancer driver genes for each cancer considered in this study. Our analysis 1) confirmed that there are several known cancer driver genes in common among different types of cancer, 2) highlighted that cancer driver genes are able to regulate crucial pathways.

  10. Constraint-based modeling and kinetic analysis of the Smad dependent TGF-beta signaling pathway.

    Directory of Open Access Journals (Sweden)

    Zhike Zi

    Full Text Available BACKGROUND: Investigation of dynamics and regulation of the TGF-beta signaling pathway is central to the understanding of complex cellular processes such as growth, apoptosis, and differentiation. In this study, we aim at using systems biology approach to provide dynamic analysis on this pathway. METHODOLOGY/PRINCIPAL FINDINGS: We proposed a constraint-based modeling method to build a comprehensive mathematical model for the Smad dependent TGF-beta signaling pathway by fitting the experimental data and incorporating the qualitative constraints from the experimental analysis. The performance of the model generated by constraint-based modeling method is significantly improved compared to the model obtained by only fitting the quantitative data. The model agrees well with the experimental analysis of TGF-beta pathway, such as the time course of nuclear phosphorylated Smad, the subcellular location of Smad and signal response of Smad phosphorylation to different doses of TGF-beta. CONCLUSIONS/SIGNIFICANCE: The simulation results indicate that the signal response to TGF-beta is regulated by the balance between clathrin dependent endocytosis and non-clathrin mediated endocytosis. This model is useful to be built upon as new precise experimental data are emerging. The constraint-based modeling method can also be applied to quantitative modeling of other signaling pathways.

  11. Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.

    Science.gov (United States)

    Jiang, Zhenhong; He, Fei; Zhang, Ziding

    2017-07-01

    Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study

  12. Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer.

    Science.gov (United States)

    Wang, Yuzhi; Zhang, Yi; Huang, Qian; Li, Chengwen

    2018-04-19

    Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non‑tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t‑tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein‑protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in 'cell division', the 'proteinaceous extracellular matrix (ECM)', 'ECM structural constituents' and 'ECM‑receptor interaction', whereas downregulated genes were mainly enriched in 'response to drugs', 'extracellular space', 'transcriptional activator activity' and the 'peroxisome proliferator‑activated receptor signaling pathway'. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2‑a, baculoviral inhibitor of apoptosis repeat‑containing protein 5, cyclin‑dependent kinase 1, G2/mitotic‑specific cyclin‑B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in 'mitotic nuclear division', 'mid‑body', 'protein binding' and 'cell cycle'. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide

  13. Analysis of hydrological and geotechnical aspects related to landslides caused by rainfall infiltration

    Science.gov (United States)

    Capparelli, Giovanna; La Sala, Gabriella; Vena, Mirko; Donato, Antonio

    2015-04-01

    equations (plane stress) and strain-displacement relationship. By means of the model it is possible to analyze subsoil water circulation, safety factor of the slope subjected to gravity loading and to the pore pressure calculated from hydraulic module, displacement, strain and stress under the effect of rainfall infiltration. As an application case, the analysis and the representative results obtained for the Torre Orsaia landslide (Campania region - Southern Italy) are described.

  14. Analysis of Groundwater Anomalies Estimated by GRACE and GLDAS Satellite-based Hydrological Model in the Gulf of Mexico

    Science.gov (United States)

    Lotfata, A.; Ambinakudige, S.

    2017-12-01

    Coastal regions face a higher risk of flooding. A rise in sea-level increases flooding chances in low-lying areas. A major concern is the effect of sea-level rise on the depth of the fresh water/salt water interface in the aquifers of the coastal regions. A sea-level change rise impacts the hydrological system of the aquifers. Salt water intrusion into fresh water aquifers increase water table levels. Flooding prone areas in the coast are at a higher risk of salt water intrusion. The Gulf coast is one of the most vulnerable flood areas due to its natural weather patterns. There is not yet a local assessment of the relation between groundwater level and sea-level rising. This study investigates the projected sea-level rise models and the anomalous groundwater level during January 2002 to December 2016. We used the NASA Gravity Recovery and Climate Experiment (GRACE) and Global Land Data Assimilation System (GLDAS) satellite data in the analysis. We accounted the leakage error and the measurement error in GRACE data. GLDAS data was used to calculate the groundwater storage from the total water storage estimated using GRACE data (ΔGW=ΔTWS (soil moisture, surface water, groundwater, and canopy water) - ΔGLDAS (soil moisture, surface water, and canopy water)). The preliminary results indicate that the total water storage is increasing in parts of the Gulf of Mexico. GRACE data show high soil wetness and groundwater levels in Mississippi, Alabama and Texas coasts. Because sea-level rise increases the probability of flooding in the Gulf coast and affects the groundwater, we will analyze probable interactions between sea-level rise and groundwater in the study area. To understand regional sea-level rise patterns, we will investigate GRACE Ocean data along the Gulf coasts. We will quantify ocean total water storage, its salinity, and its relationship with the groundwater level variations in the Gulf coast.

  15. Specification of a test problem for HYDROCOIN [Hydrologic Code Intercomparison] Level 3 Case 2: Sensitivity analysis for deep disposal in partially saturated, fractured tuff

    International Nuclear Information System (INIS)

    Prindle, R.W.

    1987-08-01

    The international Hydrologic Code Intercomparison Project (HYDROCOIN) was formed to evaluate hydrogeologic models and computer codes and their use in performance assessment for high-level radioactive waste repositories. Three principal activities in the HYDROCOIN Project are Level 1, verification and benchmarking of hydrologic codes; Level 2, validation of hydrologic models; and Level 3, sensitivity and uncertainty analyses of the models and codes. This report presents a test case defined for the HYDROCOIN Level 3 activity to explore the feasibility of applying various sensitivity-analysis methodologies to a highly nonlinear model of isothermal, partially saturated flow through fractured tuff, and to develop modeling approaches to implement the methodologies for sensitivity analysis. These analyses involve an idealized representation of a repository sited above the water table in a layered sequence of welded and nonwelded, fractured, volcanic tuffs. The analyses suggested here include one-dimensional, steady flow; one-dimensional, nonsteady flow; and two-dimensional, steady flow. Performance measures to be used to evaluate model sensitivities are also defined; the measures are related to regulatory criteria for containment of high-level radioactive waste. 14 refs., 5 figs., 4 tabs

  16. Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway

    Directory of Open Access Journals (Sweden)

    Yogesh Goyal

    2017-07-01

    Full Text Available The Ras pathway patterns the poles of the Drosophila embryo by downregulating the levels and activity of a DNA-binding transcriptional repressor Capicua (Cic. We demonstrate that the spatiotemporal pattern of Cic during this signaling event can be harnessed for functional studies of mutations in the Ras pathway in human diseases. Our approach relies on a new microfluidic device that enables parallel imaging of Cic dynamics in dozens of live embryos. We found that although the pattern of Cic in early embryos is complex, it can be accurately approximated by a product of one spatial profile and one time-dependent amplitude. Analysis of these functions of space and time alone reveals the differential effects of mutations within the Ras pathway. Given the highly conserved nature of Ras-dependent control of Cic, our approach provides new opportunities for functional analysis of multiple sequence variants from developmental abnormalities and cancers.

  17. A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility

    DEFF Research Database (Denmark)

    Damotte, V; Guillot-Noel, L; Patsopoulos, N A

    2014-01-01

    adhesion molecule (CAMs) biological pathway using Cytoscape software. This network is a strong candidate, as it is involved in the crossing of the blood-brain barrier by the T cells, an early event in MS pathophysiology, and is used as an efficient therapeutic target. We drew up a list of 76 genes...... in interaction with other genes as a group. Pathway analysis is an alternative way to highlight such group of genes. Using SNP association P-values from eight multiple sclerosis (MS) GWAS data sets, we performed a candidate pathway analysis for MS susceptibility by considering genes interacting in the cell...... belonging to the CAM network. We highlighted 64 networks enriched with CAM genes with low P-values. Filtering by a percentage of CAM genes up to 50% and rejecting enriched signals mainly driven by transcription factors, we highlighted five networks associated with MS susceptibility. One of them, constituted...

  18. Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control.

    Directory of Open Access Journals (Sweden)

    Alborz Mahdavi

    2007-07-01

    Full Text Available Directing stem cell fate requires knowledge of how signaling networks integrate temporally and spatially segregated stimuli. We developed and validated a computational model of signal transducer and activator of transcription-3 (Stat3 pathway kinetics, a signaling network involved in embryonic stem cell (ESC self-renewal. Our analysis identified novel pathway responses; for example, overexpression of the receptor glycoprotein-130 results in reduced pathway activation and increased ESC differentiation. We used a systematic in silico screen to identify novel targets and protein interactions involved in Stat3 activation. Our analysis demonstrates that signaling activation and desensitization (the inability to respond to ligand restimulation is regulated by balancing the activation state of a distributed set of parameters including nuclear export of Stat3, nuclear phosphatase activity, inhibition by suppressor of cytokine signaling, and receptor trafficking. This knowledge was used to devise a temporally modulated ligand delivery strategy that maximizes signaling activation and leads to enhanced ESC self-renewal.

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

    Science.gov (United States)

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

    2014-01-01

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

  20. Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

    Energy Technology Data Exchange (ETDEWEB)

    Hermsen, Sanne A.B., E-mail: Sanne.Hermsen@rivm.nl [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands); Pronk, Tessa E. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Brandhof, Evert-Jan van den [Centre for Environmental Quality, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Ven, Leo T.M. van der [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Piersma, Aldert H. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands)

    2013-10-01

    The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.

  1. In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Harrisham Kaur

    2017-11-01

    Full Text Available Fermentation of undigested proteins in human gastrointestinal tract (gut by the resident microbiota, a process called bacterial putrefaction, can sometimes disrupt the gut homeostasis. In this process, essential amino acids (e.g., histidine, tryptophan, etc. that are required by the host may be utilized by the gut microbes. In addition, some of the products of putrefaction, like ammonia, putrescine, cresol, indole, phenol, etc., have been implicated in the disease pathogenesis of colorectal cancer (CRC. We have investigated bacterial putrefaction pathways that are known to be associated with such metabolites. Results of the comprehensive in silico analysis of the selected putrefaction pathways across bacterial genomes revealed presence of these pathways in limited bacterial groups. Majority of these bacteria are commonly found in human gut. These include Bacillus, Clostridium, Enterobacter, Escherichia, Fusobacterium, Salmonella, etc. Interestingly, while pathogens utilize almost all the analyzed pathways, commensals prefer putrescine and H2S production pathways for metabolizing the undigested proteins. Further, comparison of the putrefaction pathways in the gut microbiomes of healthy, carcinoma and adenoma datasets indicate higher abundances of putrefying bacteria in the carcinoma stage of CRC. The insights obtained from the present study indicate utilization of possible microbiome-based therapies to minimize the adverse effects of gut microbiome in enteric diseases.

  2. Digital Hydrologic Networks Supporting Applications Related to Spatially Referenced Regression Modeling

    Science.gov (United States)

    Brakebill, J.W.; Wolock, D.M.; Terziotti, S.E.

    2011-01-01

    Digital hydrologic networks depicting surface-water pathways and their associated drainage catchments provide a key component to hydrologic analysis and modeling. Collectively, they form common spatial units that can be used to frame the descriptions of aquatic and watershed processes. In addition, they provide the ability to simulate and route the movement of water and associated constituents throughout the landscape. Digital hydrologic networks have evolved from derivatives of mapping products to detailed, interconnected, spatially referenced networks of water pathways, drainage areas, and stream and watershed characteristics. These properties are important because they enhance the ability to spatially evaluate factors that affect the sources and transport of water-quality constituents at various scales. SPAtially Referenced Regressions On Watershed attributes (SPARROW), a process-based/statistical model, relies on a digital hydrologic network in order to establish relations between quantities of monitored contaminant flux, contaminant sources, and the associated physical characteristics affecting contaminant transport. Digital hydrologic networks modified from the River Reach File (RF1) and National Hydrography Dataset (NHD) geospatial datasets provided frameworks for SPARROW in six regions of the conterminous United States. In addition, characteristics of the modified RF1 were used to update estimates of mean-annual streamflow. This produced more current flow estimates for use in SPARROW modeling. ?? 2011 American Water Resources Association. This article is a U.S. Government work and is in the public domain in the USA.

  3. Development of spatial data guidelines and standards: spatial data set documentation to support hydrologic analysis in the U.S. Geological Survey

    Science.gov (United States)

    Fulton, James L.

    1992-01-01

    Spatial data analysis has become an integral component in many surface and sub-surface hydrologic investigations within the U.S. Geological Survey (USGS). Currently, one of the largest costs in applying spatial data analysis is the cost of developing the needed spatial data. Therefore, guidelines and standards are required for the development of spatial data in order to allow for data sharing and reuse; this eliminates costly redevelopment. In order to attain this goal, the USGS is expanding efforts to identify guidelines and standards for the development of spatial data for hydrologic analysis. Because of the variety of project and database needs, the USGS has concentrated on developing standards for documenting spatial sets to aid in the assessment of data set quality and compatibility of different data sets. An interim data set documentation standard (1990) has been developed that provides a mechanism for associating a wide variety of information with a data set, including data about source material, data automation and editing procedures used, projection parameters, data statistics, descriptions of features and feature attributes, information on organizational contacts lists of operations performed on the data, and free-form comments and notes about the data, made at various times in the evolution of the data set. The interim data set documentation standard has been automated using a commercial geographic information system (GIS) and data set documentation software developed by the USGS. Where possible, USGS developed software is used to enter data into the data set documentation file automatically. The GIS software closely associates a data set with its data set documentation file; the documentation file is retained with the data set whenever it is modified, copied, or transferred to another computer system. The Water Resources Division of the USGS is continuing to develop spatial data and data processing standards, with emphasis on standards needed to support

  4. Metabolic-flux analysis of hydrogen production pathway in Citrobacter amalonaticus Y19

    Energy Technology Data Exchange (ETDEWEB)

    Oh, You-Kwan; Kim, Mi-Sun [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-343 (Korea); Kim, Heung-Joo; Park, Sunghoon [Department of Chemical and Biochemical Engineering and Institute for Environmental Technology and Industry, Pusan National University, Busan 609-735 (Korea); Ryu, Dewey D.Y. [Biochemical Engineering Program, Department of Chemical Engineering and Material Science, University of California, Davis, CA 95616 (United States)

    2008-03-15

    For the newly isolated chemoheterotrophic bacterium Citrobacter amalonaticus Y19, anaerobic glucose metabolism and hydrogen (H{sub 2}) production pathway were studied using batch cultivation and an in silico metabolic-flux analysis. Batch cultivation was conducted under varying initial glucose concentration between 1.5 and 9.5 g/L with quantitative measurement of major metabolites to obtain accurate carbon material balance. The metabolic flux of Y19 was analyzed using a metabolic-pathway model which was constructed from 81 biochemical reactions. The linear optimization program MetaFluxNet was employed for the analysis. When the specific growth rate of cells was chosen as an objective function, the model described the batch culture characteristics of Ci. amalonaticus Y19 reasonably well. When the specific H{sub 2} production rate was selected as an objective function, on the other hand, the achievable maximal H{sub 2} production yield (8.7molH{sub 2}/mol glucose) and the metabolic pathway enabling the high H{sub 2} yield were identified. The pathway involved non-native NAD(P)-linked hydrogenase and H{sub 2} production from NAD(P)H which were supplied at a high rate from glucose degradation through the pentose phosphate pathway. (author)

  5. Microarray analysis reveals genetic pathways modulated by tipifarnib in acute myeloid leukemia

    International Nuclear Information System (INIS)

    Raponi, Mitch; Belly, Robert T; Karp, Judith E; Lancet, Jeffrey E; Atkins, David; Wang, Yixin

    2004-01-01

    Farnesyl protein transferase inhibitors (FTIs) were originally developed to inhibit oncogenic ras, however it is now clear that there are several other potential targets for this drug class. The FTI tipifarnib (ZARNESTRA™, R115777) has recently demonstrated clinical responses in adults with refractory and relapsed acute leukemias. This study was conducted to identify genetic markers and pathways that are regulated by tipifarnib in acute myeloid leukemia (AML). Tipifarnib-mediated gene expression changes in 3 AML cell lines and bone marrow samples from two patients with AML were analyzed on a cDNA microarray containing approximately 7000 human genes. Pathways associated with these expression changes were identified using the Ingenuity Pathway Analysis tool. The expression analysis identified a common set of genes that were regulated by tipifarnib in three leukemic cell lines and in leukemic blast cells isolated from two patients who had been treated with tipifarnib. Association of modulated genes with biological functional groups identified several pathways affected by tipifarnib including cell signaling, cytoskeletal organization, immunity, and apoptosis. Gene expression changes were verified in a subset of genes using real time RT-PCR. Additionally, regulation of apoptotic genes was found to correlate with increased Annexin V staining in the THP-1 cell line but not in the HL-60 cell line. The genetic networks derived from these studies illuminate some of the biological pathways affected by FTI treatment while providing a proof of principle for identifying candidate genes that might be used as surrogate biomarkers of drug activity

  6. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia.

    Science.gov (United States)

    van Uitert, Miranda; Moerland, Perry D; Enquobahrie, Daniel A; Laivuori, Hannele; van der Post, Joris A M; Ris-Stalpers, Carrie; Afink, Gijs B

    2015-01-01

    Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite) and protein-protein associations (STRING). This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome). The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300) and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia.

  7. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia.

    Directory of Open Access Journals (Sweden)

    Miranda van Uitert

    Full Text Available Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite and protein-protein associations (STRING. This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome. The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300 and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia.

  8. Genome-wide analysis of a Wnt1-regulated transcriptional network implicates neurodegenerative pathways.

    Science.gov (United States)

    Wexler, Eric M; Rosen, Ezra; Lu, Daning; Osborn, Gregory E; Martin, Elizabeth; Raybould, Helen; Geschwind, Daniel H

    2011-10-04

    Wnt proteins are critical to mammalian brain development and function. The canonical Wnt signaling pathway involves the stabilization and nuclear translocation of β-catenin; however, Wnt also signals through alternative, noncanonical pathways. To gain a systems-level, genome-wide view of Wnt signaling, we analyzed Wnt1-stimulated changes in gene expression by transcriptional microarray analysis in cultured human neural progenitor (hNP) cells at multiple time points over a 72-hour time course. We observed a widespread oscillatory-like pattern of changes in gene expression, involving components of both the canonical and the noncanonical Wnt signaling pathways. A higher-order, systems-level analysis that combined independent component analysis, waveform analysis, and mutual information-based network construction revealed effects on pathways related to cell death and neurodegenerative disease. Wnt effectors were tightly clustered with presenilin1 (PSEN1) and granulin (GRN), which cause dominantly inherited forms of Alzheimer's disease and frontotemporal dementia (FTD), respectively. We further explored a potential link between Wnt1 and GRN and found that Wnt1 decreased GRN expression by hNPs. Conversely, GRN knockdown increased WNT1 expression, demonstrating that Wnt and GRN reciprocally regulate each other. Finally, we provided in vivo validation of the in vitro findings by analyzing gene expression data from individuals with FTD. These unbiased and genome-wide analyses provide evidence for a connection between Wnt signaling and the transcriptional regulation of neurodegenerative disease genes.

  9. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

    DEFF Research Database (Denmark)

    Thomassen, Mads; Tan, Qihua; Kruse, Torben

    2008-01-01

    ABSTRACT: BACKGROUND: Metastasis is believed to progress in several steps including different pathways but the determination and understanding of these mechanisms is still fragmentary. Microarray analysis of gene expression patterns in breast tumors has been used to predict outcome in recent stud...

  10. SNP-based pathway enrichment analysis for genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Potkin Steven G

    2011-04-01

    Full Text Available Abstract Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs, have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1 for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2 ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one

  11. A comparative analysis of hydrologic responses of tropical deciduous and temperate deciduous watershed ecosystems to climatic change

    Science.gov (United States)

    James M. Vose; Jose Manuel Maass

    1999-01-01

    Long-term monitoring of ecological and hydrological processes is critical to understanding ecosystem function and responses to anthropogenic and natural disturbances. Much of the world's knowledge of ecosystem responses to disturbance comes from long-term studies on gaged watersheds. However, there are relatively few long-term sites due to the large cost and...

  12. Statistical analysis of hydrological response in urbanising catchments based on adaptive sampling using inter-Amount times

    NARCIS (Netherlands)

    ten Veldhuis, J.A.E.; Schleiss, M.A.

    2017-01-01

    Urban catchments are typically characterised by a more flashy nature of the hydrological response compared to natural catchments. Predicting flow changes associated with urbanisation is not straightforward, as they are influenced by interactions between impervious cover, basin size, drainage

  13. Hydrological analysis as a technical tool to support strategic and economic development : a case study of Lake Naivasha, Kenya

    NARCIS (Netherlands)

    Yihdego, Y.; Reta, G.; Becht, R.

    2016-01-01

    Effective integrated water resources management requires reliable estimation of an overall basin water budget and of hydrologic fluctuations between groundwater and surface-water resources. Seasonal variability of groundwater-surface water exchange fluxes impacts on the water balance. The long term

  14. A Community Data Model for Hydrologic Observations

    Science.gov (United States)

    Tarboton, D. G.; Horsburgh, J. S.; Zaslavsky, I.; Maidment, D. R.; Valentine, D.; Jennings, B.

    2006-12-01

    The CUAHSI Hydrologic Information System project is developing information technology infrastructure to support hydrologic science. Hydrologic information science involves the description of hydrologic environments in a consistent way, using data models for information integration. This includes a hydrologic observations data model for the storage and retrieval of hydrologic observations in a relational database designed to facilitate data retrieval for integrated analysis of information collected by multiple investigators. It is intended to provide a standard format to facilitate the effective sharing of information between investigators and to facilitate analysis of information within a single study area or hydrologic observatory, or across hydrologic observatories and regions. The observations data model is designed to store hydrologic observations and sufficient ancillary information (metadata) about the observations to allow them to be unambiguously interpreted and used and provide traceable heritage from raw measurements to usable information. The design is based on the premise that a relational database at the single observation level is most effective for providing querying capability and cross dimension data retrieval and analysis. This premise is being tested through the implementation of a prototype hydrologic observations database, and the development of web services for the retrieval of data from and ingestion of data into the database. These web services hosted by the San Diego Supercomputer center make data in the database accessible both through a Hydrologic Data Access System portal and directly from applications software such as Excel, Matlab and ArcGIS that have Standard Object Access Protocol (SOAP) capability. This paper will (1) describe the data model; (2) demonstrate the capability for representing diverse data in the same database; (3) demonstrate the use of the database from applications software for the performance of hydrologic analysis

  15. Hydrological Impacts of Land Use Change in the Central Appalachian Mountains, U.S.: A Multi-Scale Analysis

    Science.gov (United States)

    Eshleman, K. N.; Negley, T. L.; Townsend, P. A.

    2003-12-01

    Quantifying, understanding, and predicting the hydrological impacts of land use changes and land management practices are important objectives of both the academic hydrologist and the civil engineer. Relationships between stormflow response and land use have been most readily observed at small spatial scales (e.g., hillslopes, small experimental watersheds), but have proved difficult to establish in larger basins where (1) high-resolution precipitation data are usually unavailable, (2) land use patterns are often exceedingly complex, and (3) land use changes are essentially uncontrolled. In the Central Appalachian Mountains of the U.S., conversion of forests to mined lands (through devegetation, excavation of overburden and coal deposits, and subsequent reclamation) is the dominant land use change presently occurring. In the Georges Creek basin in western Maryland, for example, the portion of the watershed classified as mined (including active, reclaimed, and abandoned surface mines) increased from 3.8 to 15.5% from 1962 to 1997; modest urbanization of the basin (2.4 to 4.7%) also occurred during this period. In 1999, we initiated a comparative field study to determine if surface coal-mining and subsequent land reclamation practices affect stormflow responses at multiple spatial scales: (1) plot, (2) small watershed, and (3) river basin scales. Results from the plot-scale experiments suggested that soil infiltration capacity is grossly reduced during mining and reclamation, apparently due to loss of forest litter and soil compaction by heavy machinery. At the small watershed (<25 ha) scale, a comparative analysis of a pair of gaged watersheds indicated that conventional methods of surface mining and reclamation can increase peak stormflow, total storm runoff, and storm runoff coefficient by about 250% relative to similar forested watersheds in the same region. Finally, frequency analysis of long-term runoff data from the larger, extensively-mined Georges Creek

  16. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    Science.gov (United States)

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  17. Mathematical modelling of fracture hydrology

    International Nuclear Information System (INIS)

    Herbert, A.W.; Hodgkinson, D.P.; Lever, D.A.; Robinson, P.C.; Rae, J.

    1985-06-01

    This report summarises the work performed between January 1983 and December 1984 for the CEC/DOE contract 'Mathematical Modelling of Fracture Hydrology', under the following headings: 1) Statistical fracture network modelling, 2) Continuum models of flow and transport, 3) Simplified models, 4) Analysis of laboratory experiments and 5) Analysis of field experiments. (author)

  18. Transcriptome Analysis of Manganese-deficient Chlamydomonas reinhardtii Provides Insight on the Chlorophyll Biosynthesis Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Lockhart, Ainsley; Zvenigorodsky, Natasha; Pedraza, Mary Ann; Lindquist, Erika

    2011-08-11

    The biosynthesis of chlorophyll and other tetrapyrroles is a vital but poorly understood process. Recent genomic advances with the unicellular green algae Chlamydomonas reinhardtii have created opportunity to more closely examine the mechanisms of the chlorophyll biosynthesis pathway via transcriptome analysis. Manganese is a nutrient of interest for complex reactions because of its multiple stable oxidation states and role in molecular oxygen coordination. C. reinhardtii was cultured in Manganese-deplete Tris-acetate-phosphate (TAP) media for 24 hours and used to create cDNA libraries for sequencing using Illumina TruSeq technology. Transcriptome analysis provided intriguing insight on possible regulatory mechanisms in the pathway. Evidence supports similarities of GTR (Glutamyl-tRNA synthase) to its Chlorella vulgaris homolog in terms of Mn requirements. Data was also suggestive of Mn-related compensatory up-regulation for pathway proteins CHLH1 (Manganese Chelatase), GUN4 (Magnesium chelatase activating protein), and POR1 (Light-dependent protochlorophyllide reductase). Intriguingly, data suggests possible reciprocal expression of oxygen dependent CPX1 (coproporphyrinogen III oxidase) and oxygen independent CPX2. Further analysis using RT-PCR could provide compelling evidence for several novel regulatory mechanisms in the chlorophyll biosynthesis pathway.

  19. Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.

    Directory of Open Access Journals (Sweden)

    Hariklia Eleftherohorinou

    2009-11-01

    Full Text Available Although the introduction of genome-wide association studies (GWAS have greatly increased the number of genes associated with common diseases, only a small proportion of the predicted genetic contribution has so far been elucidated. Studying the cumulative variation of polymorphisms in multiple genes acting in functional pathways may provide a complementary approach to the more common single SNP association approach in understanding genetic determinants of common disease. We developed a novel pathway-based method to assess the combined contribution of multiple genetic variants acting within canonical biological pathways and applied it to data from 14,000 UK individuals with 7 common diseases. We tested inflammatory pathways for association with Crohn's disease (CD, rheumatoid arthritis (RA and type 1 diabetes (T1D with 4 non-inflammatory diseases as controls. Using a variable selection algorithm, we identified variants responsible for the pathway association and evaluated their use for disease prediction using a 10 fold cross-validation framework in order to calculate out-of-sample area under the Receiver Operating Curve (AUC. The generalisability of these predictive models was tested on an independent birth cohort from Northern Finland. Multiple canonical inflammatory pathways showed highly significant associations (p 10(-3-10(-20 with CD, T1D and RA. Variable selection identified on average a set of 205 SNPs (149 genes for T1D, 350 SNPs (189 genes for RA and 493 SNPs (277 genes for CD. The pattern of polymorphisms at these SNPS were found to be highly predictive of T1D (91% AUC and RA (85% AUC, and weakly predictive of CD (60% AUC. The predictive ability of the T1D model (without any parameter refitting had good predictive ability (79% AUC in the Finnish cohort. Our analysis suggests that genetic contribution to common inflammatory diseases operates through multiple genes interacting in functional pathways.

  20. Evaluating the effect of clinical care pathways on quality of cancer care: analysis of breast, colon and rectal cancer pathways.

    Science.gov (United States)

    Bao, Han; Yang, Fengjuan; Su, Shaofei; Wang, Xinyu; Zhang, Meiqi; Xiao, Yaming; Jiang, Hao; Wang, Jiaying; Liu, Meina

    2016-05-01

    Substantial gaps exist between clinical practice and evidence-based cancer care, potentially leading to adverse clinical outcomes and decreased quality of life for cancer patients. This study aimed to evaluate the usefulness of clinical pathways as a tool for improving quality of cancer care, using breast, colon, and rectal cancer pathways as demonstrations. Newly diagnosed patients with invasive breast, colon, and rectal cancer were enrolled as pre-pathway groups, while patients with the same diagnoses treated according to clinical pathways were recruited for post-pathway groups. Compliance with preoperative core biopsy or fine-needle aspiration, utilization of sentinel lymph node biopsy, and proportion of patients whose tumor hormone receptor status was stated in pathology report were significantly increased after implementation of clinical pathway for breast cancer. For colon cancer, compliance with two care processes was significantly improved: surgical resection with anastomosis and resection of at least 12 lymph nodes. Regarding rectal cancer, there was a significant increase in compliance with preoperative evaluation of depth of tumor invasion, total mesorectal excision treatment of middle- or low-position rectal cancer, and proportion of patients who had undergone rectal cancer surgery whose pathology report included margin status. Moreover, total length of hospital stay was decreased remarkably for all three cancer types, and postoperative complications remained unchanged following implementation of the clinical pathways. Clinical pathways can improve compliance with standard care by implementing evidence-based quality indicators in daily practice, which could serve as a useful tool for narrowing the gap between clinical practice and evidence-based care.

  1. Cloning and Expression Analysis of MEP Pathway Enzyme-encoding Genes in Osmanthus fragrans

    Directory of Open Access Journals (Sweden)

    Chen Xu

    2016-09-01

    Full Text Available The 2-C-methyl-d-erythritol 4-phosphate (MEP pathway is responsible for the biosynthesis of many crucial secondary metabolites, such as carotenoids, monoterpenes, plastoquinone, and tocopherols. In this study, we isolated and identified 10 MEP pathway genes in the important aromatic plant sweet osmanthus (Osmanthus fragrans. Multiple sequence alignments revealed that 10 MEP pathway genes shared high identities with other reported proteins. The genes showed distinctive expression profiles in various tissues, or at different flower stages and diel time points. The qRT-PCR results demonstrated that these genes were highly expressed in inflorescences, which suggested a tissue-specific transcript pattern. Our results also showed that OfDXS1, OfDXS2, and OfHDR1 had a clear diurnal oscillation pattern. The isolation and expression analysis provides a strong foundation for further research on the MEP pathway involved in gene function and molecular evolution, and improves our understanding of the molecular mechanism underlying this pathway in plants.

  2. Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways.

    Science.gov (United States)

    Lee, Yun; Lafontaine Rivera, Jimmy G; Liao, James C

    2014-09-01

    Metabolic pathways in cells must be sufficiently robust to tolerate fluctuations in expression levels and changes in environmental conditions. Perturbations in expression levels may lead to system failure due to the disappearance of a stable steady state. Increasing evidence has suggested that biological networks have evolved such that they are intrinsically robust in their network structure. In this article, we presented Ensemble Modeling for Robustness Analysis (EMRA), which combines a continuation method with the Ensemble Modeling approach, for investigating the robustness issue of non-native pathways. EMRA investigates a large ensemble of reference models with different parameters, and determines the effects of parameter drifting until a bifurcation point, beyond which a stable steady state disappears and system failure occurs. A pathway is considered to have high bifurcational robustness if the probability of system failure is low in the ensemble. To demonstrate the utility of EMRA, we investigate the bifurcational robustness of two synthetic central metabolic pathways that achieve carbon conservation: non-oxidative glycolysis and reverse glyoxylate cycle. With EMRA, we determined the probability of system failure of each design and demonstrated that alternative designs of these pathways indeed display varying degrees of bifurcational robustness. Furthermore, we demonstrated that target selection for flux improvement should consider the trade-offs between robustness and performance. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Analysis of PIK3CA Mutations and Activation Pathways in Triple Negative Breast Cancer.

    Directory of Open Access Journals (Sweden)

    Paolo Cossu-Rocca

    Full Text Available Triple Negative Breast Cancer (TNBC accounts for 12-24% of all breast carcinomas, and shows worse prognosis compared to other breast cancer subtypes. Molecular studies demonstrated that TNBCs are a heterogeneous group of tumors with different clinical and pathologic features, prognosis, genetic-molecular alterations and treatment responsivity. The PI3K/AKT is a major pathway involved in the regulation of cell survival and proliferation, and is the most frequently altered pathway in breast cancer, apparently with different biologic impact on specific cancer subtypes. The most common genetic abnormality is represented by PIK3CA gene activating mutations, with an overall frequency of 20-40%. The aims of our study were to investigate PIK3CA gene mutations on a large series of TNBC, to perform a wider analysis on genetic alterations involving PI3K/AKT and BRAF/RAS/MAPK pathways and to correlate the results with clinical-pathologic data.PIK3CA mutation analysis was performed by using cobas® PIK3CA Mutation Test. EGFR, AKT1, BRAF, and KRAS genes were analyzed by sequencing. Immunohistochemistry was carried out to identify PTEN loss and to investigate for PI3K/AKT pathways components.PIK3CA mutations were detected in 23.7% of TNBC, whereas no mutations were identified in EGFR, AKT1, BRAF, and KRAS genes. Moreover, we observed PTEN loss in 11.3% of tumors. Deregulation of PI3K/AKT pathways was revealed by consistent activation of pAKT and p-p44/42 MAPK in all PIK3CA mutated TNBC.Our data shows that PIK3CA mutations and PI3K/AKT pathway activation are common events in TNBC. A deeper investigation on specific TNBC genomic abnormalities might be helpful in order to select patients who would benefit from current targeted therapy strategies.

  4. Analysis of PIK3CA Mutations and Activation Pathways in Triple Negative Breast Cancer.

    Science.gov (United States)

    Cossu-Rocca, Paolo; Orrù, Sandra; Muroni, Maria Rosaria; Sanges, Francesca; Sotgiu, Giovanni; Ena, Sara; Pira, Giovanna; Murgia, Luciano; Manca, Alessandra; Uras, Maria Gabriela; Sarobba, Maria Giuseppina; Urru, Silvana; De Miglio, Maria Rosaria

    2015-01-01

    Triple Negative Breast Cancer (TNBC) accounts for 12-24% of all breast carcinomas, and shows worse prognosis compared to other breast cancer subtypes. Molecular studies demonstrated that TNBCs are a heterogeneous group of tumors with different clinical and pathologic features, prognosis, genetic-molecular alterations and treatment responsivity. The PI3K/AKT is a major pathway involved in the regulation of cell survival and proliferation, and is the most frequently altered pathway in breast cancer, apparently with different biologic impact on specific cancer subtypes. The most common genetic abnormality is represented by PIK3CA gene activating mutations, with an overall frequency of 20-40%. The aims of our study were to investigate PIK3CA gene mutations on a large series of TNBC, to perform a wider analysis on genetic alterations involving PI3K/AKT and BRAF/RAS/MAPK pathways and to correlate the results with clinical-pathologic data. PIK3CA mutation analysis was performed by using cobas® PIK3CA Mutation Test. EGFR, AKT1, BRAF, and KRAS genes were analyzed by sequencing. Immunohistochemistry was carried out to identify PTEN loss and to investigate for PI3K/AKT pathways components. PIK3CA mutations were detected in 23.7% of TNBC, whereas no mutations were identified in EGFR, AKT1, BRAF, and KRAS genes. Moreover, we observed PTEN loss in 11.3% of tumors. Deregulation of PI3K/AKT pathways was revealed by consistent activation of pAKT and p-p44/42 MAPK in all PIK3CA mutated TNBC. Our data shows that PIK3CA mutations and PI3K/AKT pathway activation are common events in TNBC. A deeper investigation on specific TNBC genomic abnormalities might be helpful in order to select patients who would benefit from current targeted therapy strategies.

  5. A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.

    Science.gov (United States)

    Lai, En-Yu; Chen, Yi-Hau; Wu, Kun-Pin

    2017-06-01

    Approaches to identify significant pathways from high-throughput quantitative data have been developed in recent years. Still, the analysis of proteomic data stays difficult because of limited sample size. This limitation also leads to the practice of using a competitive null as common approach; which fundamentally implies genes or proteins as independent units. The independent assumption ignores the associations among biomolecules with similar functions or cellular localization, as well as the interactions among them manifested as changes in expression ratios. Consequently, these methods often underestimate the associations among biomolecules and cause false positives in practice. Some studies incorporate the sample covariance matrix into the calculation to address this issue. However, sample covariance may not be a precise estimation if the sample size is very limited, which is usually the case for the data produced by mass spectrometry. In this study, we introduce a multivariate test under a self-contained null to perform pathway analysis for quantitative proteomic data. The covariance matrix used in the test statistic is constructed by the confidence scores retrieved from the STRING database or the HitPredict database. We also design an integrating procedure to retain pathways of sufficient evidence as a pathway group. The performance of the proposed T2-statistic is demonstrated using five published experimental datasets: the T-cell activation, the cAMP/PKA signaling, the myoblast differentiation, and the effect of dasatinib on the BCR-ABL pathway are proteomic datasets produced by mass spectrometry; and the protective effect of myocilin via the MAPK signaling pathway is a gene expression dataset of limited sample size. Compared with other popular statistics, the proposed T2-statistic yields more accurate descriptions in agreement with the discussion of the original publication. We implemented the T2-statistic into an R package T2GA, which is available at https

  6. An Analysis of Land Use Change Dynamics and Its Impacts on Hydrological Processes in the Jialing River Basin

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2014-12-01

    Full Text Available Land use changes are important aspects of global change and affect regional water cycles, environmental quality, biodiversity and terrestrial ecosystems. To understand the temporal and spatial land use change in the Jialing River Basin and its impacts on the hydrological cycle, land use change models and the variable infiltration capacity (VIC model were applied separately to the Jialing River Basin. Real change and final change were analyzed to determine the consequences of land use changes and their hydrological consequences. Real change is defined as the total variation during a fixed period, including increases and decreases. Thus, real change is the sum of the absolute values of the decrease and the increase. Final change is defined as the difference between the beginning and end of a given period for a specific factor. Overall, the amounts of settlement and shrub land area changed significantly in the entire Jialing River (with final change rates of 20.77% and −16.07%, respectively, and real change rates of 34.2% and 30.1%, respectively, from 1985 to 1995, as well as final and real change rates of 29.37%, 12.40%, 39.9% and 32.8%, respectively, from 1995 to 2000. Compared with the final change, the real change highlighted the rate of change and the change in woodland area. The land use changes in the Lueyang (LY, Shehong (SH and Fengtan (FT subcatchments were more dynamic than in the other subcatchments. The economy, population and macro-policy were the main factors responsible for driving the land use changes. The decrease in woodland area in the LY subcatchment corresponded with an increase in evapotranspiration (ET and with decreases in the other hydrological elements. Overall, the final changes in the hydrological elements in the LY, SH and FT subcatchments were not significant due to the average and compensation effects. The LY subcatchment was mainly affected by the average effect, whereas the SH and FT subcatchments were affected

  7. Hydrological impacts of forest decline and regrowth: a retrospective analysis of the past 60 years in Saxony, Germany

    Science.gov (United States)

    Renner, Maik; Kristina, Brust; Christian, Bernhofer

    2013-04-01

    It is generally believed that both, climate and land use land cover (LULC) changes impact evapotranspiration and runoff; yet there is some difficulty to separate the effects of these different impacts. Here, we condense meteorological and hydrological data from the long and well established observation network over Saxony covering the period 1950-2009. The region can be considered as a typical Central European landscape with considerable anthropogenically related impacts. Certainly, one of the most severe impacts have been the air pollution driven tree dieback along the top mountain ranges peaking in the 1970s and 1980s. To address the role of environmental factors on the long term annual average and the potential role of regional scale environmental pollution we conduct a hydro-climatic data analysis of 71 small to medium range river basins covering the greatest part of Saxony. Plotting the 1950-2009 annual averages in a Budyko diagram reveals a significant linear relation of the evaporative fraction (ET/P) to the aridity index (E0-P ). It appears that topographically controlled gradients of precipitation, land use and basin water retention exist. While most basins are found to follow the Budyko curve, two groups of basins deviate. Agriculturally dominated basins at lower altitudes exceed the Budyko curve while a set of high altitude, forested basins fall well below. The latter group is characterized by significant temporal dynamics, which are consistent in space and time with tree damage data. We visualize the decadal dynamics on the relative partitioning of water and energy at the catchment scale and show that the pollution driven tree damage affected head water catchments leading to a decline of ET (P-Q) of up to 200 mm/yr in the 1980s. The apparent regrowth since effective measures on industrial pollution have been established in the 1990s, shows a significant increase of ET. This increase is visible from space and we found good coherence with increasing

  8. Proliferation Resistance: Acquisition/Diversion Pathway Analysis for the DUPIC Fuel Cycle

    International Nuclear Information System (INIS)

    Ko, Won Il; Chang, Hong Lae; Song, Dae Yong; Lee, Ho Hee; Kwon, Eun Ha; Jeong, Chang Joon; Kim, Ho Dong

    2009-07-01

    Within the International Project on Innovative Nuclear Reactors and Fuel Cycles (INPRO), a methodology for evaluating proliferation resistance (INPRO PR methodology) has been developed. However, it remains to develop the methodology to evaluate User Requirements (UR) 4 regarding multiplicity and robustness of barriers against proliferation - innovative nuclear energy systems should incorporate multiple proliferation resistance features and measures. Since this requires an acquisition/diversion pathway analysis, this report describes a systematic approach developed for the identification and analysis of pathways for the acquisition of weapons-usable nuclear material using the DUPIC fuel cycle system. At the first step, the objectives of the proliferation were identified, including the quality and quantity of the material, the time required to acquire the material for the proliferation, thr capability of the potential proliferant country, etc. At the second step, the possible strategies, which the potential proliferant country could adopt, were identified: undeclared removal of nuclear material from the fuel cycle facilities; and further treatment of the diverted nuclear materials needed to acquire weapons-usable materials. At the final step, a systematic approach to select the plausible pathways for the acquisition/diversion of nuclear material during the whole fuel cycle has been developed. The coarse material diversion pathways for the DUPIC fuel cycle and the approach developed was reviewed and discussed at the experts meeting at the IAEA for its appropriateness and comprehensiveness

  9. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

    Science.gov (United States)

    Chovancova, Eva; Pavelka, Antonin; Benes, Petr; Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

    2012-01-01

    Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

  10. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

    Directory of Open Access Journals (Sweden)

    Eva Chovancova

    Full Text Available Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

  11. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

    Science.gov (United States)

    Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

    2012-01-01

    Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. PMID:23093919

  12. Analysis of interrelation between water quality and hydrologic conditions on a small karst catchment area of sinking watercourse Trbuhovica

    International Nuclear Information System (INIS)

    Hinic, V; Grzetic, A; Ljubotina, M; Rubinic, J; Ruzic, I; Volf, G; Vuckovic, I; Kvas, N

    2008-01-01

    Sinking watercourse Trbuhovica is located at the topping karst of Gorski Kotar in Croatia, near the Slovenian border. About 900 inhabitants live in Trbuhovica catchment area. Sewage system had not been built. The project KEEP WATERS CLEAN (INTERREG III A project) was approved by EU commission and has a purpose of investigating water resources of that area, their appropriate protection and improving management of those resources. This paper presents project's 1st phase investigation results: hydrologic conditions and water quality at several locations on stream and at the springs of Trbuhovica, Mlake and Obrh. Climatologic (precipitation, air temperature and snow cover), basic hydrologic characteristics (flow and water temperature), water quality parameters (pH, electric conductivity, alkalinity, oxygen regime, nutrients and mineral oils) and microbiology indicators have been monitored. Samples of micro invertebrates and samples of periphyton have been collected in the field. Biological results have been elaborated via Saprobial Index according to Pantle-Buck. Analyses results showed a strong connection between hydrologic condition and selected water quality parameters. The groundwater quality changes are very quick. Maximum pollutions occur during the period of intensive rain. Water at the spring of Mlaka is very clean and is classified in the first to second water category, while Trbuhovica shows higher organic pollution.

  13. Analysis of interrelation between water quality and hydrologic conditions on a small karst catchment area of sinking watercourse Trbuhovica

    Science.gov (United States)

    Hinić, V.; Rubinić, J.; Vučković, I.; Ružić, I.; Gržetić, A.; Volf, G.; Ljubotina, M.; Kvas, N.

    2008-11-01

    Sinking watercourse Trbuhovica is located at the topping karst of Gorski Kotar in Croatia, near the Slovenian border. About 900 inhabitants live in Trbuhovica catchment area. Sewage system had not been built. The project KEEP WATERS CLEAN (INTERREG III A project) was approved by EU commission and has a purpose of investigating water resources of that area, their appropriate protection and improving management of those resources. This paper presents project's 1st phase investigation results: hydrologic conditions and water quality at several locations on stream and at the springs of Trbuhovica, Mlake and Obrh. Climatologic (precipitation, air temperature and snow cover), basic hydrologic characteristics (flow and water temperature), water quality parameters (pH, electric conductivity, alkalinity, oxygen regime, nutrients and mineral oils) and microbiology indicators have been monitored. Samples of micro invertebrates and samples of periphyton have been collected in the field. Biological results have been elaborated via Saprobial Index according to Pantle-Buck. Analyses results showed a strong connection between hydrologic condition and selected water quality parameters. The groundwater quality changes are very quick. Maximum pollutions occur during the period of intensive rain. Water at the spring of Mlaka is very clean and is classified in the first to second water category, while Trbuhovica shows higher organic pollution.

  14. Analysis of spatio-temporal land cover changes for hydrological impact assessment within the Nyando River Basin of Kenya.

    Science.gov (United States)

    Olang, Luke Omondi; Kundu, Peter; Bauer, Thomas; Fürst, Josef

    2011-08-01

    The spatio-temporal changes in the land cover states of the Nyando Basin were investigated for auxiliary hydrological impact assessment. The predominant land cover types whose conversions could influence the hydrological response of the region were selected. Six Landsat images for 1973, 1986, and 2000 were processed to discern the changes based on a methodology that employs a hybrid of supervised and unsupervised classification schemes. The accuracy of the classifications were assessed using reference datasets processed in a GIS with the help of ground-based information obtained through participatory mapping techniques. To assess the possible hydrological effect of the detected changes during storm events, a physically based lumped approach for infiltration loss estimation was employed within five selected sub-basins. The results obtained indicated that forests in the basin declined by 20% while agricultural fields expanded by 16% during the entire period of study. Apparent from the land cover conversion matrices was that the majority of the forest decline was a consequence of agricultural expansion. The model results revealed decreased infiltration amounts by between 6% and 15%. The headwater regions with the vast deforestation were noted to be more vulnerable to the land cover change effects. Despite the haphazard land use patterns and uncertainties related to poor data quality for environmental monitoring and assessment, the study exposed the vast degradation and hence the need for sustainable land use planning for enhanced catchment management purposes.

  15. Integrated agro-hydrological modelling and economic analysis of BMPs to support decision making and policy design

    Science.gov (United States)

    Maroy, E.; Rousseau, A. N.; Hallema, D. W.

    2012-12-01

    With recent efforts and increasing control over point source pollution of freshwater, agricultural non-point pollution sources have become responsible for most of sediment and nutrient loads in North American water systems. Environmental and agricultural agencies have recognised the need for reducing eutrophication and have developed various policies to compel or encourage producers to best management practices (BMPs). Addressing diffuse pollution is challenging considering the complex and cumulative nature of transport processes, high variability in space and time, and prohibitive costs of distributed water quality monitoring. Many policy options exist to push producers to adopt environmentally desirable behaviour while keeping their activity viable, and ensure equitable costs to consumers and tax payers. On the one hand, economic instruments (subsidies, taxes, water quality markets) are designed to maximize cost-effectiveness, so that farmers optimize their production for maximum profit while implementing BMPs. On the other hand, emission standards or regulation of inputs are often easier and less costly to implement. To study economic and environmental impacts of such policies, a distributed modelling approach is needed to deal with the complexity of the system and the large environmental and socio-economic data requirements. Our objective is to integrate agro-hydrological modelling and economic analysis to support decision and policy making processes of BMP implementation. The integrated modelling system GIBSI was developed in an earlier study within the Canadian WEBs project (Watershed Evaluation of BMPs) to evaluate the influence of BMPs on water quality. The case study involved 30 and 15 year records of discharge and water quality measurements respectively, in the Beaurivage River watershed (Quebec, Canada). GIBSI provided a risk-based overview of the impact of BMPs (including vegetated riparian buffer strips, precision slurry application, conversion to

  16. HYDROLOGY, NESHOBA COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  17. HYDROLOGY, MONTGOMERY COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  18. HYDROLOGY, DOUGLAS COUNTY, MINNESOTA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  19. HYDROLOGY, OSCEOLA COUNTY, FL

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  20. HYDROLOGY, STEARNS COUNTY, MN

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  1. HYDROLOGY, CALHOUN COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  2. HYDROLOGY, LEFLORE COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  3. HYDROLOGY, WAYNE COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  4. Hydrology, OCONEE COUNTY, SC

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  5. HYDROLOGY, NEWTON COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  6. HYDROLOGY, TIPPAH COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  7. HYDROLOGY, CALHOUN COUNTY, MICHIGAN

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  8. HYDROLOGY, SUNFLOWER COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  9. HYDROLOGY, HOUSTON COUNTY, ALABAMA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating ALood discharges for a ALood Insurance...

  10. Weber County Hydrology Report

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  11. HYDROLOGY, LEAKE COUNTY, MISSISSIPPI

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  12. HYDROLOGY, CHISAGO COUNTY, MN

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  13. HYDROLOGY, CLAIBORNE COUNTY, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  14. HYDROLOGY, LAFAYETTE COUNTY, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  15. HYDROLOGY, Yazoo COUNTY, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  16. HYDROLOGY, Lawrence County, ARKANSAS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a Flood Insurance...

  17. HYDROLOGY, Allegheny County, PA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a Flood Insurance...

  18. HYDROLOGY, SIMPSON COUNTY, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  19. HYDROLOGY, GILCHRIST COUNTY, FL

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  20. HYDROLOGY, GLADES COUNTY, FLORIDA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a Flood Insurance...

  1. HYDROLOGY, LEE COUNTY, TEXAS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a Flood Insurance...

  2. HYDROLOGY, GREENE County, ARKANSAS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a Flood Insurance...

  3. The progress of hydrology

    Energy Technology Data Exchange (ETDEWEB)

    Chow, V T [University of Illinois, Urbana, IL (United States)

    1967-05-15

    This paper discusses mainly the challenge of hydrology, recent activities, events, and major problems in hydrology, and advances in hydrological techniques. New scientific knowledge and techniques developed in many modern scientific disciplines, and the recognition of the importance of hydrology in water-resources development enable and encourage the hydrologist to advance scientific hydrology. Many programmes to promote hydrology and to expand its attendant activities have been developed in recent years. Therefore, the activities in the United States of America, such as the Universities Council on Water Resources and the President's Water for Peace Programme, and the programmes in the International Hydrological Decade are mentioned. The most important advance in theoretical hydrology is the development of a new concept of dynamic sequential systems for the hydrological cycle, thus creating new fields of systems, parametric, and stochastic hydrology. Modern scientific instrumentation provide the hydrologist with better tools for solving his problems. The most important of these, such as electronic computers, remote sensing, and nuclear techniques are discussed. Today various major problems, both theoretical and practical, face the hydrologist. Theoretical problems concern the basic understanding of hydrological systems and the mathematical simulation and physical interpretation of hydrological phenomena. Major practical problems are numerous and diversified, but they are mostly related to the multiple-purpose development of water resources. Four central problematical subjects are discussed; namely, the effects of man on his environment, the dynamics of aqueous flow systems, hydrological transport mechanism, and groundwater hydrology. Also, the use of nuclear techniques in solving various hydrological problems is discussed. It is believed that the application of nuclear techniques would prove extremely valuable in helping solve problems, but their ultimate use in

  4. The progress of hydrology

    International Nuclear Information System (INIS)

    Chow, V.T.

    1967-01-01

    This paper discusses mainly the challenge of hydrology, recent activities, events, and major problems in hydrology, and advances in hydrological techniques. New scientific knowledge and techniques developed in many modern scientific disciplines, and the recognition of the importance of hydrology in water-resources development enable and encourage the hydrologist to advance scientific hydrology. Many programmes to promote hydrology and to expand its attendant activities have been developed in recent years. Therefore, the activities in the United States of America, such as the Universities Council on Water Resources and the President's Water for Peace Programme, and the programmes in the International Hydrological Decade are mentioned. The most important advance in theoretical hydrology is the development of a new concept of dynamic sequential systems for the hydrological cycle, thus creating new fields of systems, parametric, and stochastic hydrology. Modern scientific instrumentation provide the hydrologist with better tools for solving his problems. The most important of these, such as electronic computers, remote sensing, and nuclear techniques are discussed. Today various major problems, both theoretical and practical, face the hydrologist. Theoretical problems concern the basic understanding of hydrological systems and the mathematical simulation and physical interpretation of hydrological phenomena. Major practical problems are numerous and diversified, but they are mostly related to the multiple-purpose development of water resources. Four central problematical subjects are discussed; namely, the effects of man on his environment, the dynamics of aqueous flow systems, hydrological transport mechanism, and groundwater hydrology. Also, the use of nuclear techniques in solving various hydrological problems is discussed. It is believed that the application of nuclear techniques would prove extremely valuable in helping solve problems, but their ultimate use in

  5. A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene co‑expression analysis.

    Science.gov (United States)

    Chen, Xiao-Min; Feng, Ming-Jun; Shen, Cai-Jie; He, Bin; Du, Xian-Feng; Yu, Yi-Bo; Liu, Jing; Chu, Hui-Min

    2017-07-01

    The present study was designed to develop a novel method for identifying significant pathways associated with human hypertrophic cardiomyopathy (HCM), based on gene co‑expression analysis. The microarray dataset associated with HCM (E‑GEOD‑36961) was obtained from the European Molecular Biology Laboratory‑European Bioinformatics Institute database. Informative pathways were selected based on the Reactome pathway database and screening treatments. An empirical Bayes method was utilized to construct co‑expression networks for informative pathways, and a weight value was assigned to each pathway. Differential pathways were extracted based on weight threshold, which was calculated using a random model. In order to assess whether the co‑expression method was feasible, it was compared with traditional pathway enrichment analysis of differentially expressed genes, which were identified using the significance analysis of microarrays package. A total of 1,074 informative pathways were screened out for subsequent investigations and their weight values were also obtained. According to the threshold of weight value of 0.01057, 447 differential pathways, including folding of actin by chaperonin containing T‑complex protein 1 (CCT)/T‑complex protein 1 ring complex (TRiC), purine ribonucleoside monophosphate biosynthesis and ubiquinol biosynthesis, were obtained. Compared with traditional pathway enrichment analysis, the number of pathways obtained from the co‑expression approach was increased. The results of the present study demonstrated that this method may be useful to predict marker pathways for HCM. The pathways of folding of actin by CCT/TRiC and purine ribonucleoside monophosphate biosynthesis may provide evidence of the underlying molecular mechanisms of HCM, and offer novel therapeutic directions for HCM.

  6. Statistical assessment and hydrological utility of the latest multi-satellite precipitation analysis IMERG in Ganjiang River basin

    Science.gov (United States)

    Li, Na; Tang, Guoqiang; Zhao, Ping; Hong, Yang; Gou, Yabin; Yang, Kai

    2017-01-01

    This study aims to statistically and hydrologically assess the hydrological utility of the latest Integrated Multi-satellitE Retrievals from Global Precipitation Measurement (IMERG) multi-satellite constellation over the mid-latitude Ganjiang River basin in China. The investigations are conducted at hourly and 0.1° resolutions throughout the rainy season from March 12 to September 30, 2014. Two high-quality quantitative precipitation estimation (QPE) datasets, i.e., a gauge-corrected radar mosaic QPE product (RQPE) and a highly dense network of 1200 rain gauges, are used as the reference. For the implementation of the study, first, we compare IMERG product and RQPE with rain gauge-interpolated data, respectively. The results indicate that both remote sensing products can estimate precipitation fairly well over the basin, while RQPE significantly outperforms IMERG product in almost all the studied cases. The correlation coefficients of RQPE (CC = 0.98 and CC = 0.67) are much higher than those of IMERG product (CC = 0.80 and CC = 0.33) at basin and grid scales, respectively. Then, the hydrological assessment is conducted with the Coupled Routing and Excess Storage (CREST) model under multiple parameterization scenarios, in which the model is calibrated using the rain gauge-interpolated data, RQPE, and IMERG products respectively. During the calibration period (from March 12 to May 31), the simulated streamflow based on rain gauge-interpolated data shows the highest Nash-Sutcliffe coefficient efficiency (NSCE) value (0.92), closely followed by the RQPE (NSCE = 0.84), while IMERG product performs barely acceptable (NSCE = 0.56). During the validation period (from June 1 to September 30), the three rainfall datasets are used to force the CREST model based on all the three calibrated parameter sets (i.e., nine combinations in total). RQPE outperforms rain gauge-interpolated data and IMERG product in all validation scenarios, possibly due to its advantageous capability

  7. Data mining and pathway analysis of glucose-6-phosphate dehydrogenase with natural language processing

    Science.gov (United States)

    Chen, Long; Zhang, Chunhua; Wang, Yanling; Li, Yuqian; Han, Qiaoqiao; Yang, Huixin; Zhu, Yuechun

    2017-01-01

    Human glucose-6-phosphate dehydrogenase (G6PD) is a crucial enzyme in the pentose phosphate pathway, and serves an important role in biosynthesis and the redox balance. G6PD deficiency is a major cause of neonatal jaundice and acute hemolyticanemia, and recently, G6PD has been associated with diseases including inflammation and cancer. The aim of the present study was to conduct a search of the National Center for Biotechnology Information PubMed library for articles discussing G6PD. Genes that were identified to be associated with G6PD were recorded, and the frequency at which each gene appeared was calculated. Gene ontology (GO), pathway and network analyses were then performed. A total of 98 G6PD-associated genes and 33 microRNAs (miRNAs) that potentially regulate G6PD were identified. The 98 G6PD-associated genes were then sub-classified into three functional groups by GO analysis, followed by analysis of function, pathway, network, and disease association. Out of the 47 signaling pathways identified, seven were significantly correlated with G6PD-associated genes. At least two out of four independent programs identified the 33 miRNAs that were predicted to target G6PD. miR-1207-5P, miR-1 and miR-125a-5p were predicted by all four software programs to target G6PD. The results of the present study revealed that dysregulation of G6PD was associated with cancer, autoimmune diseases, and oxidative stress-induced disorders. These results revealed the potential roles of G6PD-regulated signaling and metabolic pathways in the etiology of these diseases. PMID:28627690

  8. Hydrological inferences through morphometric analysis of lower Kosi river basin of India for water resource management based on remote sensing data

    Science.gov (United States)

    Rai, Praveen Kumar; Chandel, Rajeev Singh; Mishra, Varun Narayan; Singh, Prafull

    2018-03-01

    Satellite based remote sensing technology has proven to be an effectual tool in analysis of drainage networks, study of surface morphological features and their correlation with groundwater management prospect at basin level. The present study highlights the effectiveness and advantage of remote sensing and GIS-based analysis for quantitative and qualitative assessment of flood plain region of lower Kosi river basin based on morphometric analysis. In this study, ASTER DEM is used to extract the vital hydrological parameters of lower Kosi river basin in ARC GIS software. Morphometric parameters, e.g., stream order, stream length, bifurcation ratio, drainage density, drainage frequency, drainage texture, form factor, circularity ratio, elongation ratio, etc., have been calculated for the Kosi basin and their hydrological inferences were discussed. Most of the morphometric parameters such as bifurcation ratio, drainage density, drainage frequency, drainage texture concluded that basin has good prospect for water management program for various purposes and also generated data base that can provide scientific information for site selection of water-harvesting structures and flood management activities in the basin. Land use land cover (LULC) of the basin were also prepared from Landsat data of 2005, 2010 and 2015 to assess the change in dynamic of the basin and these layers are very noteworthy for further watershed prioritization.

  9. Integrative Analysis of Gene Expression Data Including an Assessment of Pathway Enrichment for Predicting Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Pingzhao Hu

    2006-01-01

    Full Text Available Background: Microarray technology has been previously used to identify genes that are differentially expressed between tumour and normal samples in a single study, as well as in syntheses involving multiple studies. When integrating results from several Affymetrix microarray datasets, previous studies summarized probeset-level data, which may potentially lead to a loss of information available at the probe-level. In this paper, we present an approach for integrating results across studies while taking probe-level data into account. Additionally, we follow a new direction in the analysis of microarray expression data, namely to focus on the variation of expression phenotypes in predefined gene sets, such as pathways. This targeted approach can be helpful for revealing information that is not easily visible from the changes in the individual genes. Results: We used a recently developed method to integrate Affymetrix expression data across studies. The idea is based on a probe-level based test statistic developed for testing for differentially expressed genes in individual studies. We incorporated this test statistic into a classic random-effects model for integrating data across studies. Subsequently, we used a gene set enrichment test to evaluate the significance of enriched biological pathways in the differentially expressed genes identified from the integrative analysis. We compared statistical and biological significance of the prognostic gene expression signatures and pathways identified in the probe-level model (PLM with those in the probeset-level model (PSLM. Our integrative analysis of Affymetrix microarray data from 110 prostate cancer samples obtained from three studies reveals thousands of genes significantly correlated with tumour cell differentiation. The bioinformatics analysis, mapping these genes to the publicly available KEGG database, reveals evidence that tumour cell differentiation is significantly associated with many

  10. Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

    Science.gov (United States)

    Liggi, Sonia; Drakakis, Georgios; Koutsoukas, Alexios; Cortes-Ciriano, Isidro; Martínez-Alonso, Patricia; Malliavin, Thérèse E; Velazquez-Campoy, Adrian; Brewerton, Suzanne C; Bodkin, Michael J; Evans, David A; Glen, Robert C; Carrodeguas, José Alberto; Bender, Andreas

    2014-01-01

    An in silico mechanism-of-action analysis protocol was developed, comprising molecule bioactivity profiling, annotation of predicted targets with pathways and calculation of enrichment factors to highlight targets and pathways more likely to be implicated in the studied phenotype. The method was applied to a cytotoxicity phenotypic endpoint, with enriched targets/pathways found to be statistically significant when compared with 100 random datasets. Application on a smaller apoptotic set (10 molecules) did not allowed to obtain statistically relevant results, suggesting that the protocol requires modification such as analysis of the most frequently predicted targets/annotated pathways. Pathway annotations improved the mechanism-of-action information gained by target prediction alone, allowing a better interpretation of the predictions and providing better mapping of targets onto pathways.

  11. Enhancement of Nucleoside Production in Hirsutella sinensis Based on Biosynthetic Pathway Analysis

    Science.gov (United States)

    Liu, Zhi-Qiang; Zhang, Bo; Lin, Shan; Baker, Peter James; Chen, Mao-Sheng; Xue, Ya-Ping; Wu, Hui; Xu, Feng; Yuan, Shui-Jin; Teng, Yi; Wu, Ling-Fang

    2017-01-01

    To enhance nucleoside production in Hirsutella sinensis, the biosynthetic pathways of purine and pyrimidine nucleosides were constructed and verified. The differential expression analysis showed that purine nucleoside phosphorylase, inosine monophosphate dehydrogenase, and guanosine monophosphate synthase genes involved in purine nucleotide biosynthesis were significantly upregulated 16.56-fold, 8-fold, and 5.43-fold, respectively. Moreover, dihydroorotate dehydrogenase, uridine nucleosidase, uridine/cytidine monophosphate kinase, and inosine triphosphate pyrophosphatase genes participating in pyrimidine nucleoside biosynthesis were upregulated 4.53-fold, 10.63-fold, 4.26-fold, and 5.98-fold, respectively. To enhance the nucleoside production, precursors for synthesis of nucleosides were added based on the analysis of biosynthetic pathways. Uridine and cytidine contents, respectively, reached 5.04 mg/g and 3.54 mg/g when adding 2 mg/mL of ribose, resulting in an increase of 28.6% and 296% compared with the control, respectively. Meanwhile, uridine and cytidine contents, respectively, reached 10.83 mg/g 2.12 mg/g when adding 0.3 mg/mL of uracil, leading to an increase of 176.3% and 137.1%, respectively. This report indicated that fermentation regulation was an effective way to enhance the nucleoside production in H. sinensis based on biosynthetic pathway analysis. PMID:29333435

  12. Identification of Key Pathways and Genes in Advanced Coronary Atherosclerosis Using Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Xiaowen Tan

    2017-01-01

    Full Text Available Background. Coronary artery atherosclerosis is a chronic inflammatory disease. This study aimed to identify the key changes of gene expression between early and advanced carotid atherosclerotic plaque in human. Methods. Gene expression dataset GSE28829 was downloaded from Gene Expression Omnibus (GEO, including 16 advanced and 13 early stage atherosclerotic plaque samples from human carotid. Differentially expressed genes (DEGs were analyzed. Results. 42,450 genes were obtained from the dataset. Top 100 up- and downregulated DEGs were listed. Functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG identification were performed. The result of functional and pathway enrichment analysis indicted that the immune system process played a critical role in the progression of carotid atherosclerotic plaque. Protein-protein interaction (PPI networks were performed either. Top 10 hub genes were identified from PPI network and top 6 modules were inferred. These genes were mainly involved in chemokine signaling pathway, cell cycle, B cell receptor signaling pathway, focal adhesion, and regulation of actin cytoskeleton. Conclusion. The present study indicated that analysis of DEGs would make a deeper understanding of the molecular mechanisms of atherosclerosis development and they might be used as molecular targets and diagnostic biomarkers for the treatment of atherosclerosis.

  13. Metabolic pathway analysis and kinetic studies for production of nattokinase in Bacillus subtilis.

    Science.gov (United States)

    Unrean, Pornkamol; Nguyen, Nhung H A

    2013-01-01

    We have constructed a reaction network model of Bacillus subtilis. The model was analyzed using a pathway analysis tool called elementary mode analysis (EMA). The analysis tool was used to study the network capabilities and the possible effects of altered culturing conditions on the production of a fibrinolytic enzyme, nattokinase (NK) by B. subtilis. Based on all existing metabolic pathways, the maximum theoretical yield for NK synthesis in B. subtilis under different substrates and oxygen availability was predicted and the optimal culturing condition for NK production was identified. To confirm model predictions, experiments were conducted by testing these culture conditions for their influence on NK activity. The optimal culturing conditions were then applied to batch fermentation, resulting in high NK activity. The EMA approach was also applied for engineering B. subtilis metabolism towards the most efficient pathway for NK synthesis by identifying target genes for deletion and overexpression that enable the cell to produce NK at the maximum theoretical yield. The consistency between experiments and model predictions proves the feasibility of EMA being used to rationally design culture conditions and genetic manipulations for the efficient production of desired products.

  14. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

    Science.gov (United States)

    Yang, Yunlai; Arouri, Khaled

    2016-03-01

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  15. GeneAnalytics Pathway Analysis and Genetic Overlap among Autism Spectrum Disorder, Bipolar Disorder and Schizophrenia

    Directory of Open Access Journals (Sweden)

    Naveen S. Khanzada

    2017-02-01

    Full Text Available Bipolar disorder (BPD and schizophrenia (SCH show similar neuropsychiatric behavioral disturbances, including impaired social interaction and communication, seen in autism spectrum disorder (ASD with multiple overlapping genetic and environmental influences implicated in risk and course of illness. GeneAnalytics software was used for pathway analysis and genetic profiling to characterize common susceptibility genes obtained from published lists for ASD (792 genes, BPD (290 genes and SCH (560 genes. Rank scores were derived from the number and nature of overlapping genes, gene-disease association, tissue specificity and gene functions subdivided into categories (e.g., diseases, tissues or functional pathways. Twenty-three genes were common to all three disorders and mapped to nine biological Superpathways including Circadian entrainment (10 genes, score = 37.0, Amphetamine addiction (five genes, score = 24.2, and Sudden infant death syndrome (six genes, score = 24.1. Brain tissues included the medulla oblongata (11 genes, score = 2.1, thalamus (10 genes, score = 2.0 and hypothalamus (nine genes, score = 2.0 with six common genes (BDNF, DRD2, CHRNA7, HTR2A, SLC6A3, and TPH2. Overlapping genes impacted dopamine and serotonin homeostasis and signal transduction pathways, impacting mood, behavior and physical activity level. Converging effects on pathways governing circadian rhythms support a core etiological relationship between neuropsychiatric illnesses and sleep disruption with hypoxia and central brain stem dysfunction.

  16. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways.

    Science.gov (United States)

    Yang, Yunlai; Arouri, Khaled

    2016-03-11

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  17. Data assimilation in hydrological modelling

    DEFF Research Database (Denmark)

    Drecourt, Jean-Philippe

    Data assimilation is an invaluable tool in hydrological modelling as it allows to efficiently combine scarce data with a numerical model to obtain improved model predictions. In addition, data assimilation also provides an uncertainty analysis of the predictions made by the hydrological model....... In this thesis, the Kalman filter is used for data assimilation with a focus on groundwater modelling. However the developed techniques are general and can be applied also in other modelling domains. Modelling involves conceptualization of the processes of Nature. Data assimilation provides a way to deal...... with model non-linearities and biased errors. A literature review analyzes the most popular techniques and their application in hydrological modelling. Since bias is an important problem in groundwater modelling, two bias aware Kalman filters have been implemented and compared using an artificial test case...

  18. Low flow hydrology: a review

    CSIR Research Space (South Africa)

    Smakhtin, VU

    2001-01-10

    Full Text Available The paper intends to review the current status of low-flow hydrology — a discipline which deals with minimum flow in a river during the dry periods of the year. The discussion starts with the analysis of low-flow generating mechanisms operating...

  19. Hydrologic conditions, groundwater quality, and analysis of sink hole formation in the Albany area of Dougherty County, Georgia, 2009

    Science.gov (United States)

    Gordon, Debbie W.; Painter, Jaime A.; McCranie, John M.

    2012-01-01

    The U.S. Geological Survey, in cooperation with the Albany Water, Gas, and Light Commission has conducted water resources investigations and monitored groundwater conditions and availability in the Albany, Georgia, area since 1977. This report presents an overview of hydrologic conditions, water quality, and groundwater studies in the Albany area of Dougherty County, Georgia, during 2009. Historical data also are presented for comparison with 2009 data. During 2009, groundwater-level data were collected in 29 wells in the Albany area to monitor water-level trends in the surficial, Upper Floridan, Claiborne, Clayton, and Providence aquifers. Groundwater-level data from 21 of the 29 wells indicated an increasing trend during 2008–09. Five wells show no trend due to lack of data and three wells have decreasing trends. Period-of-record water levels (period of record ranged between 1957–2009 and 2003–2009) declined slightly in 10 wells and increased slightly in 4 wells tapping the Upper Floridan aquifer; declined in 1 well and increased in 2 wells tapping the Claiborne aquifer; declined in 4 wells and increased in 2 wells tapping the Clayton aquifer; and increased in 1 well tapping the Providence aquifer. Analyses of groundwater samples collected during 2009 from 12 wells in the Upper Floridan aquifer in the vicinity of a well field located southwest of Albany indicate that overall concentrations of nitrate plus nitrite as nitrogen increased slightly from 2008 in 8 wells. A maximum concentration of 12.9 milligrams per liter was found in a groundwater sample from a well located upgradient from the well field. The distinct difference in chemical constituents of water samples collected from the Flint River and samples collected from wells located in the well-field area southwest of Albany indicates that little water exchange occurs between the Upper Floridan aquifer and Flint River where the river flows adjacent to, but downgradient of, the well field. Water

  20. A comparison of the gravity field over Central Europe from superconducting gravimeters, GRACE and global hydrological models, using EOF analysis

    Science.gov (United States)

    Crossley, David; de Linage, Caroline; Hinderer, Jacques; Boy, Jean-Paul; Famiglietti, James

    2012-05-01

    We analyse data from seven superconducting gravimeter (SG) stations in Europe from 2002 to 2007 from the Global Geodynamics Project (GGP) and compare seasonal variations with data from GRACE and several global hydrological models - GLDAS, WGHM and ERA-Interim. Our technique is empirical orthogonal function (EOF) decomposition of the fields that allows for the inherent incompatibility of length scales between ground and satellite observations. GGP stations below the ground surface pose a problem because part of the attraction from soil moisture comes from above the gravimeter, and this gives rise to a complex (mixed) gravity response. The first principle component (PC) of the EOF decomposition is the main indicator for comparing the fields, although for some of the series it accounts for only about 50 per cent of the variance reduction. PCs for GRACE solutions RL04 from CSR and GFZ are filtered with a cosine taper (degrees 20-40) and a Gaussian window (350 km). Significant differences are evident between GRACE solutions from different groups and filters, though they all agree reasonably well with the global hydrological models for the predominantly seasonal signal. We estimate the first PC at 10-d sampling to be accurate to 1 μGal for GGP data, 1.5 μGal for GRACE data and 1 μGal between the three global hydrological models. Within these limits the CNES/GRGS solution and ground GGP data agree at the 79 per cent level, and better when the GGP solution is restricted to the three above-ground stations. The major limitation on the GGP side comes from the water mass distribution surrounding the underground instruments that leads to a complex gravity effect. To solve this we propose a method for correcting the SG residual gravity series for the effects of soil moisture above the station.

  1. ANALYSIS OF THE POSSIBILITY OF USING HYDROLOGICAL MODELS IN STRATEGIC ENVIRONMENTAL ASSESSMENT OF LOCAL SPATIAL DEVELOPMENT PLANS

    OpenAIRE

    Mariusz Sojka; Sadżide Murat-Błażejewska; Rafał Wróżyński

    2014-01-01

    The paper presents the possibility of application of the hydrological model HEC-HMS in the development of a strategic environmental assessment of local spatial development plans on surface water. The practical possibility of using simulation models of catchment response to high intensity precipitation is shown on the example of the Różany Potok watercourse catchment which is subject to rapid urbanization process. The area of Różany Potok catchment is 8.1 km2 and a stream length is 5.57 km. In...

  2. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

    Directory of Open Access Journals (Sweden)

    Jesús Lascorz

    2011-01-01

    Full Text Available Background: A large number of gene expression profiling (GEP studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-regulated in colorectal carcinogenesis. Materials and Methods: We started the analysis with 242 unique annotated genes that had been reported by any of three recent meta-analyses covering GEP studies on genes differentially expressed in carcinoma vs normal mucosa. Most of these genes (218, 91.9% had been reported in at least three GEP studies. These 242 genes were submitted to bioinformatic analysis using a total of nine tools to detect enrichment of Gene Ontology (GO categories or Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. As a final consistency criterion the pathway categories had to be enriched by several tools to be taken into consideration. Results: Our pathway-based enrichment analysis identified the categories of ribosomal protein constituents, extracellular matrix receptor interaction, carbonic anhydrase isozymes, and a general category related to inflammation and cellular response as significantly and consistently overrepresented entities. Conclusions: We triaged the genes covered by the published GEP literature on colorectal carcinogenesis and subjected them to multiple enrichment tools in order to identify the consistently enriched gene categories. These turned out to have known functional relationships to cancer development and thus deserve further investigation.

  3. Uncertainty and sensitivity analysis of food pathway results with the MACCS Reactor Accident Consequence Model

    International Nuclear Information System (INIS)

    Helton, J.C.; Johnson, J.D.; Rollstin, J.A.; Shiver, A.W.; Sprung, J.L.

    1995-01-01

    Uncertainty and sensitivity analysis techniques based on Latin hypercube sampling, partial correlation analysis and stepwise regression analysis are used in an investigation with the MACCS model of the food pathways associated with a severe accident at a nuclear power station. The primary purpose of this study is to provide guidance on the variables to be considered in future review work to reduce the uncertainty in the important variables used in the calculation of reactor accident consequences. The effects of 87 imprecisely-known input variables on the following reactor accident consequences are studied: crop growing season dose, crop long-term dose, milk growing season dose, total food pathways dose, total ingestion pathways dose, total long-term pathways dose, area dependent cost, crop disposal cost, milk disposal cost, condemnation area, crop disposal area and milk disposal area. When the predicted variables are considered collectively, the following input variables were found to be the dominant contributors to uncertainty: fraction of cesium deposition on grain fields that is retained on plant surfaces and transferred directly to grain, maximum allowable ground concentrations of Cs-137 and Sr-90 for production of crops, ground concentrations of Cs-134, Cs-137 and I-131 at which the disposal of milk will be initiated due to accidents that occur during the growing season, ground concentrations of Cs-134, I-131 and Sr-90 at which the disposal of crops will be initiated due to accidents that occur during the growing season, rate of depletion of Cs-137 and Sr-90 from the root zone, transfer of Sr-90 from soil to legumes, transfer of Cs-137 from soil to pasture, transfer of cesium from animal feed to meat, and the transfer of cesium, iodine and strontium from animal feed to milk

  4. Uncertainty and sensitivity analysis of food pathway results with the MACCS reactor accident consequence model

    International Nuclear Information System (INIS)

    Helton, J.C.; Johnson, J.D.; Rollstin, J.A.; Shiver, A.W.; Sprung, J.L.

    1995-01-01

    Uncertainty and sensitivity analysis techniques based on Latin hypercube sampling, partial correlation analysis and stepwise regression analysis are used in an investigation with the MACCS model of the food pathways associated with a severe accident at a nuclear power station. The primary purpose of this study is to provide guidance on the variables to be considered in future review work to reduce the uncertainty in the important variables used in the calculation of reactor accident consequences. The effects of 87 imprecisely-known input variables on the following reactor accident consequences are studied: crop growing-season dose, crop long-term dose, milk growing-season dose, total food pathways dose, total ingestion pathways dose, total long-term pathways dose, area dependent cost, crop disposal cost, milk disposal cost, condemnation area, crop disposal area and milk disposal area. When the predicted variables are considered collectively, the following input variables were found to be the dominant contributors to uncertainty: fraction of cesium deposition on grain fields that is retained on plant surfaces and transferred directly to grain, maximum allowable ground concentrations of Cs-137 and Sr-90 for production of crops, ground concentrations of Cs-134, Cs-137 and I-131 at which the disposal of milk will be initiated due to accidents that occur during the growing season, ground concentrations of Cs-134, I-131 and Sr-90 at which the disposal of crops will be initiated due to accidents that occur during the growing season, rate of depletion of Cs-137 and Sr-90 from the root zone, transfer of Sr-90 from soil to legumes, transfer of Cs-137 from soil to pasture, transfer of cesium from animal feed to meat, and the transfer of cesium, iodine and strontium from animal feed to milk

  5. Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions

    Directory of Open Access Journals (Sweden)

    Studham Matthew E

    2012-07-01

    Full Text Available Abstract Background Phytohormones mediate plant defense responses to pests and pathogens. In particular, the hormones jasmonic acid, ethylene, salicylic acid, and abscisic acid have been shown to dictate and fine-tune defense responses, and identification of the phytohormone components of a particular defense response is commonly used to characterize it. Identification of phytohormone regulation is particularly important in transcriptome analyses. Currently there is no computational tool to determine the relative activity of these hormones that can be applied to transcriptome analyses in soybean. Findings We developed a pathway analysis method that provides a broad measure of the activation or suppression of individual phytohormone pathways based on changes in transcript expression of pathway-related genes. The magnitude and significance of these changes are used to determine a pathway score for a phytohormone for a given comparison in a microarray experiment. Scores for individual hormones can then be compared to determine the dominant phytohormone in a given defense response. To validate this method, it was applied to publicly available data from previous microarray experiments that studied the response of soybean plants to Asian soybean rust and soybean cyst nematode. The results of the analyses for these experiments agreed with our current understanding of the role of phytohormones in these defense responses. Conclusions This method is useful in providing a broad measure of the relative induction and suppression of soybean phytohormones during a defense response. This method could be used as part of microarray studies that include individual transcript analysis, gene set analysis, and other methods for a comprehensive defense response characterization.

  6. Following User Pathways: Cross Platform and Mixed Methods Analysis in Social Media Studies

    DEFF Research Database (Denmark)

    Hall, Margeret; Mazarakis, Athanasios; Peters, Isabella

    2016-01-01

    is the mixed method approach (e.g. qualitative and quantitative methods) in order to better understand how users and society interacts online. The workshop 'Following User Pathways' brings together a community of researchers and professionals to address methodological, analytical, conceptual, and technological......Social media and the resulting tidal wave of available data have changed the ways and methods researchers analyze communities at scale. But the full potential for social scientists (and others) is not yet achieved. Despite the popularity of social media analysis in the past decade, few researchers...... challenges and opportunities of cross-platform, mixed method analysis in social media ecosystems....

  7. Hanford Site Composite Analysis Technical Approach Description: Groundwater Pathway Dose Calculation.

    Energy Technology Data Exchange (ETDEWEB)

    Morgans, D. L. [CH2M Hill Plateau Remediation Company, Richland, WA (United States); Lindberg, S. L. [Intera Inc., Austin, TX (United States)

    2017-09-20

    The purpose of this technical approach document (TAD) is to document the assumptions, equations, and methods used to perform the groundwater pathway radiological dose calculations for the revised Hanford Site Composite Analysis (CA). DOE M 435.1-1, states, “The composite analysis results shall be used for planning, radiation protection activities, and future use commitments to minimize the likelihood that current low-level waste disposal activities will result in the need for future corrective or remedial actions to adequately protect the public and the environment.”

  8. Heading in the right direction: thermodynamics-based network analysis and pathway engineering.

    Science.gov (United States)

    Ataman, Meric; Hatzimanikatis, Vassily

    2015-12-01

    Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Assembly of inflammation-related genes for pathway-focused genetic analysis.

    Directory of Open Access Journals (Sweden)

    Matthew J Loza

    2007-10-01

    Full Text Available Recent identifications of associations between novel variants in inflammation-related genes and several common diseases emphasize the need for systematic evaluations of these genes in disease susceptibility. Considering that many genes are involved in the complex inflammation responses and many genetic variants in these genes have the potential to alter the functions and expression of these genes, we assembled a list of key inflammation-related genes to facilitate the identification of genetic associations of diseases with an inflammation-related etiology. We first reviewed various phases of inflammation responses, including the development of immune cells, sensing of danger, influx of cells to sites of insult, activation and functional responses of immune and non-immune cells, and resolution of the immune response. Assisted by the Ingenuity Pathway Analysis, we then identified 17 functional sub-pathways that are involved in one or multiple phases. This organization would greatly increase the chance of detecting gene-gene interactions by hierarchical clustering of genes with their functional closeness in a pathway. Finally, as an example application, we have developed tagging single nucleotide polymorphism (tSNP arrays for populations of European and African descent to capture all the common variants of these key inflammation-related genes. Assays of these tSNPs have been designed and assembled into two Affymetrix ParAllele customized chips, one each for European (12,011 SNPs and African (21,542 SNPs populations. These tSNPs have greater coverage for these inflammation-related genes compared to the existing genome-wide arrays, particularly in the African population. These tSNP arrays can facilitate systematic evaluation of inflammation pathways in disease susceptibility. For additional applications, other genotyping platforms could also be employed. For existing genome-wide association data, this list of key inflammation-related genes and

  10. Functional pathway analysis of genes associated with response to treatment for chronic hepatitis C.

    Science.gov (United States)

    Birerdinc, A; Afendy, A; Stepanova, M; Younossi, I; Manyam, G; Baranova, A; Younossi, Z M

    2010-10-01

    Chronic hepatitis C (CH-C) is among the most common causes of chronic liver disease. Approximately 50% of patients with CH-C treated with pegylated interferon-α and ribavirin (PEG-IFN-α + RBV) achieve a sustained virological response (SVR). Several factors such as genotype 1, African American (AA) race, obesity and the absence of an early virological response (EVR) are associated with low SVR. This study elucidates molecular pathways deregulated in patients with CH-C with negative predictors of response to antiviral therapy. Sixty-eight patients with CH-C who underwent a full course of treatment with PEG-IFN-α + RBV were included in the study. Pretreatment blood samples were collected in PAXgene™ RNA tubes. EVR, complete EVR (cEVR), and SVR rates were 76%, 57% and 41%, respectively. Total RNA was extracted from pretreatment peripheral blood mononuclear cells, quantified and used for one-step RT-PCR to profile 154 mRNAs. The expression of mRNAs was normalized with six 'housekeeping' genes. Differentially expressed genes were separated into up and downregulated gene lists according to the presence or absence of a risk factor and subjected to KEGG Pathway Painter which allows high-throughput visualization of the pathway-specific changes in expression profiles. The genes were consolidated into the networks associated with known predictors of response. Before treatment, various genes associated with core components of the JAK/STAT pathway were activated in the cohorts least likely to achieve SVR. Genes related to focal adhesion and TGF-β pathways were activated in some patients with negative predictors of response. Pathway-centred analysis of gene expression profiles from treated patients with CH-C points to the Janus kinase-signal transducers and activators of transcription signalling cascade as the major pathogenetic component responsible for not achieving SVR. In addition, focal adhesion and TGF-β pathways are associated with some predictors of response.

  11. Thermodynamics of metabolic pathways for penicillin production: Analysis of thermodynamic feasibility and free energy changes during fed-batch cultivation

    DEFF Research Database (Denmark)

    Pissarra, P.D.; Nielsen, Jens Bredal

    1997-01-01

    This paper describes the thermodynamic analysis of pathways related to penicillin production in Penicillium chrysogenum. First a thermodynamic feasibility analysis is performed of the L-lysine pathway of which one of the precursors for penicillin biosynthesis (alpha-aminoadipic acid......) is an intermediate. It is found that the L-lysine pathway in P. chrysogenum is thermodynamically feasible and that the calculated standard Gibbs free energy values of the two enzymes controlling the pathway flux indicate that they operate far from equilibrium. It is therefore proposed that the regulation of alpha......-aminoadipate reductase by lysine is important to maintain a high concentration of alpha-aminoadipate in order to direct the carbon flux to penicillin production. Secondly the changes in Gibbs free energy in the penicillin biosynthetic pathway during fed-batch cultivation were studied. The analysis showed that all...

  12. Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia.

    Science.gov (United States)

    Wu, Chong; Pan, Wei

    2018-04-01

    Many genetic variants affect complex traits through gene expression, which can be exploited to boost statistical power and enhance interpretation in genome-wide association studies (GWASs) as demonstrated by the transcriptome-wide association study (TWAS) approach. Furthermore, due to polygenic inheritance, a complex trait is often affected by multiple genes with similar functions as annotated in gene pathways. Here, we extend TWAS from gene-based analysis to pathway-based analysis: we integrate public pathway collections, expression quantitative trait locus (eQTL) data and GWAS summary association statistics (or GWAS individual-level data) to identify gene pathways associated with complex traits. The basic idea is to weight the SNPs of the genes in a pathway based on their estimated cis-effects on gene expression, then adaptively test for association of the pathway with a GWAS trait by effectively aggregating possibly weak association signals across the genes in the pathway. The P values can be calculated analytically and thus fast. We applied our proposed test with the KEGG and GO pathways to two schizophrenia (SCZ) GWAS summary association data sets, denoted by SCZ1 and SCZ2 with about 20,000 and 150,000 subjects, respectively. Most of the significant pathways identified by analyzing the SCZ1 data were reproduced by the SCZ2 data. Importantly, we identified 15 novel pathways associated with SCZ, such as GABA receptor complex (GO:1902710), which could not be uncovered by the standard single SNP-based analysis or gene-based TWAS. The newly identified pathways may help us gain insights into the biological mechanism underlying SCZ. Our results showcase the power of incorporating gene expression information and gene functional annotations into pathway-based association testing for GWAS. © 2018 WILEY PERIODICALS, INC.

  13. Pathway-based Analysis of the Hidden Genetic Heterogeneities in Cancers

    Directory of Open Access Journals (Sweden)

    Xiaolei Zhao

    2014-02-01

    Full Text Available Many cancers apparently showing similar phenotypes are actually distinct at the molecular level, leading to very different responses to the same treatment. It has been recently demonstrated that pathway-based approaches are robust and reliable for genetic analysis of cancers. Nevertheless, it remains unclear whether such function-based approaches are useful in deciphering molecular heterogeneities in cancers. Therefore, we aimed to test this possibility in the present study. First, we used a NCI60 dataset to validate the ability of pathways to correctly partition samples. Next, we applied the proposed method to identify the hidden subtypes in diffuse large B-cell lymphoma (DLBCL. Finally, the clinical significance of the identified subtypes was verified using survival analysis. For the NCI60 dataset, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Subsequently, for a DLBCL dataset, we identified three hidden subtypes that showed very different 10-year overall survival rates (90%, 46% and 20% and were highly significantly (P = 0.008 correlated with the clinical survival rate. This study demonstrated that the pathway-based approach is promising for unveiling genetic heterogeneities in complex human diseases.

  14. Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

    Science.gov (United States)

    Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

    2016-09-15

    Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes

    DEFF Research Database (Denmark)

    Pers, Tune H; Timshel, Pascal; Ripke, Stephan

    2016-01-01

    Over 100 associated genetic loci have been robustly associated with schizophrenia. Gene prioritization and pathway analysis have focused on a priori hypotheses and thus may have been unduly influenced by prior assumptions and missed important causal genes and pathways. Using a data-driven approac...

  16. Analysis of acyl CoA ester intermediates of the mevalonate pathway in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Seker, Tamay; Møller, Kasper; Nielsen, Jens

    2005-01-01

    The mevalonate pathway plays an important role in providing the cell with a number of essential precursors for the synthesis of biomass constituents. With respect to their chemical structure, the metabolites of this pathway can be divided into two groups: acyl esters [acetoacetyl CoA, acetyl Co......A, hydroxymethylglutaryl (HMG) CoA] and phosphorylated metabolites (isopentenyl pyrophosphate, dimethylallyl pyrophosphate, geranyl pyrophosphate, farnesyl pyrophosphate). In this study, we developed a method for the precise analysis of the intracellular concentration of acetoacetyl CoA, acetyl CoA and HMG CoA; and we...... used this method for quantification of these metabolites in Saccharomyces cerevisiae, both during batch growth on glucose and on galactose and in glucose-limited chemostat cultures operated at three different dilution rates. The level of the metabolites changed depending on the growth phase...

  17. Acquisition/Diversion Pathway Analysis of the DUPIC Fuel Cycle for the Assessment of Proliferation Resistance

    International Nuclear Information System (INIS)

    Chang, Hong Lae; Ko, Won Il

    2008-01-01

    Within the International Project on Innovative Nuclear Reactors and Fuel Cycles (INPRO) of the IAEA, a methodology for evaluating proliferation resistance (INPRO PR methodology) has been developed in order to provide guidance in using the INPRO methodology. However, it remains to develop the methodology to evaluate User Requirements (UR) 4 regarding multiplicity and robustness of barriers against proliferation (innovative nuclear energy systems should incorporate multiple proliferation resistance features and measures). To develop the assessment procedure and metrics for User Requirement 4 (UR4), the coarse acquisition/ diversion pathway analysis of the DUPIC Fuel Cycle has been performed. The most plausible pathways for the acquisition of weapons-usable nuclear material were identified and analyzed using a systematic approach herein, and future work to complete the assessment approach for the UR4 of the INPRO methodology regarding the multiplicity and robustness of barriers against proliferation are also proposed

  18. Hepatic Proteomic Analysis Revealed Altered Metabolic Pathways in Insulin Resistant Akt1+/-/Akt2-/-Mice

    Science.gov (United States)

    Pedersen, Brian A; Wang, Weiwen; Taylor, Jared F; Khattab, Omar S; Chen, Yu-Han; Edwards, Robert A; Yazdi, Puya G; Wang, Ping H

    2015-01-01

    Objective The aim of this study was to identify liver proteome changes in a mouse model of severe insulin resistance and markedly decreased leptin levels. Methods Two-dimensional differential gel electrophoresis was utilized to identify liver proteome changes in AKT1+/-/AKT2-/- mice. Proteins with altered levels were identified with tandem mass spectrometry. Ingenuity Pathway analysis was performed for the interpretation of the biological significance of the observed proteomic changes. Results 11 proteins were identified from 2 biological replicates to be differentially expressed by a ratio of at least 1.3 between age-matched insulin resistant (Akt1+/-/Akt2-/-) and wild type mice. Albumin and mitochondrial ornithine aminotransferase were detected from multiple spots, which suggest post-translational modifications. Enzymes of the urea cycle were common members of top regulated pathways. Conclusion Our results help to unveil the regulation of the liver proteome underlying altered metabolism in an animal model of severe insulin resistance. PMID:26455965

  19. Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor

    Directory of Open Access Journals (Sweden)

    Wang G

    2018-04-01

    Full Text Available Guang-Yu Wang,1,* Ling Li,2,* Bo Liu,1 Xiao Han,1 Chun-Hua Wang,1 Ji-Wen Wang3 1Department of Neurosurgery, 2Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Jinan, Shandong, 3Department of Neurology, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Pudong New District, Shanghai, People’s Republic of China *These authors contributed equally to this work Purpose: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET. Materials and methods: Gene expression profile of GSE14295 was downloaded from publicly available Gene Expression Omnibus (GEO database. Differentially expressed genes (DEGs were screened out in primary sPNET samples compared with normal fetal and adult brain reference samples (sPNET vs fetal brain and sPNET vs adult brain. Pathway enrichment analysis of these DEGs was conducted, followed by protein–protein interaction (PPI network construction and significant module selection. Additionally, transcription factors (TFs regulating the common DEGs in the two comparison groups were identified, and the regulatory network was constructed. Results: In total, 526 DEGs (99 up- and 427 downregulated in sPNET vs fetal brain and 815 DEGs (200 up- and 615 downregulated in sPNET vs adult brain were identified. DEGs in sPNET vs fetal brain and sPNET vs adult brain were associated with calcium signaling pathway, cell cycle, and p53 signaling pathway. CDK1, CDC20, BUB1B, and BUB1 were hub nodes in the PPI networks of DEGs in sPNET vs fetal brain and sPNET vs adult brain. Significant modules were extracted from the PPI networks. In addition, 64 upregulated and 200 downregulated overlapping DEGs were identified in both sPNET vs fetal brain and sPNET vs adult brain. The genes involved in the regulatory network upon overlapping DEGs and the TFs were correlated with calcium signaling pathway

  20. Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

    Science.gov (United States)

    He, Yue-E; Qiu, Hui-Xian; Jiang, Jian-Bing; Wu, Rong-Zhou; Xiang, Ru-Lian; Zhang, Yuan-Hai

    2017-01-01

    The aim of the present study was to identify key genes that may be involved in the pathogenesis of Tetralogy of Fallot (TOF) using bioinformatics methods. The GSE26125 microarray dataset, which includes cardiovascular tissue samples derived from 16 children with TOF and five healthy age-matched control infants, was downloaded from the Gene Expression Omnibus database. Differential expression analysis was performed between TOF and control samples to identify differentially expressed genes (DEGs) using Student's t-test, and the R/limma package, with a log2 fold-change of >2 and a false discovery rate of <0.01 set as thresholds. The biological functions of DEGs were analyzed using the ToppGene database. The ReactomeFIViz application was used to construct functional interaction (FI) networks, and the genes in each module were subjected to pathway enrichment analysis. The iRegulon plugin was used to identify transcription factors predicted to regulate the DEGs in the FI network, and the gene-transcription factor pairs were then visualized using Cytoscape software. A total of 878 DEGs were identified, including 848 upregulated genes and 30 downregulated genes. The gene FI network contained seven function modules, which were all comprised of upregulated genes. Genes enriched in Module 1 were enriched in the following three neurological disorder-associated signaling pathways: Parkinson's disease, Alzheimer's disease and Huntington's disease. Genes in Modules 0, 3 and 5 were dominantly enriched in pathways associated with ribosomes and protein translation. The Xbox binding protein 1 transcription factor was demonstrated to be involved in the regulation of genes encoding the subunits of cytoplasmic and mitochondrial ribosomes, as well as genes involved in neurodegenerative disorders. Therefore, dysfunction of genes involved in signaling pathways associated with neurodegenerative disorders, ribosome function and protein translation may contribute to the pathogenesis of TOF

  1. Hydrologic design methodologies for small-scale hydro at ungauged sites. Phase 2A, British Columbia. Summary report. Integrated method for power analysis (IMP)

    Energy Technology Data Exchange (ETDEWEB)

    1986-01-01

    Analysis of the feasibility of sites for small-scale hydroelectric power generation in British Columbia can be a difficult process in cases where gauged streamflow data are not available. This report outlines the capabilities of a package of computer programs, designed to aid the planner of small-scale hydro projects in evaluating the hydrology and energy potential of ungauged sites in that province. The programs were developed by using appropriate programming and hydrological research that had already been done, and taking advantage of experience already available from previous use of components of the package. As the province's mountainous terrain, with numerous microclimates, precluded use of methods of regional analysis based on regression or comparison with gauged streams, the package was developed on the basis of a conceptual model of physical processes on the land and in the atmosphere. The resulting package, the Integrated Method for Power Analysis, consists of five basic components: an atmospheric model of annual precipitation and one-in-ten-year 24-h maximum rainfall; a watershed model that will generate streamflow data based on information from the atmospheric model; a flood frequency analysis system that uses site-specific topographic information and information from the atmospheric model to generate a flood frequency curve; a hydroelectric power simulation program which determines the daily energy output for a run-of-river or reservoir storage site; and a graphics analysis package that provides direct visualization of atmospheric and streamflow data, and the results of watershed and power simulation modelling. 2 figs., 1 tab.

  2. Aligning Event Logs to Task-Time Matrix Clinical Pathways in BPMN for Variance Analysis.

    Science.gov (United States)

    Yan, Hui; Van Gorp, Pieter; Kaymak, Uzay; Lu, Xudong; Ji, Lei; Chiau, Choo Chiap; Korsten, Hendrikus H M; Duan, Huilong

    2018-03-01

    Clinical pathways (CPs) are popular healthcare management tools to standardize care and ensure quality. Analyzing CP compliance levels and variances is known to be useful for training and CP redesign purposes. Flexible semantics of the business process model and notation (BPMN) language has been shown to be useful for the modeling and analysis of complex protocols. However, in practical cases one may want to exploit that CPs often have the form of task-time matrices. This paper presents a new method parsing complex BPMN models and aligning traces to the models heuristically. A case study on variance analysis is undertaken, where a CP from the practice and two large sets of patients data from an electronic medical record (EMR) database are used. The results demonstrate that automated variance analysis between BPMN task-time models and real-life EMR data are feasible, whereas that was not the case for the existing analysis techniques. We also provide meaningful insights for further improvement.

  3. Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

    Science.gov (United States)

    Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

    2015-03-09

    Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 "pathway phenotypes" that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold ([Formula: see text]). These phenotypes are more heritable ([Formula: see text]) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. Copyright © 2015 Brown et al.

  4. A coupled hydrological-hydraulic flood inundation model calibrated using post-event measurements and integrated uncertainty analysis in a poorly gauged Mediterranean basin

    Science.gov (United States)

    Hdeib, Rouya; Abdallah, Chadi; Moussa, Roger; Colin, Francois

    2017-04-01

    Developing flood inundation maps of defined exceedance probabilities is required to provide information on the flood hazard and the associated risk. A methodology has been developed to model flood inundation in poorly gauged basins, where reliable information on the hydrological characteristics of floods are uncertain and partially captured by the traditional rain-gauge networks. Flood inundation is performed through coupling a hydrological rainfall-runoff (RR) model (HEC-HMS) with a hydraulic model (HEC-RAS). The RR model is calibrated against the January 2013 flood event in the Awali River basin, Lebanon (300 km2), whose flood peak discharge was estimated by post-event measurements. The resulting flows of the RR model are defined as boundary conditions of the hydraulic model, which is run to generate the corresponding water surface profiles and calibrated against 20 post-event surveyed cross sections after the January-2013 flood event. An uncertainty analysis is performed to assess the results of the models. Consequently, the coupled flood inundation model is simulated with design storms and flood inundation maps are generated of defined exceedance probabilities. The peak discharges estimated by the simulated RR model were in close agreement with the results from different empirical and statistical methods. This methodology can be extended to other poorly gauged basins facing common stage-gauge failure or characterized by floods with a stage exceeding the gauge measurement level, or higher than that defined by the rating curve.

  5. Analysis of uses and competitions of water resources or an original dissemination strategy of hydrological modelling results of an EU project ?

    Science.gov (United States)

    La Jeunesse, Isabelle; Fustec, Klervi; Larrue, Corinne; Trottier, Julie

    2010-05-01

    We propose to address the question of security threats through an analysis of water uses and competitions in the current situation, on one hand, and in conditions of climate change, on the other hand, in order to have an operational dissemination of hydrological modelling results. This will be carried out for each case study of the EU project CLIMB (7th EU FP). In this particular case, climate change impacts are to be considered in relation with water uses and rivalries. Taking them into account while involving stakeholders should allow us to have a deep impact on water uses regulation under conditions of climate change. The originality of this methodology, the first objective of which within the project is to disseminate project results and interact with stakeholders, is to use the dissemination phase as a means of involving stakeholder knowledge concerning water uses and competitions. The idea is to let the stakeholders identify themselves, in each case study, by means of interactive methods, the impact of the change of hydrological regime on their own water uses and competitions. We propose to use a real "bottom-up" strategy to assess the potential water uses and rivalries in the context of water scarcity (or flood) due to climate change. Such an approach will allow us to evaluate the risk of an increase in water rivalries and threats to security following climate change impacts scenarios at the river basin scale.

  6. Pathways of early fatherhood, marriage, and employment: a latent class growth analysis.

    Science.gov (United States)

    Dariotis, Jacinda K; Pleck, Joseph H; Astone, Nan M; Sonenstein, Freya L

    2011-05-01

    In the National Longitudinal Survey of Youth 1979 (NLSY79), young fathers include heterogeneous subgroups with varying early life pathways in terms of fatherhood timing, the timing of first marriage, and holding full-time employment. Using latent class growth analysis with 10 observations between ages 18 and 37, we derived five latent classes with median ages of first fatherhood below the cohort median (26.4), constituting distinct early fatherhood pathways representing 32.4% of NLSY men: (A) Young Married Fathers, (B) Teen Married Fathers, (C) Young Underemployed Married Fathers, (D) Young Underemployed Single Fathers, and (E) Young Later-Marrying Fathers. A sixth latent class of men who become fathers around the cohort median, following full-time employment and marriage (On-Time On-Sequence Fathers), is the comparison group. With sociodemographic background controlled, all early fatherhood pathways show disadvantage in at least some later-life circumstances (earnings, educational attainment, marital status, and incarceration). The extent of disadvantage is greater when early fatherhood occurs at relatively younger ages (before age 20), occurs outside marriage, or occurs outside full-time employment. The relative disadvantage associated with early fatherhood, unlike early motherhood, increases over the life course.

  7. Geographic Information System and Remote Sensing Approach with Hydrologic Rational Model for Flood Event Analysis in Jakarta

    Science.gov (United States)

    Aditya, M. R.; Hernina, R.; Rokhmatuloh

    2017-12-01

    Rapid development in Jakarta which generates more impervious surface has reduced the amount of rainfall infiltration into soil layer and increases run-off. In some events, continuous high rainfall intensity could create sudden flood in Jakarta City. This article used rainfall data of Jakarta during 10 February 2015 to compute rainfall intensity and then interpolate it with ordinary kriging technique. Spatial distribution of rainfall intensity then overlaid with run-off coefficient based on certain land use type of the study area. Peak run-off within each cell resulted from hydrologic rational model then summed for the whole study area to generate total peak run-off. For this study area, land use types consisted of 51.9 % industrial, 37.57% parks, and 10.54% residential with estimated total peak run-off 6.04 m3/sec, 0.39 m3/sec, and 0.31 m3/sec, respectively.

  8. Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE Cohorts

    Directory of Open Access Journals (Sweden)

    Unjin Shim

    2014-12-01

    Full Text Available Metabolic syndrome (MetS is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs, important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs, explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m2. A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10-6, and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10-7, Bonferroni-adjusted p < 0.05. Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF, the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.

  9. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  10. Genome-Wide Gene Set Analysis for Identification of Pathways Associated with Alcohol Dependence

    Science.gov (United States)

    Biernacka, Joanna M.; Geske, Jennifer; Jenkins, Gregory D.; Colby, Colin; Rider, David N.; Karpyak, Victor M.; Choi, Doo-Sup; Fridley, Brooke L.

    2013-01-01

    It is believed that multiple genetic variants with small individual effects contribute to the risk of alcohol dependence. Such polygenic effects are difficult to detect in genome-wide association studies that test for association of the phenotype with each single nucleotide polymorphism (SNP) individually. To overcome this challenge, gene set analysis (GSA) methods that jointly test for the effects of pre-defined groups of genes have been proposed. Rather than testing for association between the phenotype and individual SNPs, these analyses evaluate the global evidence of association with a set of related genes enabling the identification of cellular or molecular pathways or biological processes that play a role in development of the disease. It is hoped that by aggregating the evidence of association for all available SNPs in a group of related genes, these approaches will have enhanced power to detect genetic associations with complex traits. We performed GSA using data from a genome-wide study of 1165 alcohol dependent cases and 1379 controls from the Study of Addiction: Genetics and Environment (SAGE), for all 200 pathways listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Results demonstrated a potential role of the “Synthesis and Degradation of Ketone Bodies” pathway. Our results also support the potential involvement of the “Neuroactive Ligand Receptor Interaction” pathway, which has previously been implicated in addictive disorders. These findings demonstrate the utility of GSA in the study of complex disease, and suggest specific directions for further research into the genetic architecture of alcohol dependence. PMID:22717047

  11. Aligning ontologies and integrating textual evidence for pathway analysis of microarray data

    Energy Technology Data Exchange (ETDEWEB)

    Gopalan, Banu; Posse, Christian; Sanfilippo, Antonio P.; Stenzel-Poore, Mary; Stevens, S.L.; Castano, Jose; Beagley, Nathaniel; Riensche, Roderick M.; Baddeley, Bob; Simon, R.P.; Pustejovsky, James

    2006-10-08

    Expression arrays are introducing a paradigmatic change in biology by shifting experimental approaches from single gene studies to genome-level analysis, monitoring the ex-pression levels of several thousands of genes in parallel. The massive amounts of data obtained from the microarray data needs to be integrated and interpreted to infer biological meaning within the context of information-rich pathways. In this paper, we present a methodology that integrates textual information with annotations from cross-referenced ontolo-gies to map genes to pathways in a semi-automated way. We illustrate this approach and compare it favorably to other tools by analyzing the gene expression changes underlying the biological phenomena related to stroke. Stroke is the third leading cause of death and a major disabler in the United States. Through years of study, researchers have amassed a significant knowledge base about stroke, and this knowledge, coupled with new technologies, is providing a wealth of new scientific opportunities. The potential for neu-roprotective stroke therapy is enormous. However, the roles of neurogenesis, angiogenesis, and other proliferative re-sponses in the recovery process following ischemia and the molecular mechanisms that lead to these processes still need to be uncovered. Improved annotation of genomic and pro-teomic data, including annotation of pathways in which genes and proteins are involved, is required to facilitate their interpretation and clinical application. While our approach is not aimed at replacing existing curated pathway databases, it reveals multiple hidden relationships that are not evident with the way these databases analyze functional groupings of genes from the Gene Ontology.

  12. Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

    Directory of Open Access Journals (Sweden)

    Yang X

    2018-03-01

    Full Text Available Xiao Yang,1 Shaoming Zhu,2 Li Li,3 Li Zhang,1 Shu Xian,1 Yanqing Wang,1 Yanxiang Cheng1 1Department of Obstetrics and Gynecology, 2Department of Urology, Renmin Hospital of Wuhan University, 3Department of Pharmacology, Wuhan University Health Science Center, Wuhan, Hubei, People’s Republic of China Background: The mortality rate associated with ovarian cancer ranks the highest among gynecological malignancies. However, the cause and underlying molecular events of ovarian cancer are not clear. Here, we applied integrated bioinformatics to identify key pathogenic genes involved in ovarian cancer and reveal potential molecular mechanisms. Results: The expression profiles of GDS3592, GSE54388, and GSE66957 were downloaded from the Gene Expression Omnibus (GEO database, which contained 115 samples, including 85 cases of ovarian cancer samples and 30 cases of normal ovarian samples. The three microarray datasets were integrated to obtain differentially expressed genes (DEGs and were deeply analyzed by bioinformatics methods. The gene ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathway enrichments of DEGs were performed by DAVID and KOBAS online analyses, respectively. The protein–protein interaction (PPI networks of the DEGs were constructed from the STRING database. A total of 190 DEGs were identified in the three GEO datasets, of which 99 genes were upregulated and 91 genes were downregulated. GO analysis showed that the biological functions of DEGs focused primarily on regulating cell proliferation, adhesion, and differentiation and intracellular signal cascades. The main cellular components include cell membranes, exosomes, the cytoskeleton, and the extracellular matrix. The molecular functions include growth factor activity, protein kinase regulation, DNA binding, and oxygen transport activity. KEGG pathway analysis showed that these DEGs were mainly involved in the Wnt signaling pathway, amino acid metabolism, and the

  13. Automated retinofugal visual pathway reconstruction with multi-shell HARDI and FOD-based analysis.

    Science.gov (United States)

    Kammen, Alexandra; Law, Meng; Tjan, Bosco S; Toga, Arthur W; Shi, Yonggang

    2016-01-15

    Diffusion MRI tractography provides a non-invasive modality to examine the human retinofugal projection, which consists of the optic nerves, optic chiasm, optic tracts, the lateral geniculate nuclei (LGN) and the optic radiations. However, the pathway has several anatomic features that make it particularly challenging to study with tractography, including its location near blood vessels and bone-air interface at the base of the cerebrum, crossing fibers at the chiasm, somewhat-tortuous course around the temporal horn via Meyer's Loop, and multiple closely neighboring fiber bundles. To date, these unique complexities of the visual pathway have impeded the development of a robust and automated reconstruction method using tractography. To overcome these challenges, we develop a novel, fully automated system to reconstruct the retinofugal visual pathway from high-resolution diffusion imaging data. Using multi-shell, high angular resolution diffusion imaging (HARDI) data, we reconstruct precise fiber orientation distributions (FODs) with high order spherical harmonics (SPHARM) to resolve fiber crossings, which allows the tractography algorithm to successfully navigate the complicated anatomy surrounding the retinofugal pathway. We also develop automated algorithms for the identification of ROIs used for fiber bundle reconstruction. In particular, we develop a novel approach to extract the LGN region of interest (ROI) based on intrinsic shape analysis of a fiber bundle computed from a seed region at the optic chiasm to a target at the primary visual cortex. By combining automatically identified ROIs and FOD-based tractography, we obtain a fully automated system to compute the main components of the retinofugal pathway, including the optic tract and the optic radiation. We apply our method to the multi-shell HARDI data of 215 subjects from the Human Connectome Project (HCP). Through comparisons with post-mortem dissection measurements, we demonstrate the retinotopic

  14. Point Analysis in Java applied to histological images of the perforant pathway: a user's account.

    Science.gov (United States)

    Scorcioni, Ruggero; Wright, Susan N; Patrick Card, J; Ascoli, Giorgio A; Barrionuevo, Germán

    2008-01-01

    The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (x2 objective) comprised the entire perforant pathway, while the high magnification set (x100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

  15. RAMM: a system of computer programs for radionuclide pathway analysis calculations

    International Nuclear Information System (INIS)

    Lyon, R.B.

    1976-09-01

    A generalized system of computer programs, designated RAMM (Radioactive Materials Management) system, has been developed to assist in the analysis of the movement of radionuclides through the environment to man. RAMM incorporates the GASP IV continuous/discrete simulation system. A nodal approach is used whereby the system to be analyzed is split up into parts small enough that the distribution of nuclides within the node may be taken to be homogeneous. Pathways are defined between nodes, and appropriate transfer coefficients are input or generated. Output includes the time dependent contents of the nodes and dose rates, integrated doses and dose commitments of selected nodes. (author)

  16. Understanding alternative fluxes/effluxes through comparative metabolic pathway analysis of phylum actinobacteria using a simplified approach.

    Science.gov (United States)

    Verma, Mansi; Lal, Devi; Saxena, Anjali; Anand, Shailly; Kaur, Jasvinder; Kaur, Jaspreet; Lal, Rup

    2013-12-01

    Actinobacteria are known for their diverse metabolism and physiology. Some are dreadful human pathogens whereas some constitute the natural flora for human gut. Therefore, the understanding of metabolic pathways is a key feature for targeting the pathogenic bacteria without disturbing the symbiotic ones. A big challenge faced today is multiple drug resistance by Mycobacterium and other pathogens that utilize alternative fluxes/effluxes. With the availability of genome sequence, it is now feasible to conduct the comparative in silico analysis. Here we present a simplified approach to compare metabolic pathways so that the species specific enzyme may be traced and engineered for future therapeutics. The analyses of four key carbohydrate metabolic pathways, i.e., glycolysis, pyruvate metabolism, tri carboxylic acid cycle and pentose phosphate pathway suggest the presence of alternative fluxes. It was found that the upper pathway of glycolysis was highly variable in the actinobacterial genomes whereas lower glycolytic pathway was highly conserved. Likewise, pentose phosphate pathway was well conserved in contradiction to TCA cycle, which was found to be incomplete in majority of actinobacteria. The clustering based on presence and absence of genes of these metabolic pathways clearly revealed that members of different genera shared identical pathways and, therefore, provided an easy method to identify the metabolic similarities/differences between pathogenic and symbiotic organisms. The analyses could identify isoenzymes and some key enzymes that were found to be missing in some pathogenic actinobacteria. The present work defines a simple approach to explore the effluxes in four metabolic pathways within the phylum actinobacteria. The analysis clearly reflects that actinobacteria exhibit diverse routes for metabolizing substrates. The pathway comparison can help in finding the enzymes that can be used as drug targets for pathogens without effecting symbiotic organisms

  17. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and fourier transform-ion cyclotron resonance mass spectrometry

    International Nuclear Information System (INIS)

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

    2006-01-01

    It has been proposed that during growth under anaerobic or oxygen-limited conditions Shewanella oneidensis MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew S. oneidensis MR-1 on [1-13C] lactate as the sole carbon source with either trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicates that a large percentage (>75 percent) of lactate was partially oxidized to either acetate or pyruvate. The 13C isotope distributions in amino acids and other key metabolites indicate that, under anaerobic conditions, a complete serine pathway is not present, and lactate is oxidized via a highly reversible serine degradation pathway. The labeling data also suggest significant activity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutaratede hydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in S. oneidensis MR-1 under TMAO reduction condition

  18. Transcriptome analysis of bitter acid biosynthesis and precursor pathways in hop (Humulus lupulus

    Directory of Open Access Journals (Sweden)

    Clark Shawn M

    2013-01-01

    Full Text Available Abstract Background Bitter acids (e.g. humulone are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus which are important contributors to the bitter flavour and stability of beer. Bitter acids are formed from acyl-CoA precursors derived from branched-chain amino acid (BCAA degradation and C5 prenyl diphosphates from the methyl-D-erythritol 4-phosphate (MEP pathway. We used RNA sequencing (RNA-seq to obtain the transcriptomes of isolated lupulin glands, cones with glands removed and leaves from high α-acid hop cultivars, and analyzed these datasets for genes involved in bitter acid biosynthesis including the supply of major precursors. We also measured the levels of BCAAs, acyl-CoA intermediates, and bitter acids in glands, cones and leaves. Results Transcripts encoding all the enzymes of BCAA metabolism were significantly more abundant in lupulin glands, indicating that BCAA biosynthesis and subsequent degradation occurs in these specialized cells. Branched-chain acyl-CoAs and bitter acids were present at higher levels in glands compared with leaves and cones. RNA-seq analysis showed the gland-specific expression of the MEP pathway, enzymes of sucrose degradation and several transcription factors that may regulate bitter acid biosynthesis in glands. Two branched-chain aminotransferase (BCAT enzymes, HlBCAT1 and HlBCAT2, were abundant, with gene expression quantification by RNA-seq and qRT-PCR indicating that HlBCAT1 was specific to glands while HlBCAT2 was present in glands, cones and leaves. Recombinant HlBCAT1 and HlBCAT2 catalyzed forward (biosynthetic and reverse (catabolic reactions with similar kinetic parameters. HlBCAT1 is targeted to mitochondria where it likely plays a role in BCAA catabolism. HlBCAT2 is a plastidial enzyme likely involved in BCAA biosynthesis. Phylogenetic analysis of the hop BCATs and those from other plants showed that they group into distinct biosynthetic (plastidial and

  19. Identification and pathway analysis of microRNAs with no previous involvement in breast cancer.

    Directory of Open Access Journals (Sweden)

    Sandra Romero-Cordoba

    Full Text Available microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value = 0.05, Fold Change = 2 in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand. The expression of 14 microRNAs was replicated in an independent set of 55 tumors. Bioinformatic analysis of mRNA targets of the altered miRNAs, identified oncogenes like ERBB2, YY1, several MAP kinases, and known tumor-suppressors like FOXA1 and SMAD4. Pathway analysis identified that some biological process which are important in breast carcinogenesis are affected by the altered microRNA expression, including signaling through MAP kinases and TP53 pathways, as well as biological processes like cell death and communication, focal adhesion and ERBB2-ERBB3 signaling. Our data identified the altered expression of several microRNAs whose aberrant expression might have an important impact on cancer-related cellular pathways and whose role in breast cancer has not been previously described.

  20. Multi-criteria decision analysis of energy system transformation pathways: A case study for Switzerland

    International Nuclear Information System (INIS)

    Volkart, Kathrin; Weidmann, Nicolas; Bauer, Christian; Hirschberg, Stefan

    2017-01-01

    Two recent political decisions are expected to frame the development of the Swiss energy system in the coming decades: the nuclear phase-out and the greenhouse gas (GHG) emission reduction target. To accomplish both of them, low-carbon technologies based on renewable energy and Carbon Capture and Storage (CCS) are expected to gain importance. The objective of the present work is to support prospective Swiss energy policy-making by providing a detailed sustainability analysis of possible energy system transformation pathways. For this purpose, the results of the scenario quantification with an energy system model are coupled with multi-criteria sustainability analysis. Two climate protection and one reference scenario are addressed, and the trade-offs between the scenarios are analysed based on a set of 12 interdisciplinary indicators. Implementing a stringent climate policy in Switzerland is associated with co-benefits such as less fossil resource use, less fatalities in severe accidents in the energy sector, less societal conflicts and higher resource autonomy. The availability and implementation of CCS allows for achieving the GHG emission reduction target at lower costs, but at the expense of a more fossil fuel-based energy system. - Highlights: • Three energy system transformation pathways for Switzerland are analysed. • A set of policy-relevant sustainability indicators are quantified for each pathway. • Implementing a stringent climate policy in Switzerland is associated with co-benefits. • In the CCS scenario fossil fuel use increases, but the total system costs are lower. • Fossil-fuelled transport substantially contributes to most of the addressed criteria.

  1. Automated tool for virtual screening and pharmacology-based pathway prediction and analysis

    Directory of Open Access Journals (Sweden)

    Sugandh Kumar

    2017-10-01

    Full Text Available The virtual screening is an effective tool for the lead identification in drug discovery. However, there are limited numbers of crystal structures available as compared to the number of biological sequences which makes (Structure Based Drug Discovery SBDD a difficult choice. The current tool is an attempt to automate the protein structure modelling and automatic virtual screening followed by pharmacology-based prediction and analysis. Starting from sequence(s, this tool automates protein structure modelling, binding site identification, automated docking, ligand preparation, post docking analysis and identification of hits in the biological pathways that can be modulated by a group of ligands. This automation helps in the characterization of ligands selectivity and action of ligands on a complex biological molecular network as well as on individual receptor. The judicial combination of the ligands binding different receptors can be used to inhibit selective biological pathways in a disease. This tool also allows the user to systemically investigate network-dependent effects of a drug or drug candidate.

  2. Perturbations in amino acids and metabolic pathways in osteoarthritis patients determined by targeted metabolomics analysis.

    Science.gov (United States)

    Chen, Rui; Han, Su; Liu, Xuefeng; Wang, Kunpeng; Zhou, Yong; Yang, Chundong; Zhang, Xi

    2018-05-15

    Osteoarthritis (OA) is a degenerative synovial joint disease affecting people worldwide. However, the exact pathogenesis of OA remains unclear. Metabolomics analysis was performed to obtain insight into possible pathogenic mechanisms and diagnostic biomarkers of OA. Ultra-high performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-TQ-MS), followed by multivariate statistical analysis, was used to determine the serum amino acid profiles of 32 OA patients and 35 healthy controls. Variable importance for project values and Student's t-test were used to determine the metabolic abnormalities in OA. Another 30 OA patients were used as independent samples to validate the alterations in amino acids. MetaboAnalyst was used to identify the key amino acid pathways and construct metabolic networks describing their relationships. A total of 25 amino acids and four biogenic amines were detected by UPLC-TQ-MS. Differences in amino acid profiles were found between the healthy controls and OA patients. Alanine, γ-aminobutyric acid and 4-hydroxy-l-proline were important biomarkers distinguishing OA patients from healthy controls. The metabolic pathways with the most significant effects were involved in metabolism of alanine, aspartate, glutamate, arginine and proline. The results of this study improve understanding of the amino acid metabolic abnormalities and pathogenic mechanisms of OA at the molecular level. The metabolic perturbations may be important for the diagnosis and prevention of OA. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. A meta-analysis of biomarkers related to oxidative stress and nitric oxide pathway in migraine.

    Science.gov (United States)

    Neri, Monica; Frustaci, Alessandra; Milic, Mirta; Valdiglesias, Vanessa; Fini, Massimo; Bonassi, Stefano; Barbanti, Piero

    2015-09-01

    Oxidative and nitrosative stress are considered key events in the still unclear pathophysiology of migraine. Studies comparing the level of biomarkers related to nitric oxide (NO) pathway/oxidative stress in the blood/urine of migraineurs vs. unaffected controls were extracted from the PubMed database. Summary estimates of mean ratios (MR) were carried out whenever a minimum of three papers were available. Nineteen studies were included in the meta-analyses, accounting for more than 1000 patients and controls, and compared with existing literature. Most studies measuring superoxide dismutase (SOD) showed lower activity in cases, although the meta-analysis in erythrocytes gave null results. On the contrary, plasma levels of thiobarbituric acid reactive substances (TBARS), an aspecific biomarker of oxidative damage, showed a meta-MR of 2.20 (95% CI: 1.65-2.93). As for NOs, no significant results were found in plasma, serum and urine. However, higher levels were shown during attacks, in patients with aura, and an effect of diet was found. The analysis of glutathione precursor homocysteine and asymmetric dimethylarginine (ADMA), an NO synthase inhibitor, gave inconclusive results. The role of the oxidative pathway in migraine is still uncertain. Interesting evidence emerged for TBARS and SOD, and concerning the possible role of diet in the control of NOx levels. © International Headache Society 2015.

  4. Pathway-based analysis of a melanoma genome-wide association study: analysis of genes related to tumour-immunosuppression.

    Directory of Open Access Journals (Sweden)

    Nils Schoof

    Full Text Available Systemic immunosuppression is a risk factor for melanoma, and sunburn-induced immunosuppression is thought to be causal. Genes in immunosuppression pathways are therefore candidate melanoma-susceptibility genes. If variants within these genes individually have a small effect on disease risk, the association may be undetected in genome-wide association (GWA studies due to low power to reach a high significance level. Pathway-based approaches have been suggested as a method of incorporating a priori knowledge into the analysis of GWA studies. In this study, the association of 1113 single nucleotide polymorphisms (SNPs in 43 genes (39 genomic regions related to immunosuppression have been analysed using a gene-set approach in 1539 melanoma cases and 3917 controls from the GenoMEL consortium GWA study. The association between melanoma susceptibility and the whole set of tumour-immunosuppression genes, and also predefined functional subgroups of genes, was considered. The analysis was based on a measure formed by summing the evidence from the most significant SNP in each gene, and significance was evaluated empirically by case-control label permutation. An association was found between melanoma and the complete set of genes (p(emp=0.002, as well as the subgroups related to the generation of tolerogenic dendritic cells (p(emp=0.006 and secretion of suppressive factors (p(emp=0.0004, thus providing preliminary evidence of involvement of tumour-immunosuppression gene polymorphisms in melanoma susceptibility. The analysis was repeated on a second phase of the GenoMEL study, which showed no evidence of an association. As one of the first attempts to replicate a pathway-level association, our results suggest that low power and heterogeneity may present challenges.

  5. Fundamentals of watershed hydrology

    Science.gov (United States)

    Pamela J. Edwards; Karl W.J. Williard; Jon E. Schoonover

    2015-01-01

    This is a primer about hydrology, the science of water. Watersheds are the basic land unit for water resource management and their delineation, importance, and variation are explained and illustrated. The hydrologic cycle and its components (precipitation, evaporation, transpiration, soil water, groundwater, and streamflow) which collectively provide a foundation for...

  6. Hands-On Hydrology

    Science.gov (United States)

    Mathews, Catherine E.; Monroe, Louise Nelson

    2004-01-01

    A professional school and university collaboration enables elementary students and their teachers to explore hydrology concepts and realize the beneficial functions of wetlands. Hands-on experiences involve young students in determining water quality at field sites after laying the groundwork with activities related to the hydrologic cycle,…

  7. Hydrologic Services Course.

    Science.gov (United States)

    National Oceanic and Atmospheric Administration (DOC), Rockville, MD. National Weather Service.

    A course to develop an understanding of the scope of water resource activities, of the need for forecasting, of the National Weather Service's role in hydrology, and of the proper procedures to follow in fulfilling this role is presented. The course is one of self-help, guided by correspondence. Nine lessons are included: (1) Hydrology in the…

  8. Arid Zone Hydrology

    Science.gov (United States)

    Arid zone hydrology encompasses a wide range of topics and hydro-meteorological and ecological characteristics. Although arid and semi-arid watersheds perform the same functions as those in humid environments, their hydrology and sediment transport characteristics cannot be readily predicted by inf...

  9. Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database

    Directory of Open Access Journals (Sweden)

    Wang Tiansong

    2009-09-01

    Full Text Available Abstract Background Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins. Results Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription. Conclusion Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells

  10. ANALYSIS OF THE POSSIBILITY OF USING HYDROLOGICAL MODELS IN STRATEGIC ENVIRONMENTAL ASSESSMENT OF LOCAL SPATIAL DEVELOPMENT PLANS

    Directory of Open Access Journals (Sweden)

    Mariusz Sojka

    2014-10-01

    Full Text Available The paper presents the possibility of application of the hydrological model HEC-HMS in the development of a strategic environmental assessment of local spatial development plans on surface water. The practical possibility of using simulation models of catchment response to high intensity precipitation is shown on the example of the Różany Potok watercourse catchment which is subject to rapid urbanization process. The area of Różany Potok catchment is 8.1 km2 and a stream length is 5.57 km. In the years 1992–2012 there was a significant increase in impervious areas in the catchment of about 5.2 to 16%. In addition, new local spatial development plans are prepared within the catchment area. The implementation of their records may contribute to the increase in the proportion of impervious areas to over 20%. The increase in the share of impervious areas in the catchment area and traditional approach of precipitation water management can lead to doubling flood flows and increase the risk of local flooding.

  11. Flood evolution assessment and monitoring using hydrological modelling techniques: analysis of the inundation areas at a regional scale

    Science.gov (United States)

    Podhoranyi, M.; Kuchar, S.; Portero, A.

    2016-08-01

    The primary objective of this study is to present techniques that cover usage of a hydrodynamic model as the main tool for monitoring and assessment of flood events while focusing on modelling of inundation areas. We analyzed the 2010 flood event (14th May - 20th May) that occurred in the Moravian-Silesian region (Czech Republic). Under investigation were four main catchments: Opava, Odra, Olše and Ostravice. Four hydrodynamic models were created and implemented into the Floreon+ platform in order to map inundation areas that arose during the flood event. In order to study the dynamics of the water, we applied an unsteady flow simulation for the entire area (HEC-RAS 4.1). The inundation areas were monitored, evaluated and recorded semi-automatically by means of the Floreon+ platform. We focused on information about the extent and presence of the flood areas. The modeled flooded areas were verified by comparing them with real data from different sources (official reports, aerial photos and hydrological networks). The study confirmed that hydrodynamic modeling is a very useful tool for mapping and monitoring of inundation areas. Overall, our models detected 48 inundation areas during the 2010 flood event.

  12. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

    Science.gov (United States)

    Klamt, Steffen; Gerstl, Matthias P.; Jungreuthmayer, Christian; Mahadevan, Radhakrishnan; Müller, Stefan

    2017-01-01

    Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks. PMID:28406903

  13. Quantitative historical hydrology in Europe

    Czech Academy of Sciences Publication Activity Database

    Benito, J.; Brázdil, Rudolf; Herget, J.; Machado, M. J.

    2015-01-01

    Roč. 19, č. 8 (2015), s. 3517-3539 ISSN 1027-5606 R&D Projects: GA ČR GA13-19831S Institutional support: RVO:67179843 Keywords : flood frequency-analysis * ne iberian peninsula * reconstructing peak discharges * extreme floods * climate-change * ardeche river * catastrophic floods * documentary sources * paleoflood record * spanish rivers Subject RIV: DA - Hydrology ; Limnology Impact factor: 3.990, year: 2015

  14. GWAS-based pathway analysis differentiates between fluid and crystallized intelligence.

    Science.gov (United States)

    Christoforou, A; Espeseth, T; Davies, G; Fernandes, C P D; Giddaluru, S; Mattheisen, M; Tenesa, A; Harris, S E; Liewald, D C; Payton, A; Ollier, W; Horan, M; Pendleton, N; Haggarty, P; Djurovic, S; Herms, S; Hoffman, P; Cichon, S; Starr, J M; Lundervold, A; Reinvang, I; Steen, V M; Deary, I J; Le Hellard, S

    2014-09-01

    Cognitive abilities vary among people. About 40-50% of this variability is due to general intelligence (g), which reflects the positive correlation among individuals' scores on diverse cognitive ability tests. g is positively correlated with many life outcomes, such as education, occupational status and health, motivating the investigation of its underlying biology. In psychometric research, a distinction is made between general fluid intelligence (gF) - the ability to reason in novel situations - and general crystallized intelligence (gC) - the ability to apply acquired knowledge. This distinction is supported by developmental and cognitive neuroscience studies. Classical epidemiological studies and recent genome-wide association studies (GWASs) have established that these cognitive traits have a large genetic component. However, no robust genetic associations have been published thus far due largely to the known polygenic nature of these traits and insufficient sample sizes. Here, using two GWAS datasets, in which the polygenicity of gF and gC traits was previously confirmed, a gene- and pathway-based approach was undertaken with the aim of characterizing and differentiating their genetic architecture. Pathway analysis, using genes selected on the basis of relaxed criteria, revealed notable differences between these two traits. gF appeared to be characterized by genes affecting the quantity and quality of neurons and therefore neuronal efficiency, whereas long-term depression (LTD) seemed to underlie gC. Thus, this study supports the gF-gC distinction at the genetic level and identifies functional annotations and pathways worthy of further investigation. © 2014 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.

  15. Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma.

    Directory of Open Access Journals (Sweden)

    Brian J Capaldo

    Full Text Available Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein kinase (MAPK pathway inhibition, we identified the combination of PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ErbB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720. To identify potential mechanisms of resistance to PLX4720 treatment and synergy with lapatinib treatment, we performed a multi-platform functional genomics analysis to profile the genome as well as the transcriptional and proteomic responses of these cell lines to treatment with PLX4720. We found modest levels of resistance correlated with the zygosity of the BRAF V600E allele and receptor tyrosine kinase (RTK mutational status. Layered over base-line resistance was substantial upregulation of many ErbB pathway genes in response to BRaf inhibition, thus generating the vulnerability to combination with lapatinib. The transcriptional responses of ErbB pathway genes are associated with a number of transcription factors, including ETS2 and its associated cofactors that represent a convergent regulatory mechanism conferring synergistic drug susceptibility in the context of diverse mutational landscapes.

  16. GEP analysis validates high risk MDS and acute myeloid leukemia post MDS mice models and highlights novel dysregulated pathways.

    Science.gov (United States)

    Guerenne, Laura; Beurlet, Stéphanie; Said, Mohamed; Gorombei, Petra; Le Pogam, Carole; Guidez, Fabien; de la Grange, Pierre; Omidvar, Nader; Vanneaux, Valérie; Mills, Ken; Mufti, Ghulam J; Sarda-Mantel, Laure; Noguera, Maria Elena; Pla, Marika; Fenaux, Pierre; Padua, Rose Ann; Chomienne, Christine; Krief, Patricia

    2016-01-27

    In spite of the recent discovery of genetic mutations in most myelodysplasic (MDS) patients, the pathophysiology of these disorders still remains poorly understood, and only few in vivo models are available to help unravel the disease. We performed global specific gene expression profiling and functional pathway analysis in purified Sca1+ cells of two MDS transgenic mouse models that mimic human high-risk MDS (HR-MDS) and acute myeloid leukemia (AML) post MDS, with NRASD12 and BCL2 transgenes under the control of different promoters MRP8NRASD12/tethBCL-2 or MRP8[NRASD12/hBCL-2], respectively. Analysis of dysregulated genes that were unique to the diseased HR-MDS and AML post MDS mice and not their founder mice pointed first to pathways that had previously been reported in MDS patients, including DNA replication/damage/repair, cell cycle, apoptosis, immune responses, and canonical Wnt pathways, further validating these models at the gene expression level. Interestingly, pathways not previously reported in MDS were discovered. These included dysregulated genes of noncanonical Wnt pathways and energy and lipid metabolisms. These dysregulated genes were not only confirmed in a different independent set of BM and spleen Sca1+ cells from the MDS mice but also in MDS CD34+ BM patient samples. These two MDS models may thus provide useful preclinical models to target pathways previously identified in MDS patients and to unravel novel pathways highlighted by this study.

  17. GEP analysis validates high risk MDS and acute myeloid leukemia post MDS mice models and highlights novel dysregulated pathways

    Directory of Open Access Journals (Sweden)

    Laura Guerenne

    2016-01-01

    Full Text Available Abstract Background In spite of the recent discovery of genetic mutations in most myelodysplasic (MDS patients, the pathophysiology of these disorders still remains poorly understood, and only few in vivo models are available to help unravel the disease. Methods We performed global specific gene expression profiling and functional pathway analysis in purified Sca1+ cells of two MDS transgenic mouse models that mimic human high-risk MDS (HR-MDS and acute myeloid leukemia (AML post MDS, with NRASD12 and BCL2 transgenes under the control of different promoters MRP8NRASD12/tethBCL-2 or MRP8[NRASD12/hBCL-2], respectively. Results Analysis of dysregulated genes that were unique to the diseased HR-MDS and AML post MDS mice and not their founder mice pointed first to pathways that had previously been reported in MDS patients, including DNA replication/damage/repair, cell cycle, apoptosis, immune responses, and canonical Wnt pathways, further validating these models at the gene expression level. Interestingly, pathways not previously reported in MDS were discovered. These included dysregulated genes of noncanonical Wnt pathways and energy and lipid metabolisms. These dysregulated genes were not only confirmed in a different independent set of BM and spleen Sca1+ cells from the MDS mice but also in MDS CD34+ BM patient samples. Conclusions These two MDS models may thus provide useful preclinical models to target pathways previously identified in MDS patients and to unravel novel pathways highlighted by this study.

  18. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

    Science.gov (United States)

    Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

    2011-08-01

    Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

  19. Putative drug and vaccine target protein identification using comparative genomic analysis of KEGG annotated metabolic pathways of Mycoplasma hyopneumoniae.

    Science.gov (United States)

    Damte, Dereje; Suh, Joo-Won; Lee, Seung-Jin; Yohannes, Sileshi Belew; Hossain, Md Akil; Park, Seung-Chun

    2013-07-01

    In the present study, a computational comparative and subtractive genomic/proteomic analysis aimed at the identification of putative therapeutic target and vaccine candidate proteins from Kyoto Encyclopedia of Genes and Genomes (KEGG) annotated metabolic pathways of Mycoplasma hyopneumoniae was performed for drug design and vaccine production pipelines against M.hyopneumoniae. The employed comparative genomic and metabolic pathway analysis with a predefined computational systemic workflow extracted a total of 41 annotated metabolic pathways from KEGG among which five were unique to M. hyopneumoniae. A total of 234 proteins were identified to be involved in these metabolic pathways. Although 125 non homologous and predicted essential proteins were found from the total that could serve as potential drug targets and vaccine candidates, additional prioritizing parameters characterize 21 proteins as vaccine candidate while druggability of each of the identified proteins evaluated by the DrugBank database prioritized 42 proteins suitable for drug targets. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Dose-volume complication analysis for visual pathway structures of patients with advanced paranasal sinus tumors

    International Nuclear Information System (INIS)

    Martel, Mary Kaye; Sandler, Howard M.; Cornblath, Wayne T.; Marsh, Lon H.; Hazuka, Mark B.; Roa, Wilson H.; Fraass, Benedict A.; Lichter, Allen S.

    1997-01-01

    Purpose: The purpose of the present work was to relate dose and volume information to complication data for visual pathway structures in patients with advanced paranasal sinus tumors. Methods and Materials: Three-dimensional (3D) dose distributions for chiasm, optic nerve, and retina were calculated and analyzed for 20 patients with advanced paranasal sinus malignant tumors. 3D treatment planning with beam's eye view capability was used to design beam and block arrangements, striving to spare the contralateral orbit (to lessen the chance of unilateral blindness) and frequently the ipsilateral orbit (to help prevent bilateral blindness). Point doses, dose-volume histogram analysis, and normal tissue complication probability (NTCP) calculations were performed. Published tolerance doses that indicate significant risk of complications were used as guidelines for analysis of the 3D dose distributions. Results: Point doses, percent volume exceeding a specified published tolerance dose, and NTCP calculations are given in detail for patients with complications versus patients without complications. Two optic nerves receiving maximum doses below the published tolerance dose sustained damage (mild vision loss). Three patients (of 13) without optic nerve sparing and/or chiasm sparing had moderate or severe vision loss. Complication data, including individual patient analysis to estimate overall risk for loss of vision, are given. Conclusion: 3D treatment planning techniques were used successfully to provide bilateral sparing of the globe for most patients. It was more difficult to spare the optic nerves, especially on the ipsilateral side, when prescription dose exceeded the normal tissue tolerance doses. NTCP calculations may be useful in assessing complication risk better than point dose tolerance criteria for the chiasm, optic nerve, and retina. It is important to assess the overall risk of blindness for the patient in addition to the risk for individual visual pathway

  1. Development, calibration, and analysis of a hydrologic and water-quality model of the Delaware Inland Bays watershed

    Science.gov (United States)

    Gutierrez-Magness, Angelica L.; Raffensperger, Jeff P.

    2003-01-01

    Excessive nutrients and sediment are among the most significant environmental stressors in the Delaware Inland Bays (Rehoboth, Indian River, and Little Assawoman Bays). Sources of nutrients, sediment, and other contaminants within the Inland Bays watershed include point-source discharges from industries and wastewater-treatment plants, runoff and infiltration to ground water from agricultural fields and poultry operations, effluent from on-site wastewater disposal systems, and atmospheric deposition. To determine the most effective restoration methods for the Inland Bays, it is necessary to understand the relative distribution and contribution of each of the possible sources of nutrients, sediment, and other contaminants. A cooperative study involving the Delaware Department of Natural Resources and Environmental Control, the Delaware Geological Survey, and the U.S. Geological Survey was initiated in 2000 to develop a hydrologic and water-quality model of the Delaware Inland Bays watershed that can be used as a water-resources planning and management tool. The model code Hydrological Simulation Program - FORTRAN (HSPF) was used. The 719-square-kilometer watershed was divided into 45 model segments, and the model was calibrated using streamflow and water-quality data for January 1999 through April 2000 from six U.S. Geological Survey stream-gaging stations within the watershed. Calibration for some parameters was accomplished using PEST, a model-independent parameter estimator. Model parameters were adjusted systematically so that the discrepancies between the simulated values and the corresponding observations were minimized. Modeling results indicate that soil and aquifer permeability, ditching, dominant land-use class, and land-use practices affect the amount of runoff, the mechanism or flow path (surface flow, interflow, or base flow), and the loads of sediment and nutrients. In general, the edge-of-stream total suspended solids yields in the Inland Bays

  2. Point Analysis in Java applied to histological images of the perforant pathway: A user’s account

    OpenAIRE

    Scorcioni, Ruggero; Wright, Susan N.; Card, J. Patrick; Ascoli, Giorgio A.; Barrionuevo, Germán

    2008-01-01

    The freeware Java tool PAJ, created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (2× objective) comprised the entire perforant pathway, while the high magnification set (100× objective) allowed the identification of individual fibers. A preliminary stereologi...

  3. Toward evaluating the effect of climate change on investments in the water resources sector: insights from the forecast and analysis of hydrological indicators in developing countries

    International Nuclear Information System (INIS)

    Strzepek, Kenneth; Jacobsen, Michael; Boehlert, Brent; Neumann, James

    2013-01-01

    The World Bank has recently developed a method to evaluate the effects of climate change on six hydrological indicators across 8951 basins of the world. The indicators are designed for decision-makers and stakeholders to consider climate risk when planning water resources and related infrastructure investments. Analysis of these hydrological indicators shows that, on average, mean annual runoff will decline in southern Europe; most of Africa; and in southern North America and most of Central and South America. Mean reference crop water deficit, on the other hand, combines temperature and precipitation and is anticipated to increase in nearly all locations globally due to rising global temperatures, with the most dramatic increases projected to occur in southern Europe, southeastern Asia, and parts of South America. These results suggest overall guidance on which regions to focus water infrastructure solutions that could address future runoff flow uncertainty. Most important, we find that uncertainty in projections of mean annual runoff and high runoff events is higher in poorer countries, and increases over time. Uncertainty increases over time for all income categories, but basins in the lower and lower-middle income categories are forecast to experience dramatically higher increases in uncertainty relative to those in the upper-middle and upper income categories. The enhanced understanding of the uncertainty of climate projections for the water sector that this work provides strongly support the adoption of rigorous approaches to infrastructure design under uncertainty, as well as design that incorporates a high degree of flexibility, in response to both risk of damage and opportunity to exploit water supply ‘windfalls’ that might result, but would require smart infrastructure investments to manage to the greatest benefit. (letter)

  4. Toward evaluating the effect of climate change on investments in the water resources sector: insights from the forecast and analysis of hydrological indicators in developing countries

    Science.gov (United States)

    Strzepek, Kenneth; Jacobsen, Michael; Boehlert, Brent; Neumann, James

    2013-12-01

    The World Bank has recently developed a method to evaluate the effects of climate change on six hydrological indicators across 8951 basins of the world. The indicators are designed for decision-makers and stakeholders to consider climate risk when planning water resources and related infrastructure investments. Analysis of these hydrological indicators shows that, on average, mean annual runoff will decline in southern Europe; most of Africa; and in southern North America and most of Central and South America. Mean reference crop water deficit, on the other hand, combines temperature and precipitation and is anticipated to increase in nearly all locations globally due to rising global temperatures, with the most dramatic increases projected to occur in southern Europe, southeastern Asia, and parts of South America. These results suggest overall guidance on which regions to focus water infrastructure solutions that could address future runoff flow uncertainty. Most important, we find that uncertainty in projections of mean annual runoff and high runoff events is higher in poorer countries, and increases over time. Uncertainty increases over time for all income categories, but basins in the lower and lower-middle income categories are forecast to experience dramatically higher increases in uncertainty relative to those in the upper-middle and upper income categories. The enhanced understanding of the uncertainty of climate projections for the water sector that this work provides strongly support the adoption of rigorous approaches to infrastructure design under uncertainty, as well as design that incorporates a high degree of flexibility, in response to both risk of damage and opportunity to exploit water supply ‘windfalls’ that might result, but would require smart infrastructure investments to manage to the greatest benefit.

  5. Multiple Regression Analysis of mRNA-miRNA Associations in Colorectal Cancer Pathway

    Science.gov (United States)

    Wang, Fengfeng; Wong, S. C. Cesar; Chan, Lawrence W. C.; Cho, William C. S.; Yip, S. P.; Yung, Benjamin Y. M.

    2014-01-01

    Background. MicroRNA (miRNA) is a short and endogenous RNA molecule that regulates posttranscriptional gene expression. It is an important factor for tumorigenesis of colorectal cancer (CRC), and a potential biomarker for diagnosis, prognosis, and therapy of CRC. Our objective is to identify the related miRNAs and their associations with genes frequently involved in CRC microsatellite instability (MSI) and chromosomal instability (CIN) signaling pathways. Results. A regression model was adopted to identify the significantly associated miRNAs targeting a set of candidate genes frequently involved in colorectal cancer MSI and CIN pathways. Multiple linear regression analysis was used to construct the model and find the significant mRNA-miRNA associations. We identified three significantly associated mRNA-miRNA pairs: BCL2 was positively associated with miR-16 and SMAD4 was positively associated with miR-567 in the CRC tissue, while MSH6 was positively associated with miR-142-5p in the normal tissue. As for the whole model, BCL2 and SMAD4 models were not significant, and MSH6 model was significant. The significant associations were different in the normal and the CRC tissues. Conclusion. Our results have laid down a solid foundation in exploration of novel CRC mechanisms, and identification of miRNA roles as oncomirs or tumor suppressor mirs in CRC. PMID:24895601

  6. Assessing invasion process through pathway and vector analysis: case of saltcedar (Tamarix spp.

    Directory of Open Access Journals (Sweden)

    Evangelina Natale

    2012-12-01

    Full Text Available Biological invasions are one of the most pervasive environmental threats to native ecosystems worldwide. The spontaneous spread ofsaltcedar is a particular threat to biodiversity conservation in arid and semiarid environments. In Argentina, three species belonging to this genus have been recognized as invaders. The aim of the present study was to identify main dispersal vectors and pathways to refine risk analysis and increase our ability to predict new areas at risk of Tamarix establishment. We surveyed and categorized 223 populations, 39% as invasive, 26% as established, 21% as contained and 14% as detected in nature. Dispersion of saltcedar was found to be associated with watercourses and human-driven disturbances; in addition roads were found to be relevant for the introduction of propagules in newenvironments. Considering the potential impact of saltcedar invasion and that it is an easily wind-dispersed invasive, it is necessary toimplement strategies to monitor dispersal pathways and take actions to eliminate invasion foci, particularly in vulnerable and highconservation value areas.

  7. Allowable residual contamination levels of radionuclides in soil from pathway analysis

    International Nuclear Information System (INIS)

    Nyquist, J.E.; Baes, C.F. III

    1987-01-01

    The Remedial Action Program (RAP) at Oak Ridge National Laboratory will include well drilling, facility upgrades, and other waste management operations likely to involve soils contaminated with radionuclides. A preliminary protocol and generalized criteria for handling contaminated soils is needed to coordinate and plan RAP activities, but there exists only limited information on contaminate nature and distribution at ORNL RAP sites. Furthermore, projections of long-term decommissioning and closure options for these sites are preliminary. They have adapted a pathway analysis model, DECOM, to quantify risks to human health from radionuclides in soil and used it to outline preliminary criteria for determining the fate of contaminated soil produced during RAP activities. They assumed that the site could be available for unrestricted use immediately upon decontamination. The pathways considered are consumption of food grown on the contaminated soil, including direct ingestion of soil from poorly washed vegetables, direct radiation from the ground surface, inhalation of resuspended radioactive soil, and drinking water from a well drilled through or near the contaminated soil. We will discuss the assumptions and simplifications implicit in DECOM, the site-specific data required, and the results of initial calculations for the Oak Ridge Reservation

  8. Enhancement of cordyceps polysaccharide production via biosynthetic pathway analysis in Hirsutella sinensis.

    Science.gov (United States)

    Lin, Shan; Liu, Zhi-Qiang; Baker, Peter James; Yi, Ming; Wu, Hui; Xu, Feng; Teng, Yi; Zheng, Yu-Guo

    2016-11-01

    The addition of various sulfates for enhanced cordyceps polysaccharide (CP) production in submerged cultivation of H. sinensis was investigated, and manganese sulfate was found the most effective. 2mM of manganese sulfate on 0day (d) was investigated as the optimal adding condition, and the CP production reached optimum with 5.33%, increasing by 93.3% compared with the control. Furthermore, the consumption of three main precursors of CP was studied over cultivation under two conditions. Intracellular mannose content decreased by 43.1% throughout 6days cultivation, which corresponded to CP accumulation rate sharply increased from 0 d to 6 d, and mannose was considered as the most preferred precursor for generating CP. Subsequently, mannose biosynthetic pathway was constructed and verified for the first time in H. sinensis, which constituted the important part of CP biosynthesis, and transcriptional levels of the biosynthetic genes were studied. Transcriptional level of gene cpsA was significantly up-regulated 5.35-fold and it was a key gene involved both in mannose and CP biosynthesis. This study demonstrated that manganese sulfate addition is an efficient and simple way to improve CP production. Transcriptional analysis based on biosynthetic pathway was helpful to find key genes and better understand CP biosynthesis. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Afforestation, subsequent forest fires and provision of hydrological services: a model-based analysis for a Mediterranean mountainous catchment

    Science.gov (United States)

    Nunes, João Pedro; Naranjo Quintanilla, Paula; Santos, Juliana; Serpa, Dalila; Carvalho-Santos, Cláudia; Rocha, João; Keizer, Jan Jacob; Keesstra, Saskia

    2017-04-01

    Mediterranean landscapes have experienced extensive abandonment and reforestation in recent decades, which should have improved the provision of hydrological services, such as flood mitigation, soil erosion protection and water quality regulation. However, these forests are fire-prone, and the post-fire increase in runoff, erosion and sediment exports could negatively affect service provision. This issue was assessed using the SWAT model for a small mountain agroforestry catchment, which was monitored between 2010 and 2014 and where some eucalypt stands burned in 2011 and were subsequently plowed for replanting. The model was calibrated and validated for streamflow, sediment yield and erosion in agricultural fields and the burnt hillslopes, showing that it can be adapted for post-fire simulation. It was then used to perform a decadal assessment of surface runoff, erosion, and sediment exports between 2004 and 2014. Results show that the fire did not noticeably affect flood mitigation but that it increased erosion by 3 orders of magnitude, which subsequently increased sediment yield. Erosion in the burnt forest during this decade was one order of magnitude above that in agricultural fields. SWAT was also used to assess different fire and land-use scenarios during the same period. Results indicate that the impacts of fire were lower without post-fire soil management, and when the fire occurred in pine forests (i.e. before the 1990s) or in shrublands (i.e. before afforestation in the 1930s). These impacts were robust to changes in post-fire weather conditions and to a lower fire frequency (20-year intervals). The results suggest that, in the long term, fire-prone forests might not provide the anticipated soil protection and water quality regulation services in wet Mediterranean regions.

  10. Inference of miRNA targets using evolutionary conservation and pathway analysis

    Directory of Open Access Journals (Sweden)

    van Nimwegen Erik

    2007-03-01

    assigns a posterior probability to each putative target site. The results presented here indicate that our general method achieves very good performance in predicting miRNA target sites, providing at the same time insights into the evolution of target sites for individual miRNAs. Moreover, by combining our predictions with pathway analysis, we propose functions of specific miRNAs in nervous system development, inter-cellular communication and cell growth. The complete target site predictions as well as the miRNA/pathway associations are accessible on the ElMMo web server.

  11. An algorithm for modularization of MAPK and calcium signaling pathways: comparative analysis among different species.

    Science.gov (United States)

    Nayak, Losiana; De, Rajat K

    2007-12-01

    Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike studying a signaling pathway as a whole, this enables one to study the individual modules (less complex smaller units) easily and hence to study the entire pathway better. A comparative study of modules belonging to different species (for the same signaling pathway) has been made, which gives an overall idea about development of the signaling pathways over the taken set of species of calcium and MAPK signaling pathways. The superior performance, in terms of biological significance, of the proposed algorithm over an existing community finding algorithm of Newman [Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006;103(23):8577-82] has been demonstrated using the aforesaid pathways of H. sapiens.

  12. Northern hydrology and water resources in a changing environment

    International Nuclear Information System (INIS)

    Kane, D.L.

    1993-01-01

    The role that climatic change may play in altering various components of the hydrologic cycle in Arctic regions is discussed. The hydrologic setting of these regions is first described, noting the importance of subsurface freezing and thawing on hydrologic pathways and the lack of incorporation of soil freezing and thawing into climate models. Major processes of interest in the relation between climate change and hydrology are the timing and magnitude of fluxes entering and leaving a basin: precipitation, evaporation and transpiration, and runoff. The active layer of the soil could be drastically increased by only a few degrees of surface warming. The natural hydrologic cycle has considerable yearly variation, tending to mask any hydrologic changes caused by climatic change. There are too many unknowns at present for an adequate prediction of the impact of climate change on the hydrologic cycle. The biggest uncertainty is how the timing and quantity of precipitation is going to change. This quantity could be altered by any major changes in vegetation, which would be closely related to the amount of warming. In hydrologic scenarios where air temperature rises 4 degree C over 50 y, under stable, high, and low precipitation conditions, there are no significant changes in hydrologic response. 24 refs., 6 figs

  13. Phase analysis in gated blood pool tomography. Detection of accessory conduction pathway

    Energy Technology Data Exchange (ETDEWEB)

    Nakajima, Kenichi; Bunko, Hisashi; Tada, Akira; Taki, Junichi; Nanbu, Ichiro (Kanazawa Univ. (Japan). School of Medicine)

    1984-02-01

    Phase analysis of gated blood pool study has been applied to detect the site of accessory conduction pathway (ACP) in the Wolff-Parkinson-White (WPW) syndrome; however, there was a limitation to detect the precise location of ACP by phase analysis alone. In this study, we applied phase analysis to gated blood pool tomography using seven pin hole tomography (7PT) and gated emission computed tomography (GECT) in 21 patients with WPW syndrome and 3 normal subjects. In 17 patients, the sites of ACPs were confirmed by epicardial mapping and the result of the surgical division of ACP. In 7PT, the site of ACP grossly agreed to the abnormal initial phase in phase image in 5 out of 6 patients with left cardiac type. In GECT, phase images were generated in short axial, vertical and horizontal long axial sections. In 8 out of 9 patients, the site of ACP was correctly identified by phase images, and in a patient who had two ACPs, initial phase corresponded to one of the two locations. Phase analysis of gated blood pool tomography has advantages for avoiding overlap of blood pools and for estimating three-dimensional propagation of the contraction, and can be a good adjunctive method in patients with WPW syndrome.

  14. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

    International Nuclear Information System (INIS)

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

    Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both GC-MS and Fourier Transform-Ion Cyclotron Resonance mass spectrometry (FT-ICR MS) indicate the lack of oxidatively functional TCA cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80 percent of the lactate was converted to acetate and the reactions involved are the primary route of energy production (NAD(P)H and ATP production). Independent of the TCA cycle, direct cleavage of acetyl-CoA to CO and 5,10-methyl-THF also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports (the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase). These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris, and also demonstrate FT-ICR MS as a powerful tool for isotopomer analysis, overcoming problems in both GC-MS and NMR spectroscopy

  15. Hydrological change during the last 600 years as observed from landscape analysis and historical maps: a case study from the Nete catchment, Campine area, NE-Belgium

    Science.gov (United States)

    Beerten, Koen; Leterme, Bertrand

    2015-04-01

    increased from 2 km to 25 km, while land cover changed from 80% heathland and almost no trees to only 20% heathland and 50% coniferous forest. Available palaeoclimate records suggest that there is no correlation between groundwater level change and average annual temperature or precipitation. Furthermore, population density seems to be uncorrelated with the observed hydrological changes. Internal consistency checks are performed and found satisfactory. For example, the high groundwater levels predicted by the blown-out surfaces for 1400-1600 AD are confirmed by surface water features on younger historical maps (~1770 AD and ~1850 AD). Indeed, pollen analysis, topographical maps and climate records show that land cover and climate did not change significantly throughout the period 1400 AD to 1850 AD. We conclude that the proposed methods are useful tools to gather verification data (i.e., groundwater table depth) for palaeohydrological modelling in the European sand belt during the last millenium.

  16. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  17. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

    Science.gov (United States)

    Äijö, Tarmo; Huang, Yun; Mannerström, Henrik; Chavez, Lukas; Tsagaratou, Ageliki; Rao, Anjana; Lähdesmäki, Harri

    2016-03-14

    We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.

  18. Nuclear techniques in hydrology

    International Nuclear Information System (INIS)

    Moser, H.

    1976-01-01

    The nuclear techniques used in hydrology are usually tracer techniques based on the use of nuclides either intentionally introduced into, or naturally present in the water. The low concentrations of these nuclides, which must be detected in groundwater and surface water, require special measurement techniques for the concentrations of radioactive or of stable nuclides. The nuclear techniques can be used most fruitfully in conjunction with conventional methods for the solution of problems in the areas of hydrology, hydrogeology and glacier hydrology. Nuclear techniques are used in practice in the areas of prospecting for water, environment protection and engineering hydrogeology. (orig.) [de

  19. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM.

    Science.gov (United States)

    Biswas, Nidhan K; Chandra, Vikas; Sarkar-Roy, Neeta; Das, Tapojyoti; Bhattacharya, Rabindra N; Tripathy, Laxmi N; Basu, Sunandan K; Kumar, Shantanu; Das, Subrata; Chatterjee, Ankita; Mukherjee, Ankur; Basu, Pryiadarshi; Maitra, Arindam; Chattopadhyay, Ansuman; Basu, Analabha; Dhara, Surajit

    2015-01-21

    Neoplastic cells of Glioblastoma multiforme (GBM) may or may not show sustained response to temozolomide (TMZ) chemotherapy. We hypothesize that TMZ chemotherapy response in GBM is predetermined in its neoplastic clones via a specific set of mutations that alter relevant pathways. We describe exome-wide enrichment of variant allele frequencies (VAFs) in neurospheres displaying contrasting phenotypes of sustained versus reversible TMZ-responses in vitro. Enrichment of VAFs was found on genes ST5, RP6KA1 and PRKDC in cells showing sustained TMZ-effect whereas on genes FREM2, AASDH and STK36, in cells showing reversible TMZ-effect. Ingenuity pathway analysis (IPA) revealed that these genes alter cell-cycle, G2/M-checkpoint-regulation and NHEJ pathways in sustained TMZ-effect cells whereas the lysine-II&V/phenylalanine degradation and sonic hedgehog (Hh) pathways in reversible TMZ-effect cells. Next, we validated the likely involvement of the Hh-pathway in TMZ-response on additional GBM neurospheres as well as on GBM patients, by extracting RNA-sequencing-based gene expression data from the TCGA-GBM database. Finally, we demonstrated TMZ-sensitization of a TMZ non-responder neurosphere in vitro by treating them with the FDA-approved pharmacological Hh-pathway inhibitor vismodegib. Altogether, our results indicate that the Hh-pathway impedes sustained TMZ-response in GBM and could be a potential therapeutic target to enhance TMZ-response in this malignancy.

  20. Phytoplankton Ecology and Hydrological Dynamics of the Yahuarcaca Lake System, Amazonas, Colombia: Integrated Analysis of 16 Years of Study

    Directory of Open Access Journals (Sweden)

    Maria Juliana Salcedo-Hernández

    2012-09-01

    Full Text Available This article provides a synthesis of the current knowledge on the evolving relation between the Amazon River and the Yahuarcaca lagoon system, through the limnological features and the ecology of phytoplankton in a period of sixteen years. The synthesis of the information was conducted by reviewing existing data about the system, for the time indicated, and analyzing it by means of descriptive statistics and linear correlation between the variables found. Also, it contains a summary of the most important aspects of the first attempt in Colombia to evaluate the influence of the flood pulse on the phytoplankton in a daily time scale. The thermal pattern of this laggon system corresponds to a warm and constant polymicthic lake type according to the de Lewis (1983 classification. The physical, chemical and biological variables examined in this várzea system change according to the hydrologic period. The conductivity, transparency and richness of the phytoplankton increase in the low water season, while the nutrient concentration, and the density, productivity and the biomass of phytoplankton increase during the high water season. Nitrate during the low water season and phosphate during the high water season are the most restricting nutrients. The changes that have taken place through these years in the connectivity between the river and the Yahuarcaca lagoon system are reflected in the dynamics of the structure and composition of the phytoplankton. Normal 0 21 false false false ES-CO X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif"; mso-bidi-font-family:"Times New Roman"; mso-ansi-language:ES-CO; mso-fareast-language:ES-CO;}

  1. Role of Sectoral Transformation in Evolution of Water Management in Agricultural Catchments: A Socio-hydrologic Analysis

    Science.gov (United States)

    Roobavannan, Mahendran; Kandasamy, Jaya; Pande, Saket; Vigneswaran, Saravanamuthu; Sivapalan, Murugesu

    2017-04-01

    Sustainable development in society depends on an understanding of how communities interact with the natural system and how they co-evolve in time. Increasingly the livelihood and future viability of agricultural communities are being threatened by competition for water between food production and the environment. This study focused on this water-agriculture-environment nexus as it played out in the Murrumbidgee River Basin, Australia, and how co-evolution of society and water management occurred. Over 100 years of agricultural development the Murrumbidgee Basin has experienced a "pendulum swing" in terms of water allocation entirely to agriculture production at the expense of the environment, and eventually to the reallocation of water back to the environment. This pendulum swing has been attributed to a combination of increased national wealth, reduced share of agriculture in the national GDP, and to increased environment awareness of environmental degradation. Environment awareness depends on the structure of the economy, education, and socio-politic structure. As the basin economy develops accompanied by sectoral transformation, basin production becomes increasingly dependent on the industry sector. A loss of economic dependence on agriculture leads to a lower emphasis on the need to allocate water to agriculture. Society's value and preference turns around and is motivated towards the protection of the ecosystem. We hypothesize that in the competition of water use between economic livelihood and environment well being of society, economic diversification pushed the balance in towards the environment. In order to test this hypothesis, we developed a coupled socio-hydrologic model, which explicitly considers bi-directional feedbacks between human and water systems to explore how the competition for water played out in the Murrumbidgee. We demonstrate this by linking the dynamics of the economy of the whole (agriculture and industry) to community sentiment for the

  2. Well-to-wheels analysis of fast pyrolysis pathways with the GREET model.

    Energy Technology Data Exchange (ETDEWEB)

    Han, J.; Elgowainy, A.; Palou-Rivera, I.; Dunn, J.B.; Wang, M.Q. (Energy Systems)

    2011-12-01

    The pyrolysis of biomass can help produce liquid transportation fuels with properties similar to those of petroleum gasoline and diesel fuel. Argonne National Laboratory conducted a life-cycle (i.e., well-to-wheels [WTW]) analysis of various pyrolysis pathways by expanding and employing the Greenhouse Gases, Regulated Emissions, and Energy Use in Transportation (GREET) model. The WTW energy use and greenhouse gas (GHG) emissions from the pyrolysis pathways were compared with those from the baseline petroleum gasoline and diesel pathways. Various pyrolysis pathway scenarios with a wide variety of possible hydrogen sources, liquid fuel yields, and co-product application and treatment methods were considered. At one extreme, when hydrogen is produced from natural gas and when bio-char is used for process energy needs, the pyrolysis-based liquid fuel yield is high (32% of the dry mass of biomass input). The reductions in WTW fossil energy use and GHG emissions relative to those that occur when baseline petroleum fuels are used, however, is modest, at 50% and 51%, respectively, on a per unit of fuel energy basis. At the other extreme, when hydrogen is produced internally via reforming of pyrolysis oil and when bio-char is sequestered in soil applications, the pyrolysis-based liquid fuel yield is low (15% of the dry mass of biomass input), but the reductions in WTW fossil energy use and GHG emissions are large, at 79% and 96%, respectively, relative to those that occur when baseline petroleum fuels are used. The petroleum energy use in all scenarios was restricted to biomass collection and transportation activities, which resulted in a reduction in WTW petroleum energy use of 92-95% relative to that found when baseline petroleum fuels are used. Internal hydrogen production (i.e., via reforming of pyrolysis oil) significantly reduces fossil fuel use and GHG emissions because the hydrogen from fuel gas or pyrolysis oil (renewable sources) displaces that from fossil fuel

  3. Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis.

    Science.gov (United States)

    Gao, Haiyan; Yang, Mei; Zhang, Xiaolan

    2018-04-01

    The present study aimed to investigate potential recurrence-risk biomarkers based on significant pathways for Luminal A breast cancer through gene expression profile analysis. Initially, the gene expression profiles of Luminal A breast cancer patients were downloaded from The Cancer Genome Atlas database. The differentially expressed genes (DEGs) were identified using a Limma package and the hierarchical clustering analysis was conducted for the DEGs. In addition, the functional pathways were screened using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and rank ratio calculation. The multigene prognostic assay was exploited based on the statistically significant pathways and its prognostic function was tested using train set and verified using the gene expression data and survival data of Luminal A breast cancer patients downloaded from the Gene Expression Omnibus. A total of 300 DEGs were identified between good and poor outcome groups, including 176 upregulated genes and 124 downregulated genes. The DEGs may be used to effectively distinguish Luminal A samples with different prognoses verified by hierarchical clustering analysis. There were 9 pathways screened as significant pathways and a total of 18 DEGs involved in these 9 pathways were identified as prognostic biomarkers. According to the survival analysis and receiver operating characteristic curve, the obtained 18-gene prognostic assay exhibited good prognostic function with high sensitivity and specificity to both the train and test samples. In conclusion the 18-gene prognostic assay including the key genes, transcription factor 7-like 2, anterior parietal cortex and lymphocyte enhancer factor-1 may provide a new method for predicting outcomes and may be conducive to the promotion of precision medicine for Luminal A breast cancer.

  4. Modeling Subsurface Hydrology in Floodplains

    Science.gov (United States)

    Evans, Cristina M.; Dritschel, David G.; Singer, Michael B.

    2018-03-01

    Soil-moisture patterns in floodplains are highly dynamic, owing to the complex relationships between soil properties, climatic conditions at the surface, and the position of the water table. Given this complexity, along with climate change scenarios in many regions, there is a need for a model to investigate the implications of different conditions on water availability to riparian vegetation. We present a model, HaughFlow, which is able to predict coupled water movement in the vadose and phreatic zones of hydraulically connected floodplains. Model output was calibrated and evaluated at six sites in Australia to identify key patterns in subsurface hydrology. This study identifies the importance of the capillary fringe in vadose zone hydrology due to its water storage capacity and creation of conductive pathways. Following peaks in water table elevation, water can be stored in the capillary fringe for up to months (depending on the soil properties). This water can provide a critical resource for vegetation that is unable to access the water table. When water table peaks coincide with heavy rainfall events, the capillary fringe can support saturation of the entire soil profile. HaughFlow is used to investigate the water availability to riparian vegetation, producing daily output of water content in the soil over decadal time periods within different depth ranges. These outputs can be summarized to support scientific investigations of plant-water relations, as well as in management applications.

  5. Allegheny County Hydrology Areas

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Hydrology Feature Dataset contains photogrammetrically compiled water drainage features and structures including rivers, streams, drainage canals, locks, dams,...

  6. PNW Hydrologic Landscape Class

    Data.gov (United States)

    U.S. Environmental Protection Agency — Work has been done to expand the hydrologic landscapes (HLs) concept and to develop an approach for using it to address streamflow vulnerability from climate change....

  7. Hydrologic Engineering Center

    Data.gov (United States)

    Federal Laboratory Consortium — The Hydrologic Engineering Center (HEC), an organization within the Institute for Water Resources, is the designated Center of Expertise for the U.S. Army Corps of...

  8. Allegheny County Hydrology Lines

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Hydrology Feature Dataset contains photogrammetrically compiled water drainage features and structures including rivers, streams, drainage canals, locks, dams,...

  9. Hydrologic Areas of Concern

    Data.gov (United States)

    University of New Hampshire — A Hydrologic Area of Concern (HAC) is a land area surrounding a water source, which is intended to include the portion of the watershed in which land uses are likely...

  10. Use of environmental isotope techniques in groundwater hydrology

    International Nuclear Information System (INIS)

    Tirumalesh, K.; Shivanna, K.

    2009-01-01

    Environmental isotopes (stable and radioactive) have been used as tracers for investigating various hydrological problems. Wide variation in isotopic distribution ( 2 H, 13 C, 18 O, 15 N, 35 S, 3 H and 14 C) in the environment help in identifying the source, origin, pathways and processes affecting the system under consideration. In this article, a few Indian case studies covering some of the very important isotope applications in groundwater hydrology are briefly summarized. (author)