WorldWideScience

Sample records for predict target erosion

  1. Mercury erosion experiments for spallation target system

    International Nuclear Information System (INIS)

    Kinoshita, Hidetaka; Kaminaga, Masanori; Haga, Katsuhiro; Hino, Ryutaro

    2003-01-01

    The Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Research Organization (KEK) are promoting a plan to construct the spallation neutron source at the Tokai Research Establishment, JAERI, under the High-Intensity Proton Accelerator Project (J-PARC). A mercury circulation system has been designed so as to supply mercury to the target stably under the rated flow rate of 41 m 3 /hr. Then, it was necessary to confirm a mercury pump performance from the viewpoint of making the mercury circulation system feasible, and more, to investigate erosion rate under the mercury flow as well as an amount of mercury remained on the surface after drain from the viewpoints of mechanical strength relating to the lifetime and remote handling of mercury components. The mercury pump performance was tested under the mercury flow conditions by using an experimental gear pump, which had almost the same structure as a practical mercury pump to be expected in the mercury circulation system, and the erosion rates in a mercury pipeline as well as the amount of mercury remained on the surface were also investigated. The discharged flow rates of the experimental gear pump increased linearly with the rotation speed, so that the gear pump would work as the flow meter. Erosion rates obtained under the mercury velocity less than 1.6 m/s was found to be so small that decrease of pipeline wall thickness would be 390 μm after 30-year operation under the rated mercury velocity of 0.7 m/s. For the amount of remaining mercury on the pipeline, remaining rates of weight and volume were estimated at 50.7 g/m 2 and 3.74 Hg-cm 3 /m 2 , respectively. Applying these remaining rates of weight and volume to the mercury target, the remaining mercury was estimated at about 106.5 g and 7.9 cm 3 . Radioactivity of this remaining mercury volume was found to be three-order lower than that of the target casing. (author)

  2. Target fabrication using laser and spark erosion machining

    International Nuclear Information System (INIS)

    Clement, X.; Coudeville, A.; Eyharts, P.; Perrine, J.P.; Rouillard, R.

    1982-01-01

    Fabrication of laser fusion targets requires a number of special techniques. We have developed both laser and spark erosion machining to produce minute parts of complex targets. A high repetition rate YAG laser at double frequency is used to etch various materials. For example, marks or patterns are often necessary on structured or advanced targets. The laser is also used to thin down plastic coated stalks. A spark erosion system has proved to be a versatile tool and we describe current fabrication processes like cutting, drilling, and ultra precise machining. Spark erosion has interesting features for target fabrication: it is a highly controllable and reproducible technique as well as relatively inexpensive

  3. Numerical Modelling and Prediction of Erosion Induced by Hydrodynamic Cavitation

    Science.gov (United States)

    Peters, A.; Lantermann, U.; el Moctar, O.

    2015-12-01

    The present work aims to predict cavitation erosion using a numerical flow solver together with a new developed erosion model. The erosion model is based on the hypothesis that collapses of single cavitation bubbles near solid boundaries form high velocity microjets, which cause sonic impacts with high pressure amplitudes damaging the surface. The erosion model uses information from a numerical Euler-Euler flow simulation to predict erosion sensitive areas and assess the erosion aggressiveness of the flow. The obtained numerical results were compared to experimental results from tests of an axisymmetric nozzle.

  4. Cavitation erosion prediction on Francis turbines

    Energy Technology Data Exchange (ETDEWEB)

    Bourdon, P.; Farhat, M.; Simoneau, R.; Lavigne, P. [Hydro-Quebec, Montreal, PQ (Canada); Pereira, F.; Dupont, P.; Avellan, F.; Caron, J.F. [IMHEF/EPFL, (France); Dorey, J.M.; Archer, A. [Electricite de France (EDF), 92 - Clamart (France). Dir. des Etudes et Recherches; and others

    1997-12-31

    On-board aggressiveness measurement methods were tested on a severely eroded prototype blade of a 266 MW Francis turbine: pressure, pit counting, DECER electrochemical and vibration measurements. The test program provided understanding of the heterogeneous erosion distribution of the prototype blades and quantitative data for comparison in subsequent tests on the model of the machine. Model tests and flow analysis were also performed, to detect cavitation on a Francis turbine model. The results are compared to those obtained on the prototype measurements. The model used for that study is built on the basis of a geometrical recovery of one of the most eroded blade of the prototype. Different methods were investigated to predict cavitation erosion on Francis turbines from model. They are based on measurement of pitting, pressure fluctuations and acceleration. The methods proposed are suitable to measure cavitation aggressiveness on model and on prototype, and that the level on the model is several orders of magnitude smaller than on the prototype. (author) 18 refs.

  5. Geospatial application of the Water Erosion Prediction Project (WEPP) Model

    Science.gov (United States)

    D. C. Flanagan; J. R. Frankenberger; T. A. Cochrane; C. S. Renschler; W. J. Elliot

    2011-01-01

    The Water Erosion Prediction Project (WEPP) model is a process-based technology for prediction of soil erosion by water at hillslope profile, field, and small watershed scales. In particular, WEPP utilizes observed or generated daily climate inputs to drive the surface hydrology processes (infiltration, runoff, ET) component, which subsequently impacts the rest of the...

  6. The Current State of Predicting Furrow Irrigation Erosion

    Science.gov (United States)

    There continues to be a need to predict furrow irrigation erosion to estimate on- and off-site impacts of irrigation management. The objective of this paper is to review the current state of furrow erosion prediction technology considering four models: SISL, WEPP, WinSRFR and APEX. SISL is an empiri...

  7. The development of U. S. soil erosion prediction and modeling

    Directory of Open Access Journals (Sweden)

    John M. Laflen

    2013-09-01

    Full Text Available Soil erosion prediction technology began over 70 years ago when Austin Zingg published a relationship between soil erosion (by water and land slope and length, followed shortly by a relationship by Dwight Smith that expanded this equation to include conservation practices. But, it was nearly 20 years before this work's expansion resulted in the Universal Soil Loss Equation (USLE, perhaps the foremost achievement in soil erosion prediction in the last century. The USLE has increased in application and complexity, and its usefulness and limitations have led to the development of additional technologies and new science in soil erosion research and prediction. Main among these new technologies is the Water Erosion Prediction Project (WEPP model, which has helped to overcome many of the shortcomings of the USLE, and increased the scale over which erosion by water can be predicted. Areas of application of erosion prediction include almost all land types: urban, rural, cropland, forests, rangeland, and construction sites. Specialty applications of WEPP include prediction of radioactive material movement with soils at a superfund cleanup site, and near real-time daily estimation of soil erosion for the entire state of Iowa.

  8. Operational limit of a planar DC magnetron cluster source due to target erosion

    International Nuclear Information System (INIS)

    Rai, A.; Mutzke, A.; Bandelow, G.; Schneider, R.; Ganeva, M.; Pipa, A.V.; Hippler, R.

    2013-01-01

    The binary collision-based two dimensional SDTrimSP-2D model has been used to simulate the erosion process of a Cu target and its influence on the operational limit of a planar DC magnetron nanocluster source. The density of free metal atoms in the aggregation region influences the cluster formation and cluster intensity during the target lifetime. The density of the free metal atoms in the aggregation region can only be predicted by taking into account (i) the angular distribution of the sputtered flux from the primary target source and (ii) relative downwards shift of the primary source of sputtered atoms during the erosion process. It is shown that the flux of the sputtered atoms smoothly decreases with the target erosion

  9. Understanding and Predicting Gun Barrel Erosion

    National Research Council Canada - National Science Library

    Johnston, Ian A

    2005-01-01

    The Australian Defence Force will soon have to contend with gun barrel erosion issues arising from the use of new low-vulnerability gun propellants, the acquisition of new ammunition and gun systems...

  10. Water erosion risk prediction in eucalyptus plantations

    Directory of Open Access Journals (Sweden)

    Mayesse Aparecida da Silva

    2014-04-01

    Full Text Available Eucalyptus plantations are normally found in vulnerable ecosystems such as steep slope, soil with low natural fertility and lands that were degraded by agriculture. The objective of this study was to obtain Universal Soil Loss Equation (USLE factors and use them to estimate water erosion risk in regions with eucalyptus planted. The USLE factors were obtained in field plots under natural rainfall in the Rio Doce Basin, MG, Brazil, and the model applied to assess erosion risk using USLE in a Geographic Information System. The study area showed rainfall-runoff erosivity values from 10,721 to 10,642 MJ mm ha-1 h-1 yr-1. Some soils (Latosols had very low erodibility values (2.0 x 10-4 and 1.0 x 10-4t h MJ-1 mm-1, the topographic factor ranged from 0.03 to 10.57 and crop and management factor values obtained for native forest, eucalyptus and planted pasture were 0.09, 0.12 and 0.22, respectively. Water erosion risk estimates for current land use indicated that the areas where should receive more attention were mainly areas with greater topographic factors and those with Cambisols. Planning of forestry activities in this region should consider implementation of other conservation practices beyond those already used, reducing areas with a greater risk of soil erosion and increasing areas with very low risk.

  11. Predicting of soil erosion with regarding to rainfall erosivity and soil erodibility

    Science.gov (United States)

    Suif, Zuliziana; Razak, Mohd Amirun Anis Ab; Ahmad, Nordila

    2018-02-01

    The soil along the hill and slope are wearing away due to erosion and it can take place due to occurrence of weak and heavy rainfall. The aim of this study is to predict the soil erosion degree in Universiti Pertahanan Nasional Malaysia (UPNM) area focused on two major factor which is soil erodibility and rainfall erosivity. Soil erodibility is the possibilities of soil to detach and carried away during rainfall and runoff. The "ROM" scale was used in this study to determine the degree of soil erodibility, namely low, moderate, high, and very high. As for rainfall erosivity, the erosive power caused by rainfall that cause soil loss. A daily rainfall data collected from January to April was analyzed by using ROSE index classification to identify the potential risk of soil erosion. The result shows that the soil erodibilty are moderate at MTD`s hill, high at behind of block Lestari and Landslide MTD hill, and critical at behind the mess cadet. While, the highest rainfall erosivity was recorded in March and April. Overall, this study would benefit the organization greatly in saving cost in landslide protection as relevant authorities can take early measures repairing the most affected area of soil erosion.

  12. Theoretical model for cavitation erosion prediction in centrifugal pump impeller

    International Nuclear Information System (INIS)

    Rayan, M.A.; Mahgob, M.M.; Mostafa, N.H.

    1990-01-01

    Cavitation is known to have great effects on pump hydraulic and mechanical characteristics. These effects are mainly described by deviation in pump performance, increasing vibration and noise level as well as erosion of blade and casing materials. In the present work, only the hydrodynamic aspect of cavitation was considered. The efforts were directed toward the study of cavitation inception, cavity mechanics and material erosion in order to clarify the macrohydrodynamic aspects of cavitation erosive wear in real machines. As a result of this study, it was found that cavitation damage can be predicted from model data. The obtained theoretical results show good agreement with the experimental results obtained in this investigation and with results of some other investigations. The application of the findings of this work will help the design engineer in predicting the erosion rate, according to the different operating conditions. (author)

  13. Erosion prediction for alpine slopes: a symbiosis of remote sensing and a physical based erosion model

    Science.gov (United States)

    Kaiser, Andreas; Neugirg, Fabian; Haas, Florian; Schindewolf, Marcus; Schmidt, Jürgen

    2014-05-01

    As rainfall simulations represent an established tool for quantifying soil detachment on cultivated area in lowlands and low mountain ranges, they are rarely used on steep slopes high mountain ranges. Still this terrain represents productive sediment sources of high morphodynamic. A quantitative differentiation between gravitationally and fluvially relocated material reveals a major challenge in understanding erosion on steep slopes: does solifluction as a result of melting in spring or heavy convective rainstorms during summer cause the essential erosion processes? This paper aims to answer this question by separating gravitational mass movement (solifluction, landslides, mudflow and needle ice) and runoff-induced detachment. First simulated rainstorm experiments are used to assess the sediment production on bare soil on a strongly inclined plot (1 m², 42°) in the northern limestone Alps. Throughout precipitation experiments runoff and related suspended sediments were quantified. In order to enlarge slope length virtually to around 20 m a runoff feeding device is additionally implemented. Soil physical parameters were derived from on-site sampling. The generated data is introduced to the physically based and catchment-scaled erosion model EROSION 3D to upscale plot size to small watershed conditions. Thus infiltration, runoff, detachment, transport and finally deposition can be predicted for single rainstorm events and storm sequences. Secondly, in order to separate gravitational mass movements and water erosion, a LiDAR and structure-from-motion based monitoring approach is carried out to produce high-resolution digital elevation models. A time series analysis of detachment and deposition from different points in time is implemented. Absolute volume losses are then compared to sediment losses calculated by the erosion model as the latter only generates data that is connected to water induced hillside erosion. This methodology will be applied in other watersheds

  14. Geospatial application of the Water Erosion Prediction Project (WEPP) model

    Science.gov (United States)

    D. C. Flanagan; J. R. Frankenberger; T. A. Cochrane; C. S. Renschler; W. J. Elliot

    2013-01-01

    At the hillslope profile and/or field scale, a simple Windows graphical user interface (GUI) is available to easily specify the slope, soil, and management inputs for application of the USDA Water Erosion Prediction Project (WEPP) model. Likewise, basic small watershed configurations of a few hillslopes and channels can be created and simulated with this GUI. However,...

  15. A history of wind erosion prediction models in the United States Department of Agriculture: The Wind Erosion Prediction System (WEPS)

    Science.gov (United States)

    Development of the Wind Erosion Prediction System (WEPS) was officially inaugurated in 1985 by United States Department of Agriculture-Agricultural Research Service (USDA-ARS) scientists in response to customer requests, particularly those coming from the USDA Soil Conservation Service (SCS), for im...

  16. Predicting coastal cliff erosion using a Bayesian probabilistic model

    Science.gov (United States)

    Hapke, Cheryl J.; Plant, Nathaniel G.

    2010-01-01

    Regional coastal cliff retreat is difficult to model due to the episodic nature of failures and the along-shore variability of retreat events. There is a growing demand, however, for predictive models that can be used to forecast areas vulnerable to coastal erosion hazards. Increasingly, probabilistic models are being employed that require data sets of high temporal density to define the joint probability density function that relates forcing variables (e.g. wave conditions) and initial conditions (e.g. cliff geometry) to erosion events. In this study we use a multi-parameter Bayesian network to investigate correlations between key variables that control and influence variations in cliff retreat processes. The network uses Bayesian statistical methods to estimate event probabilities using existing observations. Within this framework, we forecast the spatial distribution of cliff retreat along two stretches of cliffed coast in Southern California. The input parameters are the height and slope of the cliff, a descriptor of material strength based on the dominant cliff-forming lithology, and the long-term cliff erosion rate that represents prior behavior. The model is forced using predicted wave impact hours. Results demonstrate that the Bayesian approach is well-suited to the forward modeling of coastal cliff retreat, with the correct outcomes forecast in 70–90% of the modeled transects. The model also performs well in identifying specific locations of high cliff erosion, thus providing a foundation for hazard mapping. This approach can be employed to predict cliff erosion at time-scales ranging from storm events to the impacts of sea-level rise at the century-scale.

  17. Targeting Forest Management through Fire and Erosion Modeling

    Science.gov (United States)

    Elliot, William J.; Miller, Mary Ellen; MacDonald, Lee H.

    2013-04-01

    Forests deliver a number of ecosystem services, including clean water. When forests are disturbed by wildfire, the timing and quantity of runoff can be altered, and the quality can be severely degraded. A modeling study for about 1500 km2 in the Upper Mokelumne River Watershed in California was conducted to determine the risk of wildfire and the associated potential sediment delivery should a wildfire occur, and to calculate the potential reduction in sediment delivery that might result from fuel reduction treatments. The first step was to predict wildfire severity and probability of occurrence under current vegetation conditions with FlamMap fire prediction tool. FlamMap uses current vegetation, topography, and wind characteristics to predict the speed, flame length, and direction of a simulated flame front for each 30-m pixel. As the first step in the erosion modeling, a geospatial interface for the WEPP model (GeoWEPP) was used to delineate approximately 6-ha hillslope polygons for the study area. The flame length values from FlamMap were then aggregated for each hillslope polygon to yield a predicted fire intensity. Fire intensity and pre-fire vegetation conditions were used to estimate fire severity (either unburned, low, moderate or high). The fire severity was combined with soil properties from the STATSGO database to build the vegetation and soil files needed to run WEPP for each polygon. Eight different stochastic climates were generated to account for the weather variability within the basin. A modified batching version of GeoWEPP was used to predict the first-year post-fire sediment yield from each hillslope and subwatershed. Estimated sediment yields ranged from 0 to more than 100 Mg/ha, and were typical of observed values. The polygons that generated the greatest amount of sediment or that were critical for reducing fire spread were identified, and these were "treated" by reducing the amount of fuel available for a wildfire. The erosion associated with

  18. Experience in the application of erosion-corrosion prediction programs

    International Nuclear Information System (INIS)

    Castiella Villacampa, E.; Cacho Cordero, L.; Pascual Velazquez, A.; Casar Asuar, M.

    1994-01-01

    Recently the results of the Nuclear Regulatory Commission's follow-on programme relating to the application of erosion-corrosion supervision and control programs were published. The main problems encountered in their practical application are highlighted, namely those associated with prediction, calculation of minimum thickness acceptable by code, results analyses of the thicknesses measured using ultrasound technology, cases of incorrect substitution, etc. A number of power plants in Spain are currently using a computerised prediction and monitoring program for the erosion-corrosion phenomenon. The experience gained in the application of this program has been such that it has led to a number or benefits: an improvement in the application of the program, proof of its suitability to real situation, the establishment of a series of criteria relative to the inclusion or exclusion of consideration during data input, the monitoring of the phenomenon, selection of elements for inspection, etc. The report describes these areas, using typical examples as illustrations. (Author)

  19. Forest soil erosion prediction as influenced by wildfire and roads

    Science.gov (United States)

    Cao, L.; Brooks, E. S.; Elliot, W.

    2017-12-01

    Following a wildfire, the risk of erosion is greatly increased. Forest road networks may change the underlying topography and alter natural flow paths. Flow accumulation and energy can be redistributed by roads and alter soil erosion processes. A LiDAR (Light Detection and Ranging) DEM makes it possible to quantify road topography, and estimate how roads influence surface runoff and sediment transport in a fire-disturbed watershed. With GIS technology and a soil erosion model, this study was carried out to evaluate the effect of roads on erosion and sediment yield following the Emerald Fire southwest of Lake Tahoe. The GeoWEPP model was used to estimate onsite erosion and offsite sediment delivery from each hillslope polygon and channel segment before and after fire disturbance in part of the burned area. The GeoWEPP flow path method was used to estimate the post-fire erosion rate of each GIS pixel. A 2-m resolution LiDAR DEM was used as the terrain layer. The Emerald Fire greatly increased onsite soil loss and sediment yields within the fire boundary. Following the fire, 78.71% of the burned area had predicted sediment yields greater than 4 Mg/ha/yr, compared to the preburn condition when 65.3% of the study area was estimated to generate a sediment yield less than 0.25 Mg/ha/yr. Roads had a remarkable influence on the flow path simulation and sub-catchments delineation, affecting sediment transport process spatially. Road segments acted as barriers that intercepted overland runoff and reduced downslope flow energy accumulation, therefore reducing onsite soil loss downslope of the road. Roads also changed the boundary of sub-catchment and defined new hydrological units. Road segments can transport sediment from one sub-catchment to another. This in turn leads to the redistribution of sediment and alters sediment yield for some sub-catchments. Culverts and road drain systems are of vital importance in rerouting runoff and sediment. Conservation structures can be

  20. Numerical simulation of CFC and tungsten target erosion in ITER-FEAT divertor

    International Nuclear Information System (INIS)

    Filatov, V.

    2003-01-01

    Physical, chemical and thermal surface erosion for water-cooled target armoured by CFC and tungsten is simulated by numerical code ERosion OF Immolated Layer (EROFIL-1). Some calculation results on the CFC and tungsten vertical target (VT) erosion in the ITER-FEAT divertor are presented for various operation modes (normal operations, slow transients, ELMs and disruptions). The main erosion mechanisms of CFC armour are the chemical and sublimation ones. Maximum erosion depth per 3000 cycles during normal operations and slow transients is of 2.7 mm at H phase and of 13.5 mm at DT phase. An evaluation of VT tungsten armour erosion per 3000 cycles of H and DT operations shows that no physical or chemical erosion as well as no melting are expected for tungsten armour at normal operations and slow transients. The tungsten armour melting at 2x10 6 ELMs is not allowable. The 300 disruptions are not dangerous in view of evaporation

  1. Assessment of erosion of the ITER divertor targets during type I ELMs

    Science.gov (United States)

    Federici, G.; Loarte, A.; Strohmayer, G.

    2003-09-01

    This paper presents the results of a preliminary assessment conducted to estimate the thermal response and erosion lifetime of the ITER divertor targets clad either with carbon-fibre composite or tungsten during type I ELMs. The one-dimensional thermal/erosion model, used for the analyses, is briefly described. It includes all the key surface heat transfer processes such as evaporation, melting, and radiation, and their interaction with the bulk thermal response, and it is based on an implicit finite-difference scheme, which allows for temperature-dependent material properties. The cases analysed clarify the influence of several ELM parameters on the heat transfer and erosion processes at the target (i.e. characteristic plasma ELM energy loss from the pedestal, fraction of the energy reaching the divertor, broadening of the strike-points during ELMs, duration and waveform of the ELM heat load) and design/material parameters (i.e. inclination of the target, type and thickness of the armour material, and for tungsten only, fraction of the melt layer loss). Comparison is made between cases where all ELMs are characterized by the same fixed averaged parameters, and cases where instead the characteristic parameters of each ELM are evaluated in a random fashion by using a standard Monte Carlo technique, based on distributions of some of the variables of interest derived from experiments in today's machines. Although uncertainties rule out providing firm quantitative predictions, the results of this study are useful to illustrate trends. Based on the results, the implications on the design and operation are discussed and priorities are determined for the R&D needed to reduce the remaining uncertainties.

  2. Assessment of erosion of the ITER divertor targets during type I ELMs

    International Nuclear Information System (INIS)

    Federici, G; Loarte, A; Strohmayer, G

    2003-01-01

    This paper presents the results of a preliminary assessment conducted to estimate the thermal response and erosion lifetime of the ITER divertor targets clad either with carbon-fibre composite or tungsten during type I ELMs. The one-dimensional thermal/erosion model, used for the analyses, is briefly described. It includes all the key surface heat transfer processes such as evaporation, melting, and radiation, and their interaction with the bulk thermal response, and it is based on an implicit finite-difference scheme, which allows for temperature-dependent material properties. The cases analysed clarify the influence of several ELM parameters on the heat transfer and erosion processes at the target (i.e. characteristic plasma ELM energy loss from the pedestal, fraction of the energy reaching the divertor, broadening of the strike-points during ELMs, duration and waveform of the ELM heat load) and design/material parameters (i.e. inclination of the target, type and thickness of the armour material, and for tungsten only, fraction of the melt layer loss). Comparison is made between cases where all ELMs are characterized by the same fixed averaged parameters, and cases where instead the characteristic parameters of each ELM are evaluated in a random fashion by using a standard Monte Carlo technique, based on distributions of some of the variables of interest derived from experiments in today's machines. Although uncertainties rule out providing firm quantitative predictions, the results of this study are useful to illustrate trends. Based on the results, the implications on the design and operation are discussed and priorities are determined for the R and D needed to reduce the remaining uncertainties

  3. Long-term predictive capability of erosion models

    Science.gov (United States)

    Veerabhadra, P.; Buckley, D. H.

    1983-01-01

    A brief overview of long-term cavitation and liquid impingement erosion and modeling methods proposed by different investigators, including the curve-fit approach is presented. A table was prepared to highlight the number of variables necessary for each model in order to compute the erosion-versus-time curves. A power law relation based on the average erosion rate is suggested which may solve several modeling problems.

  4. Assessing and Predicting Erosion from Off Highway Vehicle Trails in Front-Range Rocky Mountain Watersheds.

    Science.gov (United States)

    Howard, M. J.; Silins, U.; Anderson, A.

    2016-12-01

    Off highway vehicle (OHV) trails have the potential to deliver sediment to sensitive headwater streams and increased OHV use is a growing watershed management concern in many Rocky Mountain regions. Predictive tools for estimating erosion and sediment inputs are needed to support assessment and management of erosion from OHV trail networks. The objective of this study was to a) assess erodibility (K factor) and total erosion from OHV trail networks in Rocky Mountain watersheds in south-west Alberta, Canada, and to b) evaluate the applicability of the Universal Soil Loss Equation (USLE) for predicting OHV trail erosion to support erosion management strategies. Measured erosion rates and erodibility (K) from rainfall simulation plots on OHV trails during the summers of 2014 and 2015 were compared to USLE predicted erosion from these same trails. Measured erodibility (K) from 23 rainfall simulation plots was highly variable (0.001-0.273 Mg*ha*hr/ha*MJ*mm) as was total seasonal erosion from 52 large trail sections (0.0595-43.3 Mg/ha) across trail segments of variable slope, stoniness, and trail use intensity. In particular, intensity of trail use had a large effect on both erodibility and total erosion that is not presently captured by erodibility indices (K) derived from soil characteristics. Results of this study suggest that while application of USLE for predicting erosion from OHV trail networks may be useful for initial coarse erosion assessment, a better understanding of the effect of factors such as road/trail use intensity on erodibility is needed to support use of USLE or associated erosion prediction tools for road/trail erosion management.

  5. Prediction of Soil Erosion Rates in Japan where Heavily Forested Landscape with Unstable Terrain

    Science.gov (United States)

    Nanko, K.; Oguro, M.; Miura, S.; Masaki, T.

    2016-12-01

    Soil is fundamental for plant growth, water conservation, and sustainable forest management. Multidisciplinary interest in the role of the soil in areas such as biodiversity, ecosystem services, land degradation, and water security has been growing (Miura et al., 2015). Forest is usually protective land use from soil erosion because vegetation buffers rainfall power and erosivity. However, some types of forest in Japan show high susceptibility to soil erosion due to little ground cover and steep slopes exceeding thirty degree, especially young Japanese cypress (Chamaecyparis obtusa) plantations (Miura et al., 2002). This is a critical issue for sustainable forest management because C. obtusaplantations account for 10% of the total forest coverage in Japan (Forestry Agency, 2009). Prediction of soil erosion rates on nationwide scale is necessary to make decision for future forest management plan. To predict and map soil erosion rates across Japan, we applied three soil erosion models, RUSLE (Revised Universal Soil Loss Equation, Wischmeier and Smith, 1978), PESERA (Pan-European Soil Erosion Risk Assessment, Kirkby et al., 2003), and RMMF (Revised Morgan-Morgan-Finney, Morgan, 2001). The grid scale is 1-km. RUSLE and PESERA are most widely used erosion models today. RMMF includes interactions between rainfall and vegetation, such as canopy interception and ratio of canopy drainage in throughfall. Evaporated rainwater by canopy interception, generally accounts for 15-20% in annual rainfall, does not contribute soil erosion. Whereas, larger raindrops generated by canopy drainage produced higher splash erosion rates than gross rainfall (Nanko et al., 2008). Therefore, rainfall redistribution process in canopy should be considered to predict soil erosion rates in forested landscape. We compared the results from three erosion models and analyze the importance of environmental factors for the prediction of soil erosion rates. This research was supported by the Environment

  6. Challenges in soil erosion research and prediction model development

    Science.gov (United States)

    Quantification of soil erosion has been traditionally considered as a surface hydrologic process with equations for soil detachment and sediment transport derived from the mechanics and hydraulics of the rainfall and surface flow. Under the current erosion modeling framework, the soil has a constant...

  7. Advanced experimental and numerical techniques for cavitation erosion prediction

    CERN Document Server

    Chahine, Georges; Franc, Jean-Pierre; Karimi, Ayat

    2014-01-01

    This book provides a comprehensive treatment of the cavitation erosion phenomenon and state-of-the-art research in the field. It is divided into two parts. Part 1 consists of seven chapters, offering a wide range of computational and experimental approaches to cavitation erosion. It includes a general introduction to cavitation and cavitation erosion, a detailed description of facilities and measurement techniques commonly used in cavitation erosion studies, an extensive presentation of various stages of cavitation damage (including incubation and mass loss), and insights into the contribution of computational methods to the analysis of both fluid and material behavior. The proposed approach is based on a detailed description of impact loads generated by collapsing cavitation bubbles and a physical analysis of the material response to these loads. Part 2 is devoted to a selection of nine papers presented at the International Workshop on Advanced Experimental and Numerical Techniques for Cavitation Erosion (Gr...

  8. Predicting the temporal relationship between soil cesium-137 and erosion rate

    International Nuclear Information System (INIS)

    Kachanoski, R.G.; De Jong, E.

    1984-01-01

    A model was developed that predicts the amount of 137 Cs remaining in soil as a function of time and erosion rate. The model accounts for atmospheric deposition, radioactive decay, tillage dilution, and erosion transport of 137 Cs, as well as seasonal differences in 137 Cs deposition and erosion rates. The model was used to estimate minimum resolution of erosion estimates based on detection limits and accuracy of 137 Cs measurement by gamma spectroscopy, as a function of time and erosion rate. The analysis showed that under Saskatchewan conditions, changes in 137 Cs at a given site can be used to estimate erosion rates between 0.5 and 10 kg m -2 yr -1 with reasonable precision, provided the sampling interval is at least 15 yr. The relationship of fraction of 137 Cs lost vs. erosion as predicted by the model was compared with other methods being used. The model was used to estimate erosion from selected Saskatchewan soils where 137 Cs levels were measured in 1966 and again in 1981. Erosion rates calculated with the model varied from 1 kg m -2 yr -1 for a sandy loam soil in continuous forage to 19 kg m -2 yr -1 for a similar soil in a crop-fallow rotation. Erosion estimates using the model were higher than those calculated by assuming that soil loss was directly proportional to 137 Cs loss, especially when 137 Cs loss was high

  9. Predicting soil erosion risk at the Alqueva dam watershed

    OpenAIRE

    Ferreira, Vera; Panagopoulos, Thomas

    2012-01-01

    Soil erosion is serious economic and environmental concern. Assessing soil erosion risk in the Alqueva dam watershed is urgently needed to conserve soil and water resources and prevent the accelerated dam siltation, taking into account the possible land-use changes, due to tourism development, intensification of irrigated farming and biomass production, as well as climate change. A comprehensive methodology that integrates Revised Universal Soil Loss Equation (RUSLE) model and Geographic Info...

  10. Building Chinese wind data for Wind Erosion Prediction System using surrogate US data

    Science.gov (United States)

    Wind erosion is a global problem, especially in arid and semiarid regions of the world, which leads to land degradation and atmosphere pollution. The process-based Wind Erosion Prediction System (WEPS), developed by the USDA, is capable of simulating the windblown soil loss with changing weather and...

  11. Adapting the Water Erosion Prediction Project (WEPP) model for forest applications

    Science.gov (United States)

    Shuhui Dun; Joan Q. Wu; William J. Elliot; Peter R. Robichaud; Dennis C. Flanagan; James R. Frankenberger; Robert E. Brown; Arthur C. Xu

    2009-01-01

    There has been an increasing public concern over forest stream pollution by excessive sedimentation due to natural or human disturbances. Adequate erosion simulation tools are needed for sound management of forest resources. The Water Erosion Prediction Project (WEPP) watershed model has proved useful in forest applications where Hortonian flow is the major form of...

  12. The Rangeland Hydrology and Erosion Model: A dynamic approach for predicting soil loss on rangelands

    Science.gov (United States)

    In this study we present the improved Rangeland Hydrology and Erosion Model (RHEM V2.3), a process-based erosion prediction tool specific for rangeland application. The article provides the mathematical formulation of the model and parameter estimation equations. Model performance is assessed agains...

  13. The role of bathymetry, wave obliquity and coastal curvature in dune erosion prediction

    NARCIS (Netherlands)

    Den Heijer, C.

    2013-01-01

    This study aims at reducing uncertainty in dune erosion predictions, in particular at complex dune coasts, in order to improve the assessment method for dune safety against flooding. To that end, state-of-the-art process-based dune erosion models are employed to further investigate issues

  14. Comparison of WEPP and APEX runoff and erosion prediction at field scale in Goodwater Creek Experimental Watershed

    Science.gov (United States)

    The Water Erosion Prediction Project (WEPP) and the Agricultural Policy/Environmental eXtender (APEX) are process-based models that can predict spatial and temporal distributions of erosion for hillslopes and watersheds. This study applies the WEPP model to predict runoff and erosion for a 35-ha fie...

  15. Erosion Prediction Analysis and Landuse Planning in Gunggung Watershed, Bali, Indonesia

    Science.gov (United States)

    Trigunasih, N. M.; Kusmawati, T.; Yuli Lestari, N. W.

    2018-02-01

    The purpose of this research is to predict the erosion that occurs in Gunggung watershed and sustainable landuse management plan. This research used the USLE (Universal Soil Loss Equation) methodology. The method used observation / field survey and soil analysis at the Soil Laboratory of Faculty of Agriculture, Udayana University. This research is divided into 5 stages, (1) land unit determination, (2) Field observation and soil sampling, (3) Laboratory analysis and data collection, (4) Prediction of erosion using USLE (Universal Soil Loss Equation) method, (5) The permissible erosion determination (EDP) then (6) determines the level of erosion hazard based on the depth of the soil, as well as the soil conservation plan if the erosion is greater than the allowed erosion, and (7) determining landuse management plan for sustainable agriculture. Erosion which value is smaller than soil loss tolerance can be exploited in a sustainable manner, while erosion exceeds allowable erosion will be conservation measures. Conservation action is the improvement of vegetation and land management. Land management like improvements the terrace, addition of organic matter, increase plant density, planting ground cover and planting layered header system will increase the land capability classes. Land use recommended after management is mixed plantation high density with forest plants, mix plantation high density with patio bench construction, seasonal cultivation and perennial crops, cultivation of perennial crops and cultivation of seasonal crops.

  16. Target fabrication using laser and spark erosion machining

    International Nuclear Information System (INIS)

    Clement, X.; Coudeville, A.; Eyharts, P.; Perrine , J.P.; Rouillard, R.

    1981-11-01

    Lasers and E.D.M. (electrical discharge machining) are both extremely useful tools for machining the small targets needed in inertial confinement studies. Lasers are currently used in a wide range of target problems and it appears that E.D.M. has a still wider range of applications for plane and spherical targets. The problems of material deformation and tool breaking are practically eliminated as the electrode and the machined part are not in mechanical contact. In comparison with laser micromachining E.D.M. offers: larger versatility with the possibility of new developments and applications; higher production speed for thin conducting materials; lower initial and operating costs; the processes are well controlled, reproducible and can be easily automated; the operation is safe without the dangers associted with lasers

  17. Spectroscopic measurement of target plate erosion in the ASDEX Upgrade divertor

    Energy Technology Data Exchange (ETDEWEB)

    Filed, A R; Garcia-Rosales, C; Lieder, G; Pitcher, C S; Radtke, R [Association Euratom-Max-Planck-Institut fuer Plasmaphysik, Garching (Germany); ASDEX Upgrade Team

    1996-02-01

    The erosion of the graphite divertor plates in the ASDEX Upgrade tokamak is measured spectroscopically. Spatial profiles of the D{sup 0} and C{sup +} influxes across the outer target plate are determined from measured absolute line intensities. Plasma parameters (n{sub e}, T{sub e}) at the target, which are required to determine the appropriate photon emission efficiencies for these lines, are obtained from an in-vessel reciprocating Langmuir probe above the target plate. Yields for the erosion of the graphite by the incident D{sup +} flux are determined from the ratio of the measured C{sup +} to D{sup 0} fluxes. Over a range of moderate densities the measured yields of {<=} 4% are explicable in terms of physical sputtering alone. Chemical sputtering by low energy Franck-Condon neutrals probably contributes, however, to the total erosion. At higher densities detachment of the plasma from the targets occurs owing to formation of a MARFE near the X point. Under these conditions localized physical sputtering of the targets ceases. The impurity level (Z{sub eff}) is, however, maintained following detachment, indicating a corresponding maintenance of carbon influx, perhaps due to chemical erosion of the total graphite surface and/or an improvement in particle confinement in the detached state. (author). 26 refs, 14 figs, 1 tab.

  18. A history of wind erosion prediction models in the United States Department of Agriculture prior to the Wind Erosion Prediction System

    Science.gov (United States)

    Tatarko, John; Sporcic, Michael A.; Skidmore, Edward L.

    2013-09-01

    The Great Plains experienced an influx of settlers in the late 1850s-1900. Periodic drought was hard on both settlers and the soil and caused severe wind erosion. The period known as the Dirty Thirties, 1931-1939, produced many severe windstorms, and the resulting dusty sky over Washington, DC helped Hugh Hammond Bennett gain political support for the Soil Conservation Act of 1937 that started the USDA Soil Conservation Service (SCS). Austin W. Zingg and William S. Chepil began wind erosion studies at a USDA laboratory at Kansas State University in 1947. Neil P. Woodruff and Francis H. Siddoway published the first widely used model for wind erosion in 1965, called the Wind Erosion Equation (WEQ). The WEQ was solved using a series of charts and lookup tables. Subsequent improvements to WEQ included monthly magnitudes of the total wind, a computer version of WEQ programmed in FORTRAN, small-grain equivalents for range grasses, tillage systems, effects of residue management, crop row direction, cloddiness, monthly climate factors, and the weather. The SCS and the Natural Resources Conservation Service (NRCS) produced several computer versions of WEQ with the goal of standardizing and simplifying it for field personnel including a standalone version of WEQ was developed in the late 1990s using Microsoft Excel. Although WEQ was a great advancement to the science of prediction and control of wind erosion on cropland, it had many limitations that prevented its use on many lands throughout the United States and the world. In response to these limitations, the USDA developed a process-based model know as the Wind Erosion Prediction System (WEPS). The USDA Agricultural Research Service has taken the lead in developing science and technology for wind erosion prediction.

  19. Prediction method for cavitation erosion based on measurement of bubble collapse impact loads

    International Nuclear Information System (INIS)

    Hattori, S; Hirose, T; Sugiyama, K

    2009-01-01

    The prediction of cavitation erosion rates is important in order to evaluate the exact life of components. The measurement of impact loads in bubble collapses helps to predict the life under cavitation erosion. In this study, we carried out erosion tests and the measurements of impact loads in bubble collapses with a vibratory apparatus. We evaluated the incubation period based on a cumulative damage rule by measuring the impact loads of cavitation acting on the specimen surface and by using the 'constant impact load - number of impact loads curve' similar to the modified Miner's rule which is employed for fatigue life prediction. We found that the parameter Σ(F i α xn i ) (F i : impact load, n i : number of impacts and α: constant) is suitable for the evaluation of the erosion life. Moreover, we propose a new method that can predict the incubation period under various cavitation conditions.

  20. Comparison of 137Cs fallout redistribution analysis and conventional erosion-prediction models (WEPP, USLE)

    International Nuclear Information System (INIS)

    Sparovek, G.; Bacchi, O.O.S.; Ranieri, S.B.L.; Schnug, E.; De-Maria, I.C.

    2002-01-01

    Soil erosion is the most important component of the degradation of tropical agroecosystems. The rates of erosion should be considered in land evaluation and conservation planning assessment. The methods available for erosion prediction are not sufficiently well calibrated or validated for tropical soils, climates and crops. Thus, differences in estimated soil-erosion values may be expected, even if considering a single set of input data. Three methods for the estimation of soil erosion (USLE, WEPP, and 137 Cs) were applied to a watershed cultivated with sugarcane in southeastern Brazil. The absolute erosion-rate values and differences in the spatial distribution were evaluated. The overall results suggest important differences in the estimates obtained by the three methods. The differences occurred both in mean values and in geographic locations. The relative mean values for soil loss were USLE>> 137 Cs>WEPP and for standard deviations were USLE>WEPP> 137 Cs, indicating that USLE predicted the highest erosion values spread out over the widest range. The poor geographical coincidence of the results is evidence that values resulting from non-calibrated erosion methods should be considered only as qualitative indications. The method selection should consider overall site variability in relation to factors to which the methods are known to be sensitive. (author)

  1. Atomic Oxygen Erosion Yield Prediction for Spacecraft Polymers in Low Earth Orbit

    Science.gov (United States)

    Banks, Bruce A.; Backus, Jane A.; Manno, Michael V.; Waters, Deborah L.; Cameron, Kevin C.; deGroh, Kim K.

    2009-01-01

    The ability to predict the atomic oxygen erosion yield of polymers based on their chemistry and physical properties has been only partially successful because of a lack of reliable low Earth orbit (LEO) erosion yield data. Unfortunately, many of the early experiments did not utilize dehydrated mass loss measurements for erosion yield determination, and the resulting mass loss due to atomic oxygen exposure may have been compromised because samples were often not in consistent states of dehydration during the pre-flight and post-flight mass measurements. This is a particular problem for short duration mission exposures or low erosion yield materials. However, as a result of the retrieval of the Polymer Erosion and Contamination Experiment (PEACE) flown as part of the Materials International Space Station Experiment 2 (MISSE 2), the erosion yields of 38 polymers and pyrolytic graphite were accurately measured. The experiment was exposed to the LEO environment for 3.95 years from August 16, 2001 to July 30, 2005 and was successfully retrieved during a space walk on July 30, 2005 during Discovery s STS-114 Return to Flight mission. The 40 different materials tested (including Kapton H fluence witness samples) were selected specifically to represent a variety of polymers used in space as well as a wide variety of polymer chemical structures. The MISSE 2 PEACE Polymers experiment used carefully dehydrated mass measurements, as well as accurate density measurements to obtain accurate erosion yield data for high-fluence (8.43 1021 atoms/sq cm). The resulting data was used to develop an erosion yield predictive tool with a correlation coefficient of 0.895 and uncertainty of +/-6.3 10(exp -25)cu cm/atom. The predictive tool utilizes the chemical structures and physical properties of polymers to predict in-space atomic oxygen erosion yields. A predictive tool concept (September 2009 version) is presented which represents an improvement over an earlier (December 2008) version.

  2. Influence of plasma pressure gradient on melt layer macroscopic erosion of metal targets in disruption simulation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Tereshin, V.I.; Garkusha, I.E. E-mail: garkusha@ipp.kharkov.ua; Bandura, A.N.; Byrka, O.V.; Chebotarev, V.V.; Makhlaj, V.A.; Solyakov, D.G.; Wuerz, H

    2003-03-01

    Melt layer erosion of metal targets under pulsed high heat loads is discussed. Tungsten, copper, aluminum, and titanium targets were exposed to perpendicular and inclined plasma impact in the quasi-steady-state plasma accelerator QSPA Kh-50. Melt layer motion results in erosion crater formation with rather large mountains of the resolidified material at the crater edge. It is shown that macroscopic motion of the melt layer and surface cracking are the main factors responsible for tungsten erosion.

  3. Influence of plasma pressure gradient on melt layer macroscopic erosion of metal targets in disruption simulation experiments

    International Nuclear Information System (INIS)

    Tereshin, V.I.; Garkusha, I.E.; Bandura, A.N.; Byrka, O.V.; Chebotarev, V.V.; Makhlaj, V.A.; Solyakov, D.G.; Wuerz, H.

    2003-01-01

    Melt layer erosion of metal targets under pulsed high heat loads is discussed. Tungsten, copper, aluminum, and titanium targets were exposed to perpendicular and inclined plasma impact in the quasi-steady-state plasma accelerator QSPA Kh-50. Melt layer motion results in erosion crater formation with rather large mountains of the resolidified material at the crater edge. It is shown that macroscopic motion of the melt layer and surface cracking are the main factors responsible for tungsten erosion

  4. Atomic Oxygen Erosion Yield Predictive Tool for Spacecraft Polymers in Low Earth Orbit

    Science.gov (United States)

    Bank, Bruce A.; de Groh, Kim K.; Backus, Jane A.

    2008-01-01

    A predictive tool was developed to estimate the low Earth orbit (LEO) atomic oxygen erosion yield of polymers based on the results of the Polymer Erosion and Contamination Experiment (PEACE) Polymers experiment flown as part of the Materials International Space Station Experiment 2 (MISSE 2). The MISSE 2 PEACE experiment accurately measured the erosion yield of a wide variety of polymers and pyrolytic graphite. The 40 different materials tested were selected specifically to represent a variety of polymers used in space as well as a wide variety of polymer chemical structures. The resulting erosion yield data was used to develop a predictive tool which utilizes chemical structure and physical properties of polymers that can be measured in ground laboratory testing to predict the in-space atomic oxygen erosion yield of a polymer. The properties include chemical structure, bonding information, density and ash content. The resulting predictive tool has a correlation coefficient of 0.914 when compared with actual MISSE 2 space data for 38 polymers and pyrolytic graphite. The intent of the predictive tool is to be able to make estimates of atomic oxygen erosion yields for new polymers without requiring expensive and time consumptive in-space testing.

  5. Development and Life Prediction of Erosion Resistant Turbine Low Conductivity Thermal Barrier Coatings

    Science.gov (United States)

    Zhu, Dongming; Miller, Robert A.; Kuczmarski, Maria A.

    2010-01-01

    Future rotorcraft propulsion systems are required to operate under highly-loaded conditions and in harsh sand erosion environments, thereby imposing significant material design and durability issues. The incorporation of advanced thermal barrier coatings (TBC) in high pressure turbine systems enables engine designs with higher inlet temperatures, thus improving the engine efficiency, power density and reliability. The impact and erosion resistance of turbine thermal barrier coating systems are crucial to the turbine coating technology application, because a robust turbine blade TBC system is a prerequisite for fully utilizing the potential coating technology benefit in the rotorcraft propulsion. This paper describes the turbine blade TBC development in addressing the coating impact and erosion resistance. Advanced thermal barrier coating systems with improved performance have also been validated in laboratory simulated engine erosion and/or thermal gradient environments. A preliminary life prediction modeling approach to emphasize the turbine blade coating erosion is also presented.

  6. Predicted erosion and sediment delivery of fallout plutonium

    International Nuclear Information System (INIS)

    Foster, G.R.; Hakonson, T.E.

    1984-01-01

    Plutonium (Pu) from fallout after atmospheric explosion of nuclear weapons in the 1950s and 1960s is being redistributed over the landscape by soil erosion and carried on sediment by streams to oceans. Erosion rates computed with the Universal Soil Loss Equation for about 200,000 sample points on nonfederal land across the US were used to estimate Pu removal rates by soil erosion by water, Pu delivery in several major rivers, and concentration of Pu on the transported sediment. Estimates of average annual Pu delivery on sediment ranged from 0.002% of the initial fallout Pu inventory for the Savannah River basin to 0.08% for the Mississippi River basin. If the deposition of Pu had been uniformly 37 Bq/m 2 , the estimated Pu activity on suspended sediment ranged from about 0.26 Bq/kg of sediment for the Savannah River basin to 0.52 Bq/kg for the Columbia and Rio Grande river basins. After 1000 yr, about 9 to 48% of the initial Pu inventory will remain in US soils that are eroding. Much of the Pu on eroded sediment will travel only a short distance from its origin before its host sediment particles are deposited and permanently located, at least for a few hundred years. As much as 90% of the initially deposited Pu will remain, redistributed over the landscape by erosion and deposition. Although the delivery rate of Pu by rivers will not decrease greatly in the next 100 yr, a significant decrease will likely occur by 1000 yr

  7. Prediction of long-term erosion from landfill covers in the southwest

    International Nuclear Information System (INIS)

    Anderson, C.E.; Stormont, J.C.

    1997-01-01

    Erosion is a primary stressor of landfill covers, especially for climates with high intensity storms and low native plant density. Rills and gullies formed by discrete events can damage barrier layers and induce failure. Geomorphologic, empirical and physical modeling procedures are available to provide estimates of surface erosion, but numerical modeling requires accurate representation of the severe rainfall events that generate erosion. The National Weather Service precipitation frequency data and estimates of 5, 10, 15, 30 and 60-minute intensity can be statistically combined in a numerical model to obtain long-term erosion estimates. Physically based numerical models using the KINEROS and AHYMO programs have been utilized to predict the erosion from a southwestern landfill or waste containment site with 0.03, 0.05 and 0.08 meter per meter surface slopes. Results of AHYMO modeling were within 15 percent of average annual values computed with the empirical Universal Soil Loss Equation. However, the estimation of rill and gully formation that primarily degrades cover systems requires quantifying single events. For Southwestern conditions, a single 10-year storm can produce erosion quantifies equal to three times the average annual erosion and a 100-year storm can produce five times the average annual erosion

  8. Numerical Investigation of Temperature Distribution in an Eroded Bend Pipe and Prediction of Erosion Reduced Thickness

    Science.gov (United States)

    Zhu, Hongjun; Feng, Guang; Wang, Qijun

    2014-01-01

    Accurate prediction of erosion thickness is essential for pipe engineering. The objective of the present paper is to study the temperature distribution in an eroded bend pipe and find a new method to predict the erosion reduced thickness. Computational fluid dynamic (CFD) simulations with FLUENT software are carried out to investigate the temperature field. And effects of oil inlet rate, oil inlet temperature, and erosion reduced thickness are examined. The presence of erosion pit brings about the obvious fluctuation of temperature drop along the extrados of bend. And the minimum temperature drop presents at the most severe erosion point. Small inlet temperature or large inlet velocity can lead to small temperature drop, while shallow erosion pit causes great temperature drop. The dimensionless minimum temperature drop is analyzed and the fitting formula is obtained. Using the formula we can calculate the erosion reduced thickness, which is only needed to monitor the outer surface temperature of bend pipe. This new method can provide useful guidance for pipeline monitoring and replacement. PMID:24719576

  9. Chapter 4. Predicting post-fire erosion and sedimentation risk on a landscape scale

    Science.gov (United States)

    MacDonald, L.H.; Sampson, R.; Brady, D.; Juarros, L.; Martin, Deborah

    2000-01-01

    Historic fire suppression efforts have increased the likelihood of large wildfires in much of the western U.S. Post-fire soil erosion and sedimentation risks are important concerns to resource managers. In this paper we develop and apply procedures to predict post-fire erosion and sedimentation risks on a pixel-, catchment-, and landscape-scale in central and western Colorado.Our model for predicting post-fire surface erosion risk is conceptually similar to the Revised Universal Soil Loss Equation (RUSLE). One key addition is the incorporation of a hydrophobicity risk index (HY-RISK) based on vegetation type, predicted fire severity, and soil texture. Post-fire surface erosion risk was assessed for each 90-m pixel by combining HYRISK, slope, soil erodibility, and a factor representing the likely increase in soil wetness due to removal of the vegetation. Sedimentation risk was a simple function of stream gradient. Composite surface erosion and sedimentation risk indices were calculated and compared across the 72 catchments in the study area.When evaluated on a catchment scale, two-thirds of the catchments had relatively little post-fire erosion risk. Steeper catchments with higher fuel loadings typically had the highest post-fire surface erosion risk. These were generally located along the major north-south mountain chains and, to a lesser extent, in west-central Colorado. Sedimentation risks were usually highest in the eastern part of the study area where a higher proportion of streams had lower gradients. While data to validate the predicted erosion and sedimentation risks are lacking, the results appear reasonable and are consistent with our limited field observations. The models and analytic procedures can be readily adapted to other locations and should provide useful tools for planning and management at both the catchment and landscape scale.

  10. Integration of fluvial erosion factors for predicting landslides along meandering rivers

    Science.gov (United States)

    Chen, Yi-chin; Chang, Kang-tsung; Ho, Jui-yi

    2015-04-01

    River incision and lateral erosion are important geomorphologic processes in mountainous areas of Taiwan. During a typhoon or storm event, the increase of water discharge, flow velocity, and sediment discharge enhances the power of river erosion on channel bank. After the materials on toe of hillslope were removed by river erosion, landslides were triggered at outer meander bends. Although it has been long expected that river erosion can trigger landslide, studies quantifying the effects of river erosion on landslide and the application of river erosion index in landslide prediction are still overlooked. In this study, we investigated the effect of river erosion on landslide in a particular meanders landscape of the Jhoukou River, southern Taiwan. We developed a semi-automatic model to separate meandering lines into several reach segments based on the inflection points and to calculate river erosion indexes, e.g. sinuosity of meander, stream power, and stream order, for each reach segment. This model, then, built the spatial relationship between the reaches and its corresponding hillslopes, of which the toe was eroded by the reach. Based on the spatial relationship, we quantified the correlations between these indexes and landslides triggered by Typhoon Morakot in 2009 to examine the effects of river erosion on landslide. The correlated indexes were then used as landslide predictors in logistic regression model. Results of the study showed that there is no significant correlation between landslide density and meander sinuosity. This may be a result of wider channel dispersing the erosion at a meandering reach. On the other hand, landslide density at concave bank is significantly higher than that at convex bank in the downstream (stream order > 3), but that is almost the same in the upstream (stream order bank. In contrast, river sediment in the downstream is an erosion agent eroding the concave bank laterally, but also depositing on the concave side and protecting

  11. 7 CFR 610.12 - Equations for predicting soil loss due to water erosion.

    Science.gov (United States)

    2010-01-01

    .... (a) The equation for predicting soil loss due to erosion for both the USLE and the RUSLE is A = R × K... 22161.) (b) The factors in the USLE equation are: (1) A is the estimation of average annual soil loss in... 7 Agriculture 6 2010-01-01 2010-01-01 false Equations for predicting soil loss due to water...

  12. Wind erosion in semiarid landscapes: Predictive models and remote sensing methods for the influence of vegetation

    Science.gov (United States)

    Musick, H. Brad

    1993-01-01

    The objectives of this research are: to develop and test predictive relations for the quantitative influence of vegetation canopy structure on wind erosion of semiarid rangeland soils, and to develop remote sensing methods for measuring the canopy structural parameters that determine sheltering against wind erosion. The influence of canopy structure on wind erosion will be investigated by means of wind-tunnel and field experiments using structural variables identified by the wind-tunnel and field experiments using model roughness elements to simulate plant canopies. The canopy structural variables identified by the wind-tunnel and field experiments as important in determining vegetative sheltering against wind erosion will then be measured at a number of naturally vegetated field sites and compared with estimates of these variables derived from analysis of remotely sensed data.

  13. DES Prediction of Cavitation Erosion and Its Validation for a Ship Scale Propeller

    Science.gov (United States)

    Ponkratov, Dmitriy, Dr

    2015-12-01

    Lloyd's Register Technical Investigation Department (LR TID) have developed numerical functions for the prediction of cavitation erosion aggressiveness within Computational Fluid Dynamics (CFD) simulations. These functions were previously validated for a model scale hydrofoil and ship scale rudder [1]. For the current study the functions were applied to a cargo ship's full scale propeller, on which the severe cavitation erosion was reported. The performed Detach Eddy Simulation (DES) required a fine computational mesh (approximately 22 million cells), together with a very small time step (2.0E-4 s). As the cavitation for this type of vessel is primarily caused by a highly non-uniform wake, the hull was also included in the simulation. The applied method under predicted the cavitation extent and did not fully resolve the tip vortex; however, the areas of cavitation collapse were captured successfully. Consequently, the developed functions showed a very good prediction of erosion areas, as confirmed by comparison with underwater propeller inspection results.

  14. Predicting rainfall erosivity by momentum and kinetic energy in Mediterranean environment

    Science.gov (United States)

    Carollo, Francesco G.; Ferro, Vito; Serio, Maria A.

    2018-05-01

    Rainfall erosivity is an index that describes the power of rainfall to cause soil erosion and it is used around the world for assessing and predicting soil loss on agricultural lands. Erosivity can be represented in terms of both rainfall momentum and kinetic energy, both calculated per unit time and area. Contrasting results on the representativeness of these two variables are available: some authors stated that momentum and kinetic energy are practically interchangeable in soil loss estimation while other found that kinetic energy is the most suitable expression of rainfall erosivity. The direct and continuous measurements of momentum and kinetic energy by a disdrometer allow also to establish a relationship with rainfall intensity at the study site. At first in this paper a comparison between the momentum-rainfall intensity relationships measured at Palermo and El Teularet by an optical disdrometer is presented. For a fixed rainfall intensity the measurements showed that the rainfall momentum values measured at the two experimental sites are not coincident. However both datasets presented a threshold value of rainfall intensity over which the rainfall momentum assumes a quasi-constant value. Then the reliability of a theoretically deduced relationship, linking momentum, rainfall intensity and median volume diameter, is positively verified using measured raindrop size distributions. An analysis to assess which variable, momentum or kinetic energy per unit area and time, is the best predictor of erosivity in Italy and Spain was also carried out. This investigation highlighted that the rainfall kinetic energy per unit area and time can be substituted by rainfall momentum as index for estimating the rainfall erosivity, and this result does not depend on the site where precipitation occurs. Finally, rainfall intensity measurements and soil loss data collected from the bare plots equipped at Sparacia experimental area were used to verify the reliability of some

  15. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...

  16. How to diagnose rheumatoid arthritis early: a prediction model for persistent (erosive) arthritis

    NARCIS (Netherlands)

    Visser, Henk; le Cessie, Saskia; Vos, Koen; Breedveld, Ferdinand C.; Hazes, Johanna M. W.

    2002-01-01

    To develop a clinical model for the prediction, at the first visit, of 3 forms of arthritis outcome: self-limiting, persistent nonerosive, and persistent erosive arthritis. A standardized diagnostic evaluation was performed on 524 consecutive, newly referred patients with early arthritis.

  17. 75 FR 75961 - Notice of Implementation of the Wind Erosion Prediction System for Soil Erodibility System...

    Science.gov (United States)

    2010-12-07

    ... implementation of the WEPS system does not affect the Highly Erodible Map Unit List contained in the NRCS Field Office Technical Guide as of January 1, 1990. This 1990 list will continue to be used for all erodibility... plant damage, and predict PM-10 emissions when wind speeds exceed the erosion threshold. The WEPS model...

  18. Evaluation of different machine learning models for predicting and mapping the susceptibility of gully erosion

    Science.gov (United States)

    Rahmati, Omid; Tahmasebipour, Nasser; Haghizadeh, Ali; Pourghasemi, Hamid Reza; Feizizadeh, Bakhtiar

    2017-12-01

    Gully erosion constitutes a serious problem for land degradation in a wide range of environments. The main objective of this research was to compare the performance of seven state-of-the-art machine learning models (SVM with four kernel types, BP-ANN, RF, and BRT) to model the occurrence of gully erosion in the Kashkan-Poldokhtar Watershed, Iran. In the first step, a gully inventory map consisting of 65 gully polygons was prepared through field surveys. Three different sample data sets (S1, S2, and S3), including both positive and negative cells (70% for training and 30% for validation), were randomly prepared to evaluate the robustness of the models. To model the gully erosion susceptibility, 12 geo-environmental factors were selected as predictors. Finally, the goodness-of-fit and prediction skill of the models were evaluated by different criteria, including efficiency percent, kappa coefficient, and the area under the ROC curves (AUC). In terms of accuracy, the RF, RBF-SVM, BRT, and P-SVM models performed excellently both in the degree of fitting and in predictive performance (AUC values well above 0.9), which resulted in accurate predictions. Therefore, these models can be used in other gully erosion studies, as they are capable of rapidly producing accurate and robust gully erosion susceptibility maps (GESMs) for decision-making and soil and water management practices. Furthermore, it was found that performance of RF and RBF-SVM for modelling gully erosion occurrence is quite stable when the learning and validation samples are changed.

  19. Prediction for disruption erosion of ITER plasma facing components; a comparison of experimental and numerical results

    International Nuclear Information System (INIS)

    Laan, J.G. van der; Akiba, M.; Seki, M.; Hassanein, A.; Tanchuk, V.

    1991-01-01

    An evaluation is given for the prediction for disruption erosion in the International Thermonuclear Engineering Reactor (ITER). At first, a description is given of the relation between plasma operating paramters and system dimensions to the predictions of loading parameters of Plasma Facing Components (PFC) in off-normal events. Numerical results from ITER parties on the prediction of disruption erosion are compared for a few typical cases and discussed. Apart from some differences in the codes, the observed discrepancies can be ascribed to different input data of material properties and boundary conditions. Some physical models for vapour shielding and their effects on numerical results are mentioned. Experimental results from ITER parties, obtained with electron and laser beams, are also compared. Erosion rates for the candidate ITER PFC materials are shown to depend very strongly on the energy deposition parameters, which are based on plasma physics considerations, and on the assumed material loss mechanisms. Lifetimes estimates for divertor plate and first wall armour are given for carbon, tungsten and beryllium, based on the erosion in the thermal quench phase. (orig.)

  20. Real-time boronization in PBX-M using erosion of solid boronized targets

    International Nuclear Information System (INIS)

    Kugel, H.W.; Timberlake, J.; Bell, R.; LeBlanc, B.; Okabayashi, M.; Paul, S.; Tighe, W.; Hirooka, Y.

    1994-11-01

    Thirty one real-time boronizations were applied to PBX-M using the plasma erosion of solid target probes. More than 17 g of boron were deposited in PBX-M using this technique. The probes were positioned at the edge plasma to optimize vaporization and minimize spallation. Auger depth profile analysis of poloidal and toroidal deposition sample coupon arrays indicate that boron was transported by the plasma around the torus and deep into the divertors. During discharges with continuous real-time boronization, low-Z and high-Z impurities decreased rapidly as plasma surfaces were covered during the first 20-30 discharges. After boronization, a short-term improvement in plasma conditions persisted prior to significant boron erosion from plasma surfaces, and a longer term, but less significant improvement persisted as boron farther from the edge continued gettering. Real-time solid target boronization has been found to be very effective for accelerating conditioning to new regimes and maintaining high performance plasma conditions

  1. Improved USLE-K factor prediction: A case study on water erosion areas in China

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2016-09-01

    Full Text Available Soil erodibility (K-factor is an essential factor in soil erosion prediction and conservation practises. The major obstacles to any accurate, large-scale soil erodibility estimation are the lack of necessary data on soil characteristics and the misuse of variable K-factor calculators. In this study, we assessed the performance of available erodibility estimators Universal Soil Loss Equation (USLE, Revised Universal Soil Loss Equation (RUSLE, Erosion Productivity Impact Calculator (EPIC and the Geometric Mean Diameter based (Dg model for different geographic regions based on the Chinese soil erodibility database (CSED. Results showed that previous estimators overestimated almost all K-values. Furthermore, only the USLE and Dg approaches could be directly and reliably applicable to black and loess soil regions. Based on the nonlinear best fitting techniques, we improved soil erodibility prediction by combining Dg and soil organic matter (SOM. The NSE, R2 and RE values were 0.94, 0.67 and 9.5% after calibrating the results independently; similar model performance was showed for the validation process. The results obtained via the proposed approach were more accurate that the former K-value predictions. Moreover, those improvements allowed us to effectively establish a regional soil erodibility map (1:250,000 scale of water erosion areas in China. The mean K-value of Chinese water erosion regions was 0.0321 (t ha h·(ha MJ mm−1 with a standard deviation of 0.0107 (t ha h·(ha MJ mm−1; K-values present a decreasing trend from North to South in water erosion areas in China. The yield soil erodibility dataset also satisfactorily corresponded to former K-values from different scales (local, regional, and national.

  2. Soil erosion model predictions using parent material/soil texture-based parameters compared to using site-specific parameters

    Science.gov (United States)

    R. B. Foltz; W. J. Elliot; N. S. Wagenbrenner

    2011-01-01

    Forested areas disturbed by access roads produce large amounts of sediment. One method to predict erosion and, hence, manage forest roads is the use of physically based soil erosion models. A perceived advantage of a physically based model is that it can be parameterized at one location and applied at another location with similar soil texture or geological parent...

  3. Pelton turbine Needle erosion prediction based on 3D three- phase flow simulation

    International Nuclear Information System (INIS)

    Chongji, Z; Yexiang, X; Wei, Z; Yangyang, Y; Lei, C; Zhengwei, W

    2014-01-01

    Pelton turbine, which applied to the high water head and small flow rate, is widely used in the mountainous area. During the operation period the sediment contained in the water does not only induce the abrasion of the buckets, but also leads to the erosion at the nozzle which may damage the needle structure. The nozzle and needle structure are mainly used to form high quality cylindrical jet and increase the efficiency of energy exchange in the runner to the most. Thus the needle erosion will lead to the deformation of jet, and then may cause the efficiency loss and cavitation. The favourable prediction of abrasion characteristic of needle can effectively guide the optimization design and maintenance of needle structure. This paper simulated the unsteady three-dimensional multi-phase flow in the nozzle and injected jet flow. As the jet containing water and sediment is injected into the free atmosphere air with high velocity, the VOF model was adopted to predict the water and air flow. The sediment is simplified into round solid particle and the discrete particle model (DPM) was employed to predict the needle abrasion characteristic. The sand particle tracks were analyzed to interpret the mechanism of sand erosion on the needle surface. And the numerical result of needle abrasion was obtained and compared with the abrasion field observation. The similarity of abrasion pattern between the numerical results and field observation illustrated the validity of the 3D multi-phase flow simulation method

  4. Pelton turbine Needle erosion prediction based on 3D three- phase flow simulation

    Science.gov (United States)

    Chongji, Z.; Yexiang, X.; Wei, Z.; Yangyang, Y.; Lei, C.; Zhengwei, W.

    2014-03-01

    Pelton turbine, which applied to the high water head and small flow rate, is widely used in the mountainous area. During the operation period the sediment contained in the water does not only induce the abrasion of the buckets, but also leads to the erosion at the nozzle which may damage the needle structure. The nozzle and needle structure are mainly used to form high quality cylindrical jet and increase the efficiency of energy exchange in the runner to the most. Thus the needle erosion will lead to the deformation of jet, and then may cause the efficiency loss and cavitation. The favourable prediction of abrasion characteristic of needle can effectively guide the optimization design and maintenance of needle structure. This paper simulated the unsteady three-dimensional multi-phase flow in the nozzle and injected jet flow. As the jet containing water and sediment is injected into the free atmosphere air with high velocity, the VOF model was adopted to predict the water and air flow. The sediment is simplified into round solid particle and the discrete particle model (DPM) was employed to predict the needle abrasion characteristic. The sand particle tracks were analyzed to interpret the mechanism of sand erosion on the needle surface. And the numerical result of needle abrasion was obtained and compared with the abrasion field observation. The similarity of abrasion pattern between the numerical results and field observation illustrated the validity of the 3D multi-phase flow simulation method.

  5. Computer simulation of sputtering of graphite target in magnetron sputtering device with two zones of erosion

    Directory of Open Access Journals (Sweden)

    Bogdanov R.V.

    2015-03-01

    Full Text Available A computer simulation program for discharge in a magnetron sputtering device with two erosion zones was developed. Basic laws of the graphite target sputtering process and transport of sputtered material to the substrate were taken into account in the Monte Carlo code. The results of computer simulation for radial distributions of density and energy flux of carbon atoms on the substrate (at different values of discharge current and pressure of the working gas confirmed the possibility of obtaining qualitative homogeneous films using this magnetron sputtering device. Also the discharge modes were determined for this magnetron sputtering device, in which it was possible to obtain such energy and density of carbon atoms fluxes, which were suitable for deposition of carbon films containing carbon nanotubes and other nanoparticles.

  6. [Advance in researches on vegetation cover and management factor in the soil erosion prediction model].

    Science.gov (United States)

    Zhang, Yan; Yuan, Jianping; Liu, Baoyuan

    2002-08-01

    Vegetation cover and land management are the main limiting factors of soil erosion, and quantitative evaluation on the effect of different vegetation on soil erosion is essential to land use and soil conservation planning. The vegetation cover and management factor (C) in the universal soil loss equation (USLE) is an index to evaluate this effect, which has been studied deeply and used widely. However, the C factor study is insufficient in China. In order to strengthen the research of C factor, this paper reviewed the developing progress of C factor, and compared the methods of estimating C value in different USLE versions. The relative studies in China were also summarized from the aspects of vegetation canopy coverage, soil surface cover, and root density. Three problems in C factor study were pointed out. The authors suggested that cropland C factor research should be furthered, and its methodology should be unified in China to represent reliable C values for soil loss prediction and conservation planning.

  7. Uncertainty Prediction in Passive Target Motion Analysis

    Science.gov (United States)

    2016-05-12

    Number 15/152,696 Filing Date 12 May 2016 Inventor John G. Baylog et al Address any questions concerning this matter to the Office of...300118 1 of 25 UNCERTAINTY PREDICTION IN PASSIVE TARGET MOTION ANALYSIS STATEMENT OF GOVERNMENT INTEREST [0001] The invention described herein...at an unknown location and following an unknown course relative to an observer 12. Observer 12 has a sensor array such as a passive sonar or radar

  8. Development of a mobile application based on RUSLE model to predict erosion in olive groves

    Science.gov (United States)

    Marín Moreno, Víctor Javier; Redel, María Dolores; Taguas, Encarnación V.

    2017-04-01

    Apache Cordova, which are very efficient to facilitate its implementation in most of mobile platforms. The first evaluations from farmers and technicians are also presented in order to improve the first version. References: - Areal, F.J., Riesgo, L., 2014. Farmers' views on the future of olive farming in Andalusia, Spain. Land Use Policy 36 (2014) 543- 553. - CAPyDR, 2016. Aforo de producción de olivar en Andalucía, Campaña 2016-2017. Consejería de Agricultura, Pesca y Desarrollo Rural - Junta de Andalucía. Regional Government of Andalusia, Seville (2016) (Spain) - FAOSTAT -2016. FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS STATISTICS. Accessed at: http://www.fao.org/faostat - Franco, J.A., 2011. Análisis de los factores de participación en programas agroambientales de lucha contra la erosión en el olivar. ITEA 107 (3), 169-183. - Renard, K. G., Foster, G. R., Wessies, G. A., Mccool, D. K., and Yoder, D. C., 1997. Predicting Soil Ero¬sion by Water: A Guide to Conservation Planning with the Revised Universal LossEquation (RUSLE). USDA Agriculture Handbook, No. 703. - Taguas, E.V., Gómez, J.A., 2015. Vulnerability of olive orchards under the current CAP (Common Agricultural Policy) regulations on soil erosion: a study case in Southern Spain. Land Use Policy, 42, 683-694

  9. Study on the erosion of refractory metals in interaction with low energy ions at high temperatures of a target

    International Nuclear Information System (INIS)

    Vaulin, E.P.; Georgieva, N.E.; Martynenko, T.P.; Feoktistov, L.V.

    1981-01-01

    The experimental study on the erosion of a polycrystalline tungsten by argon ions with 50-100 eV energy in the temperature range 1000-1900 K is carried out and a theoretical analysis of sputtering rate under these conditions is given. It is shown that the sputtering rate is determined not only by ion energy but depends essentially on surface temperature. On the basis of the thermal spot'' model a semiempiric formula is obtained for dependence of sputtering coefficient on ion energy and target temperature. The estimation of cathode specific errosion in high-current discharges due to the sputtering and evaporation is performed. It is shown that depending on cathode temperature, cathode potential jump value as well as on relation of ion and electron current on a cathode the specific erosion due to individual ions shock can be higher and much higher than the specific erosion for account of evaporation [ru

  10. Testing and prediction of erosion-corrosion for corrosion resistant alloys used in the oil and gas production industry

    Science.gov (United States)

    Rincon, Hernan E.

    The corrosion behavior of CRAs has been thoroughly investigated and documented in the public literature by many researchers; however, little work has been done to investigate erosion-corrosion of such alloys. When sand particles are entrained in the flow, the degradation mechanism is different from that observed for sand-free corrosive environment. There is a need in the oil and gas industry to define safe service limits for utilization of such materials. The effects of flow conditions, sand rate, pH and temperature on the erosion-corrosion of CRAs were widely studied. An extensive experimental work was conducted using scratch tests and flow loop tests using several experimental techniques. At high erosivity conditions, a synergistic effect between erosion and corrosion was observed. Under the high sand rate conditions tested, erosivity is severe enough to damage the passive layer protecting the CRA thereby enhancing the corrosion rate. In most cases there is likely a competition between the rates of protective film removal due to mechanical erosion and protective film healing. Synergism occurs for each of the three alloys examined (13Cr and Super13Cr and 22Cr); however, the degree of synergism is quite different for the three alloys and may not be significant for 22Cr for field conditions where erosivities are typically much lower that those occurring in the small bore loop used in this research. Predictions of the corrosion component of erosion-corrosion based on scratch test data compared reasonably well to test results from flow loops for the three CRAs at high erosivity conditions. Second order behavior appears to be an appropriate and useful model for representing the repassivation process of CRAs. A framework for a procedure to predict penetration rates for erosion-corrosion conditions was developed based on the second order model behavior observed for the re-healing process of the passive film of CRAs and on computational fluid dynamics (CFD) simulations

  11. Particle Impact Erosion. Volume 4. User’s Manual Erosion Prediction Procedure for Rocket Nozzle Expansion Region

    Science.gov (United States)

    1983-05-01

    empirical erosion model, with use of the debris-layer model optional. 1.1 INTERFACE WITH ISPP ISPP is a collection of computer codes designed to calculate...expansion with the ODK code, 4. A two-dimensional, two-phase nozzle expansion with the TD2P code, 5. A turbulent boundary layer solution along the...INPUT THERMODYNAMIC DATA FOR TEMPERATURESBELOW 300°K OIF NEEDED) NO A• 11 READ SSP NAMELIST (ODE. BAL. ODK . TD2P. TEL. NOZZLE GEOMETRY) PROfLM 2

  12. KwaZulu-Natal coastal erosion events of 2006/2007 and 2011: A predictive tool?

    OpenAIRE

    Alan Smith; Lisa A. Guastella; Andrew A. Mather; Simon C. Bundy; Ivan D. Haigh

    2013-01-01

    Severe coastal erosion occurred along the KwaZulu-Natal coastline between mid-May and November 2011. Analysis of this erosion event and comparison with previous coastal erosion events in 2006/2007 offered the opportunity to extend the understanding of the time and place of coastal erosion strikes. The swells that drove the erosion hotspots of the 2011 erosion season were relatively low (significant wave heights were between 2 m and 4.5 m) but of long duration. Although swell height was import...

  13. Measurement of erosion: Is it possible?

    NARCIS (Netherlands)

    Stroosnijder, L.

    2005-01-01

    Reasons for erosion measurements are: (1) to determine the environmental impact of erosion and conservation practices, (2) scientific erosion research; (3) development and evaluation of erosion control technology; (4) development of erosion prediction technology and (5) allocation of conservation

  14. Predictive geophysics: geochemical simulations to geophysical targets

    Science.gov (United States)

    Chopping, R. G.; Cleverley, J.

    2017-12-01

    With an increasing focus on deep exploration for covered targets, new methods are required to target mineral systems under cover. Geophysical responses are driven by physical property contrasts; for example, density contrasts provide a gravity signal, acoustic impedance contrasts provide a seismic reflection signal. In turn, the physical properties for basement, crystalline rocks which host the vast majority of mineral systems are determined almost wholly by the mineralogy of the rocks in question. Mineral systems, through the transport of heat and reactive fluids, will serve to modify the physical properties of country rock as they chemically alter the hosting strata. To understand these changes, we have performed 2D reactive transport modelling that simulates the formation of Archean gold deposits of the Yilgarn Craton, Western Australia. From this, we derive a model of mineralogy that we can use to predict the density, magnetic susceptibility and seismic reflection changes associated with ore formation. It is then possible to predict the gravity, magnetic and seismic reflection responses associated with these deposits. Scenario mapping, such as testing the ability to resolve buried ore bodies or the geophysical survey spacing required to resolve the mineral system, can be performed to produce geophysical targets from these geochemical simulations. We find that there is a gravity response of around 9% of the unaltered response for deposits even buried by 1km of cover, and there is a magnetic spike associated with proximal alteration of the ore system. Finally, seismic reflection response is mostly characterised by additional reflections along faults that plumb the alteration system.

  15. Melt layer erosion of metallic armour targets during off-normal events in tokamaks

    International Nuclear Information System (INIS)

    Bazylev, B.; Wuerz, H.

    2002-01-01

    Melt layer erosion by melt motion is the dominating erosion mechanism for metallic armours under high heat loads. A 1-D fluid dynamics simulation model for calculation of melt motion was developed and validated against experimental results for tungsten from the e-beam facility JEBIS and beryllium from the e-beam facility JUDITH. The driving force in each case is the gradient of the surface tension. Due to the high velocity which develops in the Be melt considerable droplet splashing occurs

  16. Melt layer erosion of metallic armour targets during off-normal events in tokamaks

    Science.gov (United States)

    Bazylev, B.; Wuerz, H.

    2002-12-01

    Melt layer erosion by melt motion is the dominating erosion mechanism for metallic armours under high heat loads. A 1-D fluid dynamics simulation model for calculation of melt motion was developed and validated against experimental results for tungsten from the e-beam facility JEBIS and beryllium from the e-beam facility JUDITH. The driving force in each case is the gradient of the surface tension. Due to the high velocity which develops in the Be melt considerable droplet splashing occurs.

  17. Evaluating water erosion prediction project model using Cesium-137-derived spatial soil redistribution data

    Science.gov (United States)

    The lack of spatial soil erosion data has been a major constraint on the refinement and application of physically based erosion models. Spatially distributed models can only be thoroughly validated with distributed erosion data. The fallout cesium-137 has been widely used to generate spatial soil re...

  18. The influence of target erosion grade in the optoelectronic properties of AZO coatings growth by magnetron sputtering

    Science.gov (United States)

    Zubizarreta, C.; G-Berasategui, E.; Ciarsolo, I.; Barriga, J.; Gaspar, D.; Martins, R.; Fortunato, E.

    2016-09-01

    Aluminum-doped zinc oxide (AZO) transparent conductor coating has emerged as promising substitute to tin-doped indium oxide (ITO) as electrode in optoelectronic applications such as photovoltaics or light emitting diodes (LEDs). Besides its high transmission in the visible spectral region and low resistivity, AZO presents a main advantage over other candidates such as graphene, carbon nanotubes or silver nanowires; it can be deposited using the technology industrially implemented to manufacture ITO layers, the magnetron sputtering (MS). This is a productive, reliable and green manufacturing technique. But to guarantee the robustness, reproducibility and reliability of the process there are still some issues to be addressed, such as the effect and control of the target state. In this paper a thorough study of the influence of the target erosion grade in developed coatings has been performed. AZO films have been deposited from a ceramic target by RF MS. Structure, optical transmittance and electrical properties of the produced coatings have been analyzed as function of the target erosion grade. No noticeable differences have been found neither in optoelectronic properties nor in the structure of the coatings, indicating that the RF MS is a stable and consistent process through the whole life of the target.

  19. A history of wind erosion prediction models in the United States Department of Agriculture Prior to the Wind Erosion Prediction System

    Science.gov (United States)

    The Great Plains experienced an influx of settlers in the late 1850s to 1900. Periodic drought was hard on both settlers and the soil and caused severe wind erosion. The period known as the Dirty Thirties, 1931 to 1939, produced many severe windstorms, and the resulting dusty sky over Washington, D....

  20. Usability and Functional Enhancements to an Online Interface for Predicting Post Fire Erosion (WEPP-PEP)

    Science.gov (United States)

    Lew, Roger; Dobre, Mariana; Elliot, William; Robichaud, Pete; Brooks, Erin; Frankenberger, Jim

    2017-04-01

    There is an increased interest in the United States to use soil burn severity maps in watershed-scale hydrologic models to estimate post-fire sediment erosion from burned areas. This information is needed by stakeholders in order to concentrate their pre- or post-fire management efforts in ecologically sensitive areas to decrease the probability of post-fire sediment delivery. But these tools traditionally have been time consuming and difficult to use by managers because input datasets must be obtained and correctly processed for valid results. The Water Erosion Prediction Project (WEPP) has previously been developed as an online and easy-to-use interface to help land managers with running simulations without any knowledge of computer programming or hydrologic modeling. The interface automates the acquisition of DEM, climate, soils, and landcover data, and also automates channel and hillslope delineation for the users. The backend is built with Mapserver, GDAL, PHP, C++, Python while the front end uses OpenLayers, and, of course, JavaScript. The existing WEPP online interface was enhanced to provide better usability to stakeholders in United States (Forest Service, BLM, USDA) as well as to provide enhanced functionality for managing both pre-fire and post-fire treatments. Previously, only site administrators could add burn severity maps. The interface now allows users to create accounts to upload and share FlamMap prediction maps, differenced Normalized Burned Ratio (dNBR), or Burned Area Reflectance Classification (BARC) maps. All maps are loaded into a sortable catalog so users can quickly find their area of interest. Once loaded, the interface has been modified to support running comparisons between baseline condition with "no burn" and with a burn severity classification map. The interface has also been enhanced to allow users to conduct single storm analyses to examine, for example, how much soil loss would result after a 100-year storm. An OpenLayers map

  1. Watershed-scale evaluation of the Water Erosion Prediction Project (WEPP) model in the Lake Tahoe basin

    Science.gov (United States)

    Erin S. Brooks; Mariana Dobre; William J. Elliot; Joan Q. Wu; Jan Boll

    2016-01-01

    Forest managers need methods to evaluate the impacts of management at the watershed scale. The Water Erosion Prediction Project (WEPP) has the ability to model disturbed forested hillslopes, but has difficulty addressing some of the critical processes that are important at a watershed scale, including baseflow and water yield. In order to apply WEPP to...

  2. The influence of target erosion grade in the optoelectronic properties of AZO coatings growth by magnetron sputtering

    International Nuclear Information System (INIS)

    Zubizarreta, C.; G-Berasategui, E.; Ciarsolo, I.; Barriga, J.; Gaspar, D.; Martins, R.; Fortunato, E.

    2016-01-01

    Graphical abstract: - Highlights: • High quality AZO films deposited at low temperature by RF magnetron sputtering. • Transmittance values of 84% and resistivity of 1.9 × 10"−"3 Ω cm were obtained. • Stable optoelectronic and structural properties during whole life of the target. • RF MS: robust and reliable for the industrial manufacture of AZO frontal electrode. - Abstract: Aluminum-doped zinc oxide (AZO) transparent conductor coating has emerged as promising substitute to tin-doped indium oxide (ITO) as electrode in optoelectronic applications such as photovoltaics or light emitting diodes (LEDs). Besides its high transmission in the visible spectral region and low resistivity, AZO presents a main advantage over other candidates such as graphene, carbon nanotubes or silver nanowires; it can be deposited using the technology industrially implemented to manufacture ITO layers, the magnetron sputtering (MS). This is a productive, reliable and green manufacturing technique. But to guarantee the robustness, reproducibility and reliability of the process there are still some issues to be addressed, such as the effect and control of the target state. In this paper a thorough study of the influence of the target erosion grade in developed coatings has been performed. AZO films have been deposited from a ceramic target by RF MS. Structure, optical transmittance and electrical properties of the produced coatings have been analyzed as function of the target erosion grade. No noticeable differences have been found neither in optoelectronic properties nor in the structure of the coatings, indicating that the RF MS is a stable and consistent process through the whole life of the target.

  3. The influence of target erosion grade in the optoelectronic properties of AZO coatings growth by magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Zubizarreta, C., E-mail: cristina.zubizarreta@tekniker.es [IK4-Tekniker, Research Centre, c/ Iñaki Goenaga, 5, 20600 Eibar, Guipuzkoa (Spain); G-Berasategui, E.; Ciarsolo, I.; Barriga, J. [IK4-Tekniker, Research Centre, c/ Iñaki Goenaga, 5, 20600 Eibar, Guipuzkoa (Spain); Gaspar, D.; Martins, R.; Fortunato, E. [i3N/CENIMAT, Department of Materials Science, Faculty of Science and Technology, Universidade NOVA de Lisboa (Portugal)

    2016-09-01

    Graphical abstract: - Highlights: • High quality AZO films deposited at low temperature by RF magnetron sputtering. • Transmittance values of 84% and resistivity of 1.9 × 10{sup −3} Ω cm were obtained. • Stable optoelectronic and structural properties during whole life of the target. • RF MS: robust and reliable for the industrial manufacture of AZO frontal electrode. - Abstract: Aluminum-doped zinc oxide (AZO) transparent conductor coating has emerged as promising substitute to tin-doped indium oxide (ITO) as electrode in optoelectronic applications such as photovoltaics or light emitting diodes (LEDs). Besides its high transmission in the visible spectral region and low resistivity, AZO presents a main advantage over other candidates such as graphene, carbon nanotubes or silver nanowires; it can be deposited using the technology industrially implemented to manufacture ITO layers, the magnetron sputtering (MS). This is a productive, reliable and green manufacturing technique. But to guarantee the robustness, reproducibility and reliability of the process there are still some issues to be addressed, such as the effect and control of the target state. In this paper a thorough study of the influence of the target erosion grade in developed coatings has been performed. AZO films have been deposited from a ceramic target by RF MS. Structure, optical transmittance and electrical properties of the produced coatings have been analyzed as function of the target erosion grade. No noticeable differences have been found neither in optoelectronic properties nor in the structure of the coatings, indicating that the RF MS is a stable and consistent process through the whole life of the target.

  4. Automated lake-wide erosion predictions and economic damage calculations upstream of the Moses-Saunders power dam

    International Nuclear Information System (INIS)

    Zuzek, P.; Baird, W.F.; International Joint Commission, Ottawa, ON

    2008-01-01

    This presentation discussed an automated flood and erosion prediction system designed for the upstream sections of the Moses-Saunders power dam. The system included a wave prediction component along with 3-D maps, hourly run-ups, geographic information system (GIS) tools and a hazard analysis tool. Parcel, reach, township, and county databases were used to populate the system. The prediction system was used to develop detailed study sites of shore units in the study area. Shoreline classes included sand and cohesive buffs, low banks, coarse beaches, and cobble or boulder lags. Time series plots for Lake Ontario water and wave levels were presented. Great Lakes ice cover data were also included in the system as well as erosion predictions from 1961 to 1995. The system was also used to develop bluff recession equations and cumulative recession analyses for different regulation plans. Cumulative bluff recession and protection requirements were outlined. Screenshots of the flood and erosion prediction system interface were also included. tabs., figs

  5. Soil Erosion Prediction Using Morgan-Morgan-Finney Model in a GIS Environment in Northern Ethiopia Catchment

    Directory of Open Access Journals (Sweden)

    Gebreyesus Brhane Tesfahunegn

    2014-01-01

    Full Text Available Even though scientific information on spatial distribution of hydrophysical parameters is critical for understanding erosion processes and designing suitable technologies, little is known in Geographical Information System (GIS application in developing spatial hydrophysical data inputs and their application in Morgan-Morgan-Finney (MMF erosion model. This study was aimed to derive spatial distribution of hydrophysical parameters and apply them in the Morgan-Morgan-Finney (MMF model for estimating soil erosion in the Mai-Negus catchment, northern Ethiopia. Major data input for the model include climate, topography, land use, and soil data. This study demonstrated using MMF model that the rate of soil detachment varied from 170 t ha−1 y−1, whereas the soil transport capacity of overland flow (TC ranged from 5 t ha−1 y−1 to >42 t ha−1 y−1. The average soil loss estimated by TC using MMF model at catchment level was 26 t ha−1 y−1. In most parts of the catchment (>80%, the model predicted soil loss rates higher than the maximum tolerable rate (18 t ha−1 y−1 estimated for Ethiopia. Hence, introducing appropriate interventions based on the erosion severity predicted by MMF model in the catchment is crucial for sustainable natural resources management.

  6. Development of Erosive Burning Models for CFD Predictions of Solid Rocket Motor Internal Environments

    Science.gov (United States)

    Wang, Qun-Zhen

    2003-01-01

    Four erosive burning models, equations (11) to (14). are developed in this work by using a power law relationship to correlate (1) the erosive burning ratio and the local velocity gradient at propellant surfaces; (2) the erosive burning ratio and the velocity gradient divided by centerline velocity; (3) the erosive burning difference and the local velocity gradient at propellant surfaces; and (4) the erosive burning difference and the velocity gradient divided by centerline velocity. These models depend on the local velocity gradient at the propellant surface (or the velocity gradient divided by centerline velocity) only and, unlike other empirical models, are independent of the motor size. It was argued that, since the erosive burning is a local phenomenon occurring near the surface of the solid propellant, the erosive burning ratio should be independent of the bore diameter if it is correlated with some local flow parameters such as the velocity gradient at the propellant surface. This seems to be true considering the good results obtained by applying these models, which are developed from the small size 5 inch CP tandem motor testing, to CFD simulations of much bigger motors.

  7. IFE Target Injection Tracking and Position Prediction Update

    International Nuclear Information System (INIS)

    Petzoldt, Ronald W.; Jonestrask, Kevin

    2005-01-01

    To achieve high gain in an inertial fusion energy power plant, driver beams must hit direct drive targets with ±20 μm accuracy (±100 μm for indirect drive). Targets will have to be tracked with even greater accuracy. The conceptual design for our tracking system, which predicts target arrival position and timing based on position measurements outside of the reaction chamber was previously described. The system has been built and has begun tracking targets at the first detector station. Additional detector stations are being modified for increased field of view. After three tracking stations are operational, position predictions at the final station will be compared to position measurements at that station as a measure of target position prediction accuracy.The as-installed design will be described together with initial target tracking and position prediction accuracy results. Design modifications that allow for improved accuracy and/or in-chamber target tracking will also be presented

  8. Crust behavior and erosion rate prediction of EPR sacrificial material impinged by core melt jet

    Energy Technology Data Exchange (ETDEWEB)

    Li, Gen; Liu, Ming, E-mail: ming.liu@mail.xjtu.edu.cn; Wang, Jinshi; Chong, Daotong; Yan, Junjie

    2017-04-01

    Highlights: • A numerical code was developed to analyze melt jet-concrete interaction in the frame of MPS method. • Crust and ablated concrete layer at UO{sub 2}-ZrO{sub 2} melt and concrete interface periodically developed and collapsed. • Concrete surface temperature fluctuated around a low temperature and ablation temperature. • Concrete erosion by Fe-Zr melt jet was significantly faster than that by UO{sub 2}-ZrO{sub 2} melt jet. - Abstract: Sacrificial material is a special ferro-siliceous concrete, designed in the ex-vessel core melt stabilization system of European Pressurized water Reactor (EPR). Given a localized break of RPV lower head, the melt directly impinges onto the dry concrete in form of compact jet. The concrete erosion behavior influences the failure of melt plug, and further affects melt spreading. In this study, a numerical code was developed in the frame of Moving Particle Semi-implicit (MPS) method, to analyze the crust behavior and erosion rate of sacrificial concrete, impinged by prototypic melt jet. In validation of numerical modeling, the time-dependent erosion depth and erosion configuration matched well with the experimental data. Sensitivity study of sacrificial concrete erosion indicates that the crust and ablated concrete layer presented at UO{sub 2}-ZrO{sub 2} melt and concrete interface, whereas no crust could be found in the interaction of Fe-Zr melt with concrete. The crust went through stabilization-fracture-reformation periodic process, accompanied with accumulating and collapsing of molten concrete layer. The concrete surface temperature fluctuated around a low temperature and ablation temperature. It increased as the concrete surface layer was heated to melting, and dropped down when the cold concrete was revealed. The erosion progression was fast in the conditions of small jet diameter and large concrete inclination angle, and it was significantly faster in the erosion by metallic melt jet than by oxidic melt jet.

  9. Developing relations between soil erodibilty factors in two different soil erosion prediction models (USLE/RUSLE and wWEPP) and fludization bed technique for mechanical soil cohesion

    Science.gov (United States)

    Soil erosion models are valuable analysis tools that scientists and engineers use to examine observed data sets and predict the effects of possible future soil loss. In the area of water erosion, a variety of modeling technologies are available, ranging from solely qualitative models, to merely quan...

  10. Prediction of potential drug targets based on simple sequence properties

    Directory of Open Access Journals (Sweden)

    Lai Luhua

    2007-09-01

    Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

  11. Runoff erosion

    OpenAIRE

    Evelpidou, Niki (Ed.); Cordier, Stephane (Ed.); Merino, Agustin (Ed.); Figueiredo, Tomás de (Ed.); Centeri, Csaba (Ed.)

    2013-01-01

    Table of Contents PART I – THEORY OF RUNOFF EROSION CHAPTER 1 - RUNOFF EROSION – THE MECHANISMS CHAPTER 2 - LARGE SCALE APPROACHES OF RUNOFF EROSION CHAPTER 3 - MEASURING PRESENT RUNOFF EROSION CHAPTER 4 - MODELLING RUNOFF EROSION CHAPTER 5 - RUNOFF EROSION AND HUMAN SOCIETIES: THE INFLUENCE OF LAND USE AND MANAGEMENT PRACTICES ON SOIL EROSION PART II - CASE STUDIES CASE STUDIES – INTRODUCTION: RUNOFF EROSION IN MEDITERRANEAN AREA CASE STUDY 1: Soil Erosion Risk...

  12. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  13. Erosion corrosion in power plant piping systems - Calculation code for predicting wall thinning

    International Nuclear Information System (INIS)

    Kastner, W.; Erve, M.; Henzel, N.; Stellwag, B.

    1990-01-01

    Extensive experimental and theoretical investigations have been performed to develop a calculation code for wall thinning due to erosion corrosion in power plant piping systems. The so-called WATHEC code can be applied to single-phase water flow as well as to two-phase water/steam flow. Only input data which are available to the operator of the plant are taken into consideration. Together with a continuously updated erosion corrosion data base the calculation code forms one element of a weak point analysis for power plant piping systems which can be applied to minimize material loss due to erosion corrosion, reduce non-destructive testing and curtail monitoring programs for piping systems, recommend life-extending measures. (author). 12 refs, 17 figs

  14. Damage diagnostic of localized impact erosion by measuring acoustic vibration

    International Nuclear Information System (INIS)

    Futakawa, Masatoshi; Kogawa, Hiroyuki; Ikeda, Yujiro

    2004-01-01

    High power spallation targets for neutron sources are being developed in the world. Mercury target will be installed at the material and life science facility in J-PARC, which will promote innovative science. The mercury target is subject to the pressure wave caused by the proton bombarding mercury. The pressure wave propagation induces the cavitation in mercury that imposes localized impact erosion damage on the target vessel. The impact erosion is a critical issue to decide the lifetime of the target. The electric Magnetic IMpact Testing Machine, MIMTM, was developed to produce the localized impact erosion damage and evaluate the damage formation. Acoustic vibration measurement was carried out to investigate the correlation between the erosion damage and the damage potential derived from acoustic vibration. It was confirmed that the damage potential related with acoustic vibration is useful to predict the damage due to the localized impact erosion and to diagnose the structural integrity. (author)

  15. A critical discussion on the applicability of Compound Topographic Index (CTI) for predicting ephemeral gully erosion

    Science.gov (United States)

    Casalí, Javier; Chahor, Youssef; Giménez, Rafael; Campo-Bescós, Miguel

    2016-04-01

    The so-called Compound Topographic Index (CTI) can be calculated for each grid cell in a DEM and be used to identify potential locations for ephemeral gullies (e. g.) based on land topography (CTI = A.S.PLANC, where A is upstream drainage area, S is local slope and PLANC is planform curvature, a measure of the landscape convergence) (Parker et al., 2007). It can be shown that CTI represents stream power per unit bed area and it considers the major parameters controlling the pattern and intensity of concentrated surface runoff in the field (Parker et al., 2007). However, other key variables controlling e.g. erosion (e. g. e.) such as soil characteristics, land-use and management, are not had into consideration. The critical CTI value (CTIc) "represents the intensity of concentrated overland flow necessary to initiate erosion and channelised flow under a given set of circumstances" (Parker et al., 2007). AnnAGNPS (Annualized Agriculture Non-Point Source) pollution model is an important management tool developed by (USDA) and uses CTI to locate potential ephemeral gullies. Then, and depending on rainfall characteristics of the period simulated by AnnAGNPS, potential e. g. can become "actual", and be simulated by the model accordingly. This paper presents preliminary results and a number of considerations after evaluating the CTI tool in Navarre. CTIc values found are similar to those cited by other authors, and the e. g. networks that on average occur in the area have been located reasonably well. After our experience we believe that it is necessary to distinguish between the CTIc corresponding to the location of headcuts whose migrations originate the e. g. (CTIc1); and the CTIc necessary to represent the location of the gully networks in the watershed (CTIc2), where gully headcuts are located in the upstream end of the gullies. Most scientists only consider one CTIc value, although, from our point of view, the two situations are different. CTIc1 would represent the

  16. Synthesising empirical results to improve predictions of post-wildfire runoff and erosion response

    Science.gov (United States)

    Richard A. Shakesby; John A. Moody; Deborah A. Martin; Pete Robichaud

    2016-01-01

    Advances in research into wildfire impacts on runoff and erosion have demonstrated increasing complexity of controlling factors and responses, which, combined with changing fire frequency, present challenges for modellers. We convened a conference attended by experts and practitioners in post-wildfire impacts, meteorology and related research, including...

  17. Predicting soil erosion using Rusle and NDVI time series from TM Landsat 5

    Directory of Open Access Journals (Sweden)

    Daniel Fonseca de Carvalho

    2014-03-01

    Full Text Available The objective of this work was to evaluate the seasonal variation of soil cover and rainfall erosivity, and their influences on the revised universal soil loss equation (Rusle, in order to estimate watershed soil losses in a temporal scale. Twenty-two TM Landsat 5 images from 1986 to 2009 were used to estimate soil use and management factor (C factor. A corresponding rainfall erosivity factor (R factor was considered for each image, and the other factors were obtained using the standard Rusle method. Estimated soil losses were grouped into classes and ranged from 0.13 Mg ha-1 on May 24, 2009 (dry season to 62.0 Mg ha-1 on March 11, 2007 (rainy season. In these dates, maximum losses in the watershed were 2.2 and 781.5 Mg ha-1 , respectively. Mean annual soil loss in the watershed was 109.5 Mg ha-1 , but the central area, with a loss of nearly 300.0 Mg ha-1 , was characterized as a site of high water-erosion risk. The use of C factor obtained from remote sensing data, associated to corresponding R factor, was fundamental to evaluate the soil erosion estimated by the Rusle in different seasons, unlike of other studies which keep these factors constant throughout time.

  18. Drug-Target Interactions: Prediction Methods and Applications.

    Science.gov (United States)

    Anusuya, Shanmugam; Kesherwani, Manish; Priya, K Vishnu; Vimala, Antonydhason; Shanmugam, Gnanendra; Velmurugan, Devadasan; Gromiha, M Michael

    2018-01-01

    Identifying the interactions between drugs and target proteins is a key step in drug discovery. This not only aids to understand the disease mechanism, but also helps to identify unexpected therapeutic activity or adverse side effects of drugs. Hence, drug-target interaction prediction becomes an essential tool in the field of drug repurposing. The availability of heterogeneous biological data on known drug-target interactions enabled many researchers to develop various computational methods to decipher unknown drug-target interactions. This review provides an overview on these computational methods for predicting drug-target interactions along with available webservers and databases for drug-target interactions. Further, the applicability of drug-target interactions in various diseases for identifying lead compounds has been outlined. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  19. Development of a catchment/landscape erosion prediction model (MINErosion 4) for post-mining landscapes in Central Queensland, Australia.

    Science.gov (United States)

    Khalifa, Ashraf; Yu, Bofu; Ghadiri, Hossain; Carroll, Chris; So, Hwat-Bing

    2010-05-01

    industry further require a tool that enables them to predict and manage the impact of on-site and offsite discharges from storm events and to identify the areas of high erosion risk. Work is in progress to develop a user friendly package MINErosion 4 by combining the hillslope model MINErosion 3 with ARC-GIS 9, which allows the prediction of sediment losses and deposition from proposed post-mining landscapes (designed based on criteria derived from MINErosion3) subjected to rainstorms with known recurrence intervals for selected locations. An option is provided to derive mean annual soil loss from these catchments and landscapes. Soil samples were collected from various locations on 6 minesites to provide a measure of variability in erodibilities across a minesite. The model was validated against 9 years of catchment data collected from previous projects and the agreement between predicted (Y) and measured (X) soil losses are good with regression equations of Y = 0.919 X (R2 = 0.81) for individual rainstorms, and Y= 1.473 X (R2 = 0.726) for average annual soil loss.

  20. Deep-Learning-Based Drug-Target Interaction Prediction.

    Science.gov (United States)

    Wen, Ming; Zhang, Zhimin; Niu, Shaoyu; Sha, Haozhi; Yang, Ruihan; Yun, Yonghuan; Lu, Hongmei

    2017-04-07

    Identifying interactions between known drugs and targets is a major challenge in drug repositioning. In silico prediction of drug-target interaction (DTI) can speed up the expensive and time-consuming experimental work by providing the most potent DTIs. In silico prediction of DTI can also provide insights about the potential drug-drug interaction and promote the exploration of drug side effects. Traditionally, the performance of DTI prediction depends heavily on the descriptors used to represent the drugs and the target proteins. In this paper, to accurately predict new DTIs between approved drugs and targets without separating the targets into different classes, we developed a deep-learning-based algorithmic framework named DeepDTIs. It first abstracts representations from raw input descriptors using unsupervised pretraining and then applies known label pairs of interaction to build a classification model. Compared with other methods, it is found that DeepDTIs reaches or outperforms other state-of-the-art methods. The DeepDTIs can be further used to predict whether a new drug targets to some existing targets or whether a new target interacts with some existing drugs.

  1. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.

    Science.gov (United States)

    Bonnet, Eric; He, Ying; Billiau, Kenny; Van de Peer, Yves

    2010-06-15

    We present a new web server called TAPIR, designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. The TAPIR web server can be accessed at: http://bioinformatics.psb.ugent.be/webtools/tapir. Supplementary data are available at Bioinformatics online.

  2. DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-03-16

    Background Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient computational methods for the accurate prediction of potential DTIs. To-date, many computational methods have been proposed for this purpose, but they suffer the drawback of a high rate of false positive predictions. Results Here, we developed a novel computational DTI prediction method, DASPfind. DASPfind uses simple paths of particular lengths inferred from a graph that describes DTIs, similarities between drugs, and similarities between the protein targets of drugs. We show that on average, over the four gold standard DTI datasets, DASPfind significantly outperforms other existing methods when the single top-ranked predictions are considered, resulting in 46.17 % of these predictions being correct, and it achieves 49.22 % correct single top ranked predictions when the set of all DTIs for a single drug is tested. Furthermore, we demonstrate that our method is best suited for predicting DTIs in cases of drugs with no known targets or with few known targets. We also show the practical use of DASPfind by generating novel predictions for the Ion Channel dataset and validating them manually. Conclusions DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery. DASPfind

  3. Predicting drug-target interactions using restricted Boltzmann machines.

    Science.gov (United States)

    Wang, Yuhao; Zeng, Jianyang

    2013-07-01

    In silico prediction of drug-target interactions plays an important role toward identifying and developing new uses of existing or abandoned drugs. Network-based approaches have recently become a popular tool for discovering new drug-target interactions (DTIs). Unfortunately, most of these network-based approaches can only predict binary interactions between drugs and targets, and information about different types of interactions has not been well exploited for DTI prediction in previous studies. On the other hand, incorporating additional information about drug-target relationships or drug modes of action can improve prediction of DTIs. Furthermore, the predicted types of DTIs can broaden our understanding about the molecular basis of drug action. We propose a first machine learning approach to integrate multiple types of DTIs and predict unknown drug-target relationships or drug modes of action. We cast the new DTI prediction problem into a two-layer graphical model, called restricted Boltzmann machine, and apply a practical learning algorithm to train our model and make predictions. Tests on two public databases show that our restricted Boltzmann machine model can effectively capture the latent features of a DTI network and achieve excellent performance on predicting different types of DTIs, with the area under precision-recall curve up to 89.6. In addition, we demonstrate that integrating multiple types of DTIs can significantly outperform other predictions either by simply mixing multiple types of interactions without distinction or using only a single interaction type. Further tests show that our approach can infer a high fraction of novel DTIs that has been validated by known experiments in the literature or other databases. These results indicate that our approach can have highly practical relevance to DTI prediction and drug repositioning, and hence advance the drug discovery process. Software and datasets are available on request. Supplementary data are

  4. Upper Gastrointestinal Symptoms Predictive of Candida Esophagitis and Erosive Esophagitis in HIV and Non-HIV Patients

    Science.gov (United States)

    Takahashi, Yuta; Nagata, Naoyoshi; Shimbo, Takuro; Nishijima, Takeshi; Watanabe, Koji; Aoki, Tomonori; Sekine, Katsunori; Okubo, Hidetaka; Watanabe, Kazuhiro; Sakurai, Toshiyuki; Yokoi, Chizu; Mimori, Akio; Oka, Shinichi; Uemura, Naomi; Akiyama, Junichi

    2015-01-01

    Abstract Upper gastrointestinal (GI) symptoms are common in both HIV and non-HIV-infected patients, but the difference of GI symptom severity between 2 groups remains unknown. Candida esophagitis and erosive esophagitis, 2 major types of esophagitis, are seen in both HIV and non-HIV-infected patients, but differences in GI symptoms that are predictive of esophagitis between 2 groups remain unknown. We aimed to determine whether GI symptoms differ between HIV-infected and non-HIV-infected patients, and identify specific symptoms of candida esophagitis and erosive esophagitis between 2 groups. We prospectively enrolled 6011 patients (HIV, 430; non-HIV, 5581) who underwent endoscopy and completed questionnaires. Nine upper GI symptoms (epigastric pain, heartburn, acid regurgitation, hunger cramps, nausea, early satiety, belching, dysphagia, and odynophagia) were evaluated using a 7-point Likert scale. Associations between esophagitis and symptoms were analyzed by the multivariate logistic regression model adjusted for age, sex, and proton pump inhibitors. Endoscopy revealed GI-organic diseases in 33.4% (2010/6.011) of patients. The prevalence of candida esophagitis and erosive esophagitis was 11.2% and 12.1% in HIV-infected patients, respectively, whereas it was 2.9% and 10.7 % in non-HIV-infected patients, respectively. After excluding GI-organic diseases, HIV-infected patients had significantly (P symptom scores for heartburn, hunger cramps, nausea, early satiety, belching, dysphagia, and odynophagia than non-HIV-infected patients. In HIV-infected patients, any symptom was not significantly associated with CD4 cell count. In multivariate analysis, none of the 9 GI symptoms were associated with candida esophagitis in HIV-infected patients, whereas dysphagia and odynophagia were independently (P HIV-infected patients. However, heartburn and acid regurgitation were independently (P symptom scores were reliable in both HIV (α, 0.86) and non-HIV-infected patients

  5. NASA's Evolutionary Xenon Thruster (NEXT) Project Qualification Propellant Throughput Milestone: Performance, Erosion, and Thruster Service Life Prediction After 450 kg

    Science.gov (United States)

    Herman, Daniel A.

    2010-01-01

    The NASA s Evolutionary Xenon Thruster (NEXT) program is tasked with significantly improving and extending the capabilities of current state-of-the-art NSTAR thruster. The service life capability of the NEXT ion thruster is being assessed by thruster wear test and life-modeling of critical thruster components, such as the ion optics and cathodes. The NEXT Long-Duration Test (LDT) was initiated to validate and qualify the NEXT thruster propellant throughput capability. The NEXT thruster completed the primary goal of the LDT; namely to demonstrate the project qualification throughput of 450 kg by the end of calendar year 2009. The NEXT LDT has demonstrated 28,500 hr of operation and processed 466 kg of xenon throughput--more than double the throughput demonstrated by the NSTAR flight-spare. Thruster performance changes have been consistent with a priori predictions. Thruster erosion has been minimal and consistent with the thruster service life assessment, which predicts the first failure mode at greater than 750 kg throughput. The life-limiting failure mode for NEXT is predicted to be loss of structural integrity of the accelerator grid due to erosion by charge-exchange ions.

  6. A GIS-model for predicting the impact of climate change on shore erosion in hydroelectric reservoirs

    International Nuclear Information System (INIS)

    Penner, L.A.; Zimmer, T.A.M.; St Laurent, M.

    2008-01-01

    Shoreline erosion affects inland lakes and hydroelectric reservoirs in several ways. This poster described a vector-based geographic information system (GIS) model designed to predict changes in shore zone geometry, top-of-bluff recession, and eroded sediment volumes. The model was designed for use in Manitoba Hydro's reservoirs in northern Manitoba, and simulated near-shore downcutting and bank recession caused by wind-generated waves. Parameters for the model included deep water wave energy, and water level fluctuations. Effective wave energy was seen as a function of the water level fluctuation range, wave conditions, and near-shore slope. The model was validated by field monitoring studies that included repeated shore zone transect surveys and sediment coring studies. Results of the study showed that the model provides a systematic method of predicting potential changes in erosion associated with climatic change. The volume and mass of eroded sediment predicted for the different modelling scenarios will be used as input data for future sedimentation models. tabs., figs

  7. Quantitative self-assembly prediction yields targeted nanomedicines

    Science.gov (United States)

    Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

    2018-02-01

    Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

  8. Gaussian interaction profile kernels for predicting drug-target interaction.

    Science.gov (United States)

    van Laarhoven, Twan; Nabuurs, Sander B; Marchiori, Elena

    2011-11-01

    The in silico prediction of potential interactions between drugs and target proteins is of core importance for the identification of new drugs or novel targets for existing drugs. However, only a tiny portion of all drug-target pairs in current datasets are experimentally validated interactions. This motivates the need for developing computational methods that predict true interaction pairs with high accuracy. We show that a simple machine learning method that uses the drug-target network as the only source of information is capable of predicting true interaction pairs with high accuracy. Specifically, we introduce interaction profiles of drugs (and of targets) in a network, which are binary vectors specifying the presence or absence of interaction with every target (drug) in that network. We define a kernel on these profiles, called the Gaussian Interaction Profile (GIP) kernel, and use a simple classifier, (kernel) Regularized Least Squares (RLS), for prediction drug-target interactions. We test comparatively the effectiveness of RLS with the GIP kernel on four drug-target interaction networks used in previous studies. The proposed algorithm achieves area under the precision-recall curve (AUPR) up to 92.7, significantly improving over results of state-of-the-art methods. Moreover, we show that using also kernels based on chemical and genomic information further increases accuracy, with a neat improvement on small datasets. These results substantiate the relevance of the network topology (in the form of interaction profiles) as source of information for predicting drug-target interactions. Software and Supplementary Material are available at http://cs.ru.nl/~tvanlaarhoven/drugtarget2011/. tvanlaarhoven@cs.ru.nl; elenam@cs.ru.nl. Supplementary data are available at Bioinformatics online.

  9. TargetSpy: a supervised machine learning approach for microRNA target prediction.

    Science.gov (United States)

    Sturm, Martin; Hackenberg, Michael; Langenberger, David; Frishman, Dmitrij

    2010-05-28

    Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila

  10. TargetSpy: a supervised machine learning approach for microRNA target prediction

    Directory of Open Access Journals (Sweden)

    Langenberger David

    2010-05-01

    Full Text Available Abstract Background Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. Results We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I no seed match requirement, II seed match requirement, and III conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Conclusion Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on

  11. TargetRNA: a tool for predicting targets of small RNA action in bacteria

    OpenAIRE

    Tjaden, Brian

    2008-01-01

    Many small RNA (sRNA) genes in bacteria act as posttranscriptional regulators of target messenger RNAs. Here, we present TargetRNA, a web tool for predicting mRNA targets of sRNA action in bacteria. TargetRNA takes as input a genomic sequence that may correspond to an sRNA gene. TargetRNA then uses a dynamic programming algorithm to search each annotated message in a specified genome for mRNAs that evince basepair-binding potential to the input sRNA sequence. Based on the calculated basepair-...

  12. Drug-target interaction prediction from PSSM based evolutionary information.

    Science.gov (United States)

    Mousavian, Zaynab; Khakabimamaghani, Sahand; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-01-01

    The labor-intensive and expensive experimental process of drug-target interaction prediction has motivated many researchers to focus on in silico prediction, which leads to the helpful information in supporting the experimental interaction data. Therefore, they have proposed several computational approaches for discovering new drug-target interactions. Several learning-based methods have been increasingly developed which can be categorized into two main groups: similarity-based and feature-based. In this paper, we firstly use the bi-gram features extracted from the Position Specific Scoring Matrix (PSSM) of proteins in predicting drug-target interactions. Our results demonstrate the high-confidence prediction ability of the Bigram-PSSM model in terms of several performance indicators specifically for enzymes and ion channels. Moreover, we investigate the impact of negative selection strategy on the performance of the prediction, which is not widely taken into account in the other relevant studies. This is important, as the number of non-interacting drug-target pairs are usually extremely large in comparison with the number of interacting ones in existing drug-target interaction data. An interesting observation is that different levels of performance reduction have been attained for four datasets when we change the sampling method from the random sampling to the balanced sampling. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization.

    Science.gov (United States)

    Ezzat, Ali; Zhao, Peilin; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2017-01-01

    Experimental determination of drug-target interactions is expensive and time-consuming. Therefore, there is a continuous demand for more accurate predictions of interactions using computational techniques. Algorithms have been devised to infer novel interactions on a global scale where the input to these algorithms is a drug-target network (i.e., a bipartite graph where edges connect pairs of drugs and targets that are known to interact). However, these algorithms had difficulty predicting interactions involving new drugs or targets for which there are no known interactions (i.e., "orphan" nodes in the network). Since data usually lie on or near to low-dimensional non-linear manifolds, we propose two matrix factorization methods that use graph regularization in order to learn such manifolds. In addition, considering that many of the non-occurring edges in the network are actually unknown or missing cases, we developed a preprocessing step to enhance predictions in the "new drug" and "new target" cases by adding edges with intermediate interaction likelihood scores. In our cross validation experiments, our methods achieved better results than three other state-of-the-art methods in most cases. Finally, we simulated some "new drug" and "new target" cases and found that GRMF predicted the left-out interactions reasonably well.

  14. Cavitation damage prediction for the JSNS mercury target vessel

    Energy Technology Data Exchange (ETDEWEB)

    Naoe, Takashi, E-mail: naoe.takashi@jaea.go.jp; Kogawa, Hiroyuki; Wakui, Takashi; Haga, Katsuhiro; Teshigawara, Makoto; Kinoshita, Hidetaka; Takada, Hiroshi; Futakawa, Masatoshi

    2016-01-15

    The liquid mercury target system for the Japan Spallation Neutron Source (JSNS) at the Materials and Life science experimental Facility (MLF) in the Japan Proton Accelerator Research Complex (J-PARC) is designed to produce pulsed neutrons. The mercury target vessel in this system, which is made of type 316L stainless steel, is damaged by pressure wave-induced cavitation due to proton beam bombardment. Currently, cavitation damage is considered to be the dominant factor influencing the service life of the target vessel rather than radiation damage. In this study, cavitation damage to the interior surface of the target vessel was predicted on the basis of accumulated damage data from off-beam and on-beam experiments. The predicted damage was compared with the damage observed in a used target vessel. Furthermore, the effect of injecting gas microbubbles on cavitation damage was predicted through the measurement of the acoustic vibration of the target vessel. It was shown that the predicted depth of cavitation damage is reasonably coincident with the observed results. Moreover, it was confirmed that the injection of gas microbubbles had an effect on cavitation damage.

  15. Macromolecular target prediction by self-organizing feature maps.

    Science.gov (United States)

    Schneider, Gisbert; Schneider, Petra

    2017-03-01

    Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

  16. A quick reality check for microRNA target prediction.

    Science.gov (United States)

    Kast, Juergen

    2011-04-01

    The regulation of protein abundance by microRNA (miRNA)-mediated repression of mRNA translation is a rapidly growing area of interest in biochemical research. In animal cells, the miRNA seed sequence does not perfectly match that of the mRNA it targets, resulting in a large number of possible miRNA targets and varied extents of repression. Several software tools are available for the prediction of miRNA targets, yet the overlap between them is limited. Jovanovic et al. have developed and applied a targeted, quantitative approach to validate predicted miRNA target proteins. Using a proteome database, they have set up and tested selected reaction monitoring assays for approximately 20% of more than 800 predicted let-7 targets, as well as control genes in Caenorhabditis elegans. Their results demonstrate that such assays can be developed quickly and with relative ease, and applied in a high-throughput setup to verify known and identify novel miRNA targets. They also show, however, that the choice of the biological system and material has a noticeable influence on the frequency, extent and direction of the observed changes. Nonetheless, selected reaction monitoring assays, such as those developed by Jovanovic et al., represent an attractive new tool in the study of miRNA function at the organism level.

  17. Assessment of CASP7 structure predictions for template free targets.

    Science.gov (United States)

    Jauch, Ralf; Yeo, Hock Chuan; Kolatkar, Prasanna R; Clarke, Neil D

    2007-01-01

    In CASP7, protein structure prediction targets that lacked substantial similarity to a protein in the PDB at the time of assessment were considered to be free modeling targets (FM). We assessed predictions for 14 FM targets as well as four other targets that were deemed to be on the borderline between FM targets and template based modeling targets (TBM/FM). GDT_TS was used as one measure of model quality. Model quality was also assessed by visual inspection. Visual inspection was performed by three independent assessors who were blinded to GDT_TS scores and other quantitative measures of model quality. The best models by visual inspection tended to rank among the top few percent by GDT_TS, but were typically not the highest scoring models. Thus, visual inspection remains an essential component of assessment for FM targets. Overall, group TS020 (Baker) performed best, but success on individual targets was widely distributed among many groups. Among these other groups, TS024 and TS025 (Zhang and Zhang server) performed notably well without exceptionally large computing resources. This should be considered encouraging for future CASPs. There was a sense of progress in template FM relative to CASP6, but we were unable to demonstrate this progress objectively. (c) 2007 Wiley-Liss, Inc.

  18. User manual of Soil and Cesium Transport (SACT), a program to predict long-term Cs distribution using USLE for soil erosion, transportation and deposition

    International Nuclear Information System (INIS)

    Saito, Hiroshi; Yamaguchi, Masaaki; Kitamura, Akihiro

    2016-12-01

    This manual provides useful and necessary information to users of 'SACT' (Soil and Cesium Transport), which Japan Atomic Energy Agency (JAEA) has developed to predict a long-term distribution of Cs deposited on the land surface of Fukushima due to the Fukushima Daiichi Nuclear Power Station accident on March 11, 2011. SACT calculates soil movement (erosion, transportation and deposition) and resulting Cs migration, and predicts its future distribution, with the assumption that Cs is adhered to soil initially. SACT uses USLE (Universal Soil Loss Equation) for potential soil loss and simple hydraulic equations for soil transportation and deposition in which soil is divided into course-grained sand and fine-grained silt/clay. The amount of Cs moved with soil is predicted by the amount of above-mentioned soil movement and concentration ratio of Cs for each grain-size. SACT utilizes the 'ArcGIS' software and the GIS (Geographical Information System). SACT is characterized by its simplicity which enables fast calculation for wide area for long-term duration, using existing simple equations including USLE. Data for used parameters are widely available, and site-specific calculations are possible by using data obtained from the targeted area. (author)

  19. Formation of Valley Networks in a Cold and Icy Early Mars Climate: Predictions for Erosion Rates and Channel Morphology

    Science.gov (United States)

    Cassanelli, J.

    2017-12-01

    Mars is host to a diverse array of valley networks, systems of linear-to-sinuous depressions which are widely distributed across the surface and which exhibit branching patterns similar to the dendritic drainage patterns of terrestrial fluvial systems. Characteristics of the valley networks are indicative of an origin by fluvial activity, providing among the most compelling evidence for the past presence of flowing liquid water on the surface of Mars. Stratigraphic and crater age dating techniques suggest that the formation of the valley networks occurred predominantly during the early geologic history of Mars ( 3.7 Ga). However, whether the valley networks formed predominantly by rainfall in a relatively warm and wet early Mars climate, or by snowmelt and episodic rainfall in an ambient cold and icy climate, remains disputed. Understanding the formative environment of the valley networks will help distinguish between these warm and cold end-member early Mars climate models. Here we test a conceptual model for channel incision and evolution under cold and icy conditions with a substrate characterized by the presence of an ice-free dry active layer and subjacent ice-cemented regolith, similar to that found in the Antarctic McMurdo Dry Valleys. We implement numerical thermal models, quantitative erosion and transport estimates, and morphometric analyses in order to outline predictions for (1) the precise nature and structure of the substrate, (2) fluvial erosion/incision rates, and (3) channel morphology. Model predictions are compared against morphologic and morphometric observational data to evaluate consistency with the assumed cold climate scenario. In the cold climate scenario, the substrate is predicted to be characterized by a kilometers-thick globally-continuous cryosphere below a 50-100 meter thick desiccated ice-free zone. Initial results suggest that, with the predicted substrate structure, fluvial channel erosion and morphology in a cold early Mars

  20. Calculation Methods of Topographic Factors Modification Using Data Digital Elevation Model (DEM To Predict Erosion

    Directory of Open Access Journals (Sweden)

    Hengki Simanjuntak

    2018-03-01

    Full Text Available Erosion  is a crucial information for sustainable management of land resources within a particular watershed. The information of erosion is needed for land resource management planning, and is generally counted by USLE (Universal Soil Loss Equation. One of the parameters in USLE is topographic factor (LS. The determinations of LS in erosion estimation model are vary, both in terms of LS factor equation, as well as in terms of the length of the slope (λ and slope (s measurements. There are at least 3 methods used to calculate slope factors in spatial operation, i.e (1 Input of the LS Value from Table (INT, (2 Flow accumulation, and (3 Cell Size. The study was designed to obtain a method of calculation that gives the smallest topographic factor and in order to obtain a LS factors that similar to the slope information. Research location in Kampa Sub watershed, The LS determination in Kampa Sub watershed basically are with (INT and without calculating λ and s. INT method is determination without calculating λ and s, LS value is generate from the contour map and DEM SRTM by giving LS value from table reference of LS value. The Flow Accumulation and Cell Size are determination of LS Value by calculating λ and s. The Flow Accumulation method modifies the determination of λ and s using the middle value of s, λ per land use, and λ and s per cell. Cell Size method determines λ using the amount of cell size. The results showed that the “cell size” and "INT" methods were the best method for topographic factor (LS calculation, because LS value of “cell size” and "INT" methods are smaller than the flow accumulation method and the LS value similar to the slope information. LS value from that methods generated weighted value in average of 0,55−0,58. Keywords: cell size, flow accumulation, flow direction, the length of the slope, USLE

  1. Predicting the Rate of River Bank Erosion Caused by Large Wood Log

    Science.gov (United States)

    Zhang, N.; Rutherfurd, I.; Ghisalberti, M.

    2016-12-01

    When a single tree falls into a river channel, flow is deflected and accelerated between the tree roots and the bank face, increasing shear stress and scouring the bank. The scallop shaped erosion increases the diversity of the channel morphology, but also causes concern for adjacent landholders. Concern about increased bank erosion is one of the main reasons for large wood to still be removed from channels in SE Australia. Further, the hydraulic effect of many logs in the channel can reduce overall bank erosion rates. Although both phenomena have been described before, this research develops a hydraulic model that estimates their magnitude, and tests and calibrates this model with flume and field measurements, with logs with various configurations and sizes. Specifically, the model estimates the change in excess shear stress on the bank associated . The model addresses the effect of the log angle, distance from bank, and log size and flow condition by solving the mass continuity and energy conservation between the cross section at the approaching flow and contracted flow. Then, we evaluate our model against flume experiment preformed with semi-realistic log models to represent logs in different sizes and decay stages by comparing the measured and simulated velocity increase in the gap between the log and the bank. The log angle, distance from bank, and flow condition are systemically varied for each log model during the experiment. Final, the calibrated model is compared with the field data collected in anabranching channels of Murray River in SE Australia where there are abundant instream logs and regulated and consistent high flow for irrigation. Preliminary results suggest that a log can significantly increase the shear stress on the bank, especially when it positions perpendicular to the flow. The shear stress increases with the log angle in a rising curve (The log angle is the angle between log trunk and flow direction. 0o means log is parallel to flow with

  2. TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models.

    Science.gov (United States)

    Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

    2016-05-01

    Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com .

  3. TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models

    Science.gov (United States)

    Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

    2016-05-01

    Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com.

  4. Drug-target interaction prediction: A Bayesian ranking approach.

    Science.gov (United States)

    Peska, Ladislav; Buza, Krisztian; Koller, Júlia

    2017-12-01

    In silico prediction of drug-target interactions (DTI) could provide valuable information and speed-up the process of drug repositioning - finding novel usage for existing drugs. In our work, we focus on machine learning algorithms supporting drug-centric repositioning approach, which aims to find novel usage for existing or abandoned drugs. We aim at proposing a per-drug ranking-based method, which reflects the needs of drug-centric repositioning research better than conventional drug-target prediction approaches. We propose Bayesian Ranking Prediction of Drug-Target Interactions (BRDTI). The method is based on Bayesian Personalized Ranking matrix factorization (BPR) which has been shown to be an excellent approach for various preference learning tasks, however, it has not been used for DTI prediction previously. In order to successfully deal with DTI challenges, we extended BPR by proposing: (i) the incorporation of target bias, (ii) a technique to handle new drugs and (iii) content alignment to take structural similarities of drugs and targets into account. Evaluation on five benchmark datasets shows that BRDTI outperforms several state-of-the-art approaches in terms of per-drug nDCG and AUC. BRDTI results w.r.t. nDCG are 0.929, 0.953, 0.948, 0.897 and 0.690 for G-Protein Coupled Receptors (GPCR), Ion Channels (IC), Nuclear Receptors (NR), Enzymes (E) and Kinase (K) datasets respectively. Additionally, BRDTI significantly outperformed other methods (BLM-NII, WNN-GIP, NetLapRLS and CMF) w.r.t. nDCG in 17 out of 20 cases. Furthermore, BRDTI was also shown to be able to predict novel drug-target interactions not contained in the original datasets. The average recall at top-10 predicted targets for each drug was 0.762, 0.560, 1.000 and 0.404 for GPCR, IC, NR, and E datasets respectively. Based on the evaluation, we can conclude that BRDTI is an appropriate choice for researchers looking for an in silico DTI prediction technique to be used in drug

  5. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.

    Science.gov (United States)

    Ahmadi, Hamed; Ahmadi, Ali; Azimzadeh-Jamalkandi, Sadegh; Shoorehdeli, Mahdi Aliyari; Salehzadeh-Yazdi, Ali; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

    2013-02-01

    MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail; Soufan, Othman; Essack, Magbubah; Kalnis, Panos; Bajic, Vladimir B.

    2016-01-01

    DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery. DASPfind can be accessed online at: http://​www.​cbrc.​kaust.​edu.​sa/​daspfind.

  7. Adapting SWAT hillslope erosion model to predict sediment concentrations and yields in large Basins.

    Science.gov (United States)

    Vigiak, Olga; Malagó, Anna; Bouraoui, Fayçal; Vanmaercke, Matthias; Poesen, Jean

    2015-12-15

    The Soil and Water Assessment Tool (SWAT) is used worldwide for water quality assessment and planning. This paper aimed to assess and adapt SWAT hillslope sediment yield model (Modified Universal Soil Loss Equation, MUSLE) for applications in large basins, i.e. when spatial data is coarse and model units are large; and to develop a robust sediment calibration method for large regions. The Upper Danube Basin (132,000km(2)) was used as case study representative of large European Basins. The MUSLE was modified to reduce sensitivity of sediment yields to the Hydrologic Response Unit (HRU) size, and to identify appropriate algorithms for estimating hillslope length (L) and slope-length factor (LS). HRUs gross erosion was broadly calibrated against plot data and soil erosion map estimates. Next, mean annual SWAT suspended sediment concentrations (SSC, mg/L) were calibrated and validated against SSC data at 55 gauging stations (622 station-years). SWAT annual specific sediment yields in subbasin reaches (RSSY, t/km(2)/year) were compared to yields measured at 33 gauging stations (87station-years). The best SWAT configuration combined a MUSLE equation modified by the introduction of a threshold area of 0.01km(2) where L and LS were estimated with flow accumulation algorithms. For this configuration, the SSC residual interquartile was less than +/-15mg/L both for the calibration (1995-2004) and the validation (2005-2009) periods. The mean SSC percent bias for 1995-2009 was 24%. RSSY residual interquartile was within +/-10t/km(2)/year, with a mean RSSY percent bias of 12%. Residuals showed no bias with respect to drainage area, slope, or spatial distribution. The use of multiple data types at multiple sites enabled robust simulation of sediment concentrations and yields of the region. The MUSLE modifications are recommended for use in large basins. Based on SWAT simulations, we present a sediment budget for the Upper Danube Basin. Copyright © 2015. Published by Elsevier B.V.

  8. Precision comparison of the erosion rates derived from 137Cs measurements models with predictions based on empirical relationship

    International Nuclear Information System (INIS)

    Yang Mingyi; Liu Puling; Li Liqing

    2004-01-01

    The soil samples were collected in 6 cultivated runoff plots with grid sampling method, and the soil erosion rates derived from 137 Cs measurements were calculated. The models precision of Zhang Xinbao, Zhou Weizhi, Yang Hao and Walling were compared with predictions based on empirical relationship, data showed that the precision of 4 models is high within 50m slope length except for the slope with low slope angle and short length. Relatively, the precision of Walling's model is better than that of Zhang Xinbao, Zhou Weizhi and Yang Hao. In addition, the relationship between parameter Γ in Walling's improved model and slope angle was analyzed, the ralation is: Y=0.0109 X 1.0072 . (authors)

  9. Rill erosion rates in burned forests

    Science.gov (United States)

    Joseph W. Wagenbrenner; Peter R. Robichaud

    2011-01-01

    Introduction Wildfires often produce large increases in runoff and erosion rates (e.g., Moody and Martin, 2009), and land managers need to predict the frequency and magnitude of postfire erosion to determine the needs for hazard response and possible erosion mitigation to reduce the impacts of increased erosion on public safety and valued resources. The Water Erosion...

  10. Evaluation of the rusle and disturbed wepp erosion models for predicting soil loss in the first year after wildfire in NW Spain.

    Science.gov (United States)

    Fernández, Cristina; Vega, José A

    2018-05-04

    Severe fire greatly increases soil erosion rates and overland-flow in forest land. Soil erosion prediction models are essential for estimating fire impacts and planning post-fire emergency responses. We evaluated the performance of a) the Revised Universal Soil Loss Equation (RUSLE), modified by inclusion of an alternative equation for the soil erodibility factor, and b) the Disturbed WEPP model, by comparing the soil loss predicted by the models and the soil loss measured in the first year after wildfire in 44 experimental field plots in NW Spain. The Disturbed WEPP has not previously been validated with field data for use in NW Spain; validation studies are also very scarce in other areas. We found that both models underestimated the erosion rates. The accuracy of the RUSLE model was low, even after inclusion of a modified soil erodibility factor accounting for high contents of soil organic matter. We conclude that neither model is suitable for predicting soil erosion in the first year after fire in NW Spain and suggest that soil burn severity should be given greater weighting in post-fire soil erosion modelling. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Erosion and erosion-corrosion

    International Nuclear Information System (INIS)

    Isomoto, Yoshinori

    2008-01-01

    It is very difficult to interpret the technical term of erosion-corrosion' which is sometimes encountered in piping systems of power plants, because of complicated mechanisms and several confusing definitions of erosion-corrosion phenomena. 'FAC (flow accelerated corrosion)' is recently introduced as wall thinning of materials in power plant systems, as a representative of 'erosion-corrosion'. FAC is, however, not necessarily well understood and compared with erosion-corrosion. This paper describes firstly the origin, definition and fundamental understandings of erosion and erosion-corrosion, in order to reconsider and reconfirm the phenomena of erosion, erosion-corrosion and FAC. Next, typical mapping of erosion, corrosion, erosion-corrosion and FAC are introduced in flow velocity and environmental corrosiveness axes. The concept of damage rate in erosion-corrosion is finally discussed, connecting dissolution rate, mass transfer of metal ions in a metal oxide film and film growth. (author)

  12. Heartburn Severity Does Not Predict Disease Severity in Patients With Erosive Esophagitis

    Science.gov (United States)

    Fennerty, M. Brian; Johnson, David A.

    2006-01-01

    Background For patients with gastroesophageal reflux disease (GERD), it is often assumed by treating physicians that the severity of heartburn correlates with the severity of erosive esophagitis (EE). Objective This is a post hoc analysis of data from 5 clinical trials that investigate the relationship between the baseline severity of heartburn and the baseline severity of EE. Methods Patients with endoscopically confirmed EE were assessed for heartburn symptoms with a 4-point scale at baseline and during treatment for 8 weeks with various proton pump inhibitors in 5 double-blind trials in which esomeprazole was the common comparator. EE was graded with the Los Angeles (LA) classification system. In these trials, healing and symptom response were evaluated by endoscopy and questionnaire after 4 weeks of treatment. Patients who were not healed were treated for an additional 4 weeks and reevaluated. Results A total of 11,945 patients with endoscopically confirmed EE participated in the 5 trials, with patients receiving esomeprazole 40 mg (n = 5068), esomeprazole 20 mg (n = 1243), omeprazole 20 mg (n = 3018), or lansoprazole 30 mg (n = 2616). Approximately one quarter of the 11,945 GERD patients in these 5 trials had severe EE (defined as LA grades C or D), regardless of their baseline heartburn severity. Conclusion The severity of GERD symptoms does not correlate well with disease severity. These findings indicate that endoscopy may have value in GERD patients in identifying those with EE, and if empirical therapy is chosen, then longer courses (4-8 weeks) of antisecretory therapy may be necessary to ensure healing of unrecognized esophagitis. PMID:16926745

  13. Fuels planning: science synthesis and integration; environmental consequences fact sheet 12: Water Erosion Prediction Project (WEPP) Fuel Management (FuMe) tool

    Science.gov (United States)

    William Elliot; David Hall

    2005-01-01

    The Water Erosion Prediction Project (WEPP) Fuel Management (FuMe) tool was developed to estimate sediment generated by fuel management activities. WEPP FuMe estimates sediment generated for 12 fuel-related conditions from a single input. This fact sheet identifies the intended users and uses, required inputs, what the model does, and tells the user how to obtain the...

  14. MRI of the wrist and finger joints in inflammatory joint diseases at 1-year interval: MRI features to predict bone erosions

    International Nuclear Information System (INIS)

    Savnik, Anette; Malmskov, Hanne; Graff, Lykke B.; Danneskiold-Samsoee, Bente; Bliddal, Henning; Thomsen, Henrik S.; Nielsen, Henrik; Boesen, Jens

    2002-01-01

    The aim of this study was to assess the ability of MRI determined synovial volumes and bone marrow oedema to predict progressions in bone erosions after 1 year in patients with different types of inflammatory joint diseases. Eighty-four patients underwent MRI, laboratory and clinical examination at baseline and 1 year later. Magnetic resonance imaging of the wrist and finger joints was performed in 22 patients with rheumatoid arthritis less than 3 years (group 1) who fulfilled the American College of Rheumatology (ACR) criteria for rheumatoid arthritis, 18 patients with reactive arthritis or psoriatic arthritis (group 2), 22 patients with more than 3 years duration of rheumatoid arthritis, who fulfilled the ACR criteria for rheumatoid arthritis (group 3), and 20 patients with arthralgia (group 4). The volume of the synovial membrane was outlined manually before and after gadodiamide injection on the T1-weighted sequences in the finger joints. Bones with marrow oedema were summed up in the wrist and fingers on short-tau inversion recovery sequences. These MRI features was compared with the number of bone erosions 1 year later. The MR images were scored independently under masked conditions. The synovial volumes in the finger joints assessed on pre-contrast images was highly predictive of bone erosions 1 year later in patients with rheumatoid arthritis (groups 1 and 3). The strongest individual predictor of bone erosions at 1-year follow-up was bone marrow oedema, if present at the wrist at baseline. Bone erosions on baseline MRI were in few cases reversible at follow-up MRI. The total synovial volume in the finger joints, and the presence of bone oedema in the wrist bones, seems to be predictive for the number of bone erosions 1 year later and may be used in screening. The importance of very early bone changes on MRI and the importance of the reversibility of these findings remain to be clarified. (orig.)

  15. Predicting local distributions of erosion-corrosion wear sites for the piping in the nuclear power plant using CFD models

    International Nuclear Information System (INIS)

    Ferng, Y.M.

    2008-01-01

    The erosion-corrosion (E/C) wear is an essential degradation mechanism for the piping in the nuclear power plant, which results in the oxide mass loss from the inside of piping, the wall thinning, and even the pipe break. The pipe break induced by the E/C wear may cause costly plant repairs and personal injures. The measurement of pipe wall thickness is a useful tool for the power plant to prevent this incident. In this paper, CFD models are proposed to predict the local distributions of E/C wear sites, which include both the two-phase hydrodynamic model and the E/C models. The impacts of centrifugal and gravitational forces on the liquid droplet behaviors within the piping can be reasonably captured by the two-phase model. Coupled with these calculated flow characteristics, the E/C models can predicted the wear site distributions that show satisfactory agreement with the plant measurements. Therefore, the models proposed herein can assist in the pipe wall monitoring program for the nuclear power plant by way of concentrating the measuring point on the possible sites of severe E/C wear for the piping and reducing the measurement labor works

  16. Predicting Drug-Target Interactions Based on Small Positive Samples.

    Science.gov (United States)

    Hu, Pengwei; Chan, Keith C C; Hu, Yanxing

    2018-01-01

    A basic task in drug discovery is to find new medication in the form of candidate compounds that act on a target protein. In other words, a drug has to interact with a target and such drug-target interaction (DTI) is not expected to be random. Significant and interesting patterns are expected to be hidden in them. If these patterns can be discovered, new drugs are expected to be more easily discoverable. Currently, a number of computational methods have been proposed to predict DTIs based on their similarity. However, such as approach does not allow biochemical features to be directly considered. As a result, some methods have been proposed to try to discover patterns in physicochemical interactions. Since the number of potential negative DTIs are very high both in absolute terms and in comparison to that of the known ones, these methods are rather computationally expensive and they can only rely on subsets, rather than the full set, of negative DTIs for training and validation. As there is always a relatively high chance for negative DTIs to be falsely identified and as only partial subset of such DTIs is considered, existing approaches can be further improved to better predict DTIs. In this paper, we present a novel approach, called ODT (one class drug target interaction prediction), for such purpose. One main task of ODT is to discover association patterns between interacting drugs and proteins from the chemical structure of the former and the protein sequence network of the latter. ODT does so in two phases. First, the DTI-network is transformed to a representation by structural properties. Second, it applies a oneclass classification algorithm to build a prediction model based only on known positive interactions. We compared the best AUROC scores of the ODT with several state-of-art approaches on Gold standard data. The prediction accuracy of the ODT is superior in comparison with all the other methods at GPCRs dataset and Ion channels dataset. Performance

  17. [Anti-erosion effect of hedgerows in hillside croplands of Danjiangkou based on the evaluation with water erosion prediction project (WEPP) model].

    Science.gov (United States)

    Xiong, Qin-xue; Liu, Zhang-yong; Yao, Gui-zhi; Li, Ben-zhou

    2010-09-01

    Based on the data of field experiments on the hillside croplands of Danjiangkou, Hubei Province of China, the input files of crop characters, management measures, slope gradient and length, and soil properties for running WEPP model (Hillslope version) were established. Combining with the local weather data, a simulation study with the model was made on the runoff and soil loss of the croplands protected by four kinds of hedgerows (Amorpha fruticosa, Lonicera japonica, Hemerocallis fulva, and Poa sphondylodes) in Danjiangkou area. The resulted showed that WEPP model could accurately simulate the anti-erosion effect of hedgerows in hillside farmlands in the study area. Using this model not only reduced test number, but also saved time and effort, being able to provide scientific basis for the popularization and application of hedgerows. Among the four hedgerows, Amorpha fruticosa had the best anti-erosion effect. According to the simulation, the optimal planting density of A. fruticosa hedgerows in the farmlands was 1 m x 15 m at slope gradient 5 degrees, 1 m x 10 m at slope gradient 15 degrees, and 1 m x 3 m at slope gradient 25 degrees.

  18. Imbalanced target prediction with pattern discovery on clinical data repositories.

    Science.gov (United States)

    Chan, Tak-Ming; Li, Yuxi; Chiau, Choo-Chiap; Zhu, Jane; Jiang, Jie; Huo, Yong

    2017-04-20

    Clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted. We specifically target for interpretability for domain users where the model can be conveniently explained and applied in clinical practice. We propose an interpretable pattern model which is noise (missing) tolerant for practice data. To address the challenge of imbalanced targets of interest in clinical research, e.g., deaths less than a few percent, the geometric mean of sensitivity and specificity (G-mean) optimization criterion is employed, with which a simple but effective heuristic algorithm is developed. We compared pattern discovery to clinically interpretable methods on two retrospective clinical datasets. They contain 14.9% deaths in 1 year in the thoracic dataset and 9.1% deaths in the cardiac dataset, respectively. In spite of the imbalance challenge shown on other methods, pattern discovery consistently shows competitive cross-validated prediction performance. Compared to logistic regression, Naïve Bayes, and decision tree, pattern discovery achieves statistically significant (p-values repositories with imbalance and noise. The prediction results and interpretable patterns can provide insights in an agile and inexpensive way for the potential formal studies.

  19. Enhanced clinical pharmacy service targeting tools: risk-predictive algorithms.

    Science.gov (United States)

    El Hajji, Feras W D; Scullin, Claire; Scott, Michael G; McElnay, James C

    2015-04-01

    This study aimed to determine the value of using a mix of clinical pharmacy data and routine hospital admission spell data in the development of predictive algorithms. Exploration of risk factors in hospitalized patients, together with the targeting strategies devised, will enable the prioritization of clinical pharmacy services to optimize patient outcomes. Predictive algorithms were developed using a number of detailed steps using a 75% sample of integrated medicines management (IMM) patients, and validated using the remaining 25%. IMM patients receive targeted clinical pharmacy input throughout their hospital stay. The algorithms were applied to the validation sample, and predicted risk probability was generated for each patient from the coefficients. Risk threshold for the algorithms were determined by identifying the cut-off points of risk scores at which the algorithm would have the highest discriminative performance. Clinical pharmacy staffing levels were obtained from the pharmacy department staffing database. Numbers of previous emergency admissions and admission medicines together with age-adjusted co-morbidity and diuretic receipt formed a 12-month post-discharge and/or readmission risk algorithm. Age-adjusted co-morbidity proved to be the best index to predict mortality. Increased numbers of clinical pharmacy staff at ward level was correlated with a reduction in risk-adjusted mortality index (RAMI). Algorithms created were valid in predicting risk of in-hospital and post-discharge mortality and risk of hospital readmission 3, 6 and 12 months post-discharge. The provision of ward-based clinical pharmacy services is a key component to reducing RAMI and enabling the full benefits of pharmacy input to patient care to be realized. © 2014 John Wiley & Sons, Ltd.

  20. Modeling soil erosion in a watershed

    OpenAIRE

    Lanuza, R.

    1999-01-01

    Most erosion models have been developed based on a plot scale and have limited application to a watershed due to the differences in aerial scale. In order to address this limitation, a GIS-assisted methodology for modeling soil erosion was developed using PCRaster to predict the rate of soil erosion at watershed level; identify the location of erosion prone areas; and analyze the impact of landuse changes on soil erosion. The general methodology of desktop modeling or soil erosion at watershe...

  1. Prediction of soil stability and erosion in semiarid regions using numerical hydrological model (MCAT) and airborne hyperspectral imagery

    Science.gov (United States)

    Brook, Anna; Wittenberg, Lea

    2015-04-01

    promising models is the MCAT, which is a MATLAB library of visual and numerical analysis tools for the evaluation of hydrological and environmental models. The model applied in this paper presents an innovative infrastructural system for predicting soil stability and erosion impacts. This integrated model is applicable to mixed areas with spatially varying soil properties, landscape, and land-cover characteristics. Data from a semiarid site in southern Israel was used to evaluate the model and analyze fundamental erosion mechanisms. The findings estimate the sensitivity of the suggested model to the physical parameters and encourage the use of hyperspectral remote sensing imagery (HSI). The proposed model is integrated according to the following stages: 1. The soil texture, aggregation, soil moisture estimated via airborne HSI data, including soil surface clay and calcium carbonate erosions; 2. The mechanical stability of soil assessed via pedo-transfer function corresponding to load dependent changes in soil physical properties due to pre-compression stress (set of equations study shear strength parameters take into account soil texture, aggregation, soil moisture and ecological soil variables); 3. The precipitation-related runoff model program (RMP) satisfactorily reproduces the observed seasonal mean and variation of surface runoff for the current climate simulation; 4. The Monte Carlo Analysis Toolbox (MCAT), a library of visual and numerical analysis tools for the evaluation of hydrological and environmental models, is proposed as a tool for integrate all the approaches to an applicable model. The presented model overcomes the limitations of existing modeling methods by integrating physical data produced via HSI and yet stays generic in terms of space and time independency.

  2. RANS Based Methodology for Predicting the Influence of Leading Edge Erosion on Airfoil Performance

    Energy Technology Data Exchange (ETDEWEB)

    Langel, Christopher M. [Univ. of California, Davis, CA (United States). Dept. of Mechanical and Aerospace Engineering; Chow, Raymond C. [Univ. of California, Davis, CA (United States). Dept. of Mechanical and Aerospace Engineering; van Dam, C. P. [Univ. of California, Davis, CA (United States). Dept. of Mechanical and Aerospace Engineering; Maniaci, David Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Wind Energy Technologies Dept.

    2017-10-01

    The impact of surface roughness on flows over aerodynamically designed surfaces is of interested in a number of different fields. It has long been known the surface roughness will likely accelerate the laminar- turbulent transition process by creating additional disturbances in the boundary layer. However, there are very few tools available to predict the effects surface roughness will have on boundary layer flow. There are numerous implications of the premature appearance of a turbulent boundary layer. Increases in local skin friction, boundary layer thickness, and turbulent mixing can impact global flow properties compounding the effects of surface roughness. With this motivation, an investigation into the effects of surface roughness on boundary layer transition has been conducted. The effort involved both an extensive experimental campaign, and the development of a high fidelity roughness model implemented in a R ANS solver. Vast a mounts of experimental data was generated at the Texas A&M Oran W. Nicks Low Speed Wind Tunnel for the calibration and validation of the roughness model described in this work, as well as future efforts. The present work focuses on the development of the computational model including a description of the calibration process. The primary methodology presented introduces a scalar field variable and associated transport equation that interacts with a correlation based transition model. The additional equation allows for non-local effects of surface roughness to be accounted for downstream of rough wall sections while maintaining a "local" formulation. The scalar field is determined through a boundary condition function that has been calibrated to flat plate cases with sand grain roughness. The model was initially tested on a NACA 0012 airfoil with roughness strips applied to the leading edge. Further calibration of the roughness model was performed using results from the companion experimental study on a NACA 633 -418 airfoil

  3. On the prediction of threshold friction velocity of wind erosion using soil reflectance spectroscopy

    Science.gov (United States)

    Li, Junran; Flagg, Cody B.; Okin, Gregory S.; Painter, Thomas H.; Dintwe, Kebonye; Belnap, Jayne

    2015-01-01

    Current approaches to estimate threshold friction velocity (TFV) of soil particle movement, including both experimental and empirical methods, suffer from various disadvantages, and they are particularly not effective to estimate TFVs at regional to global scales. Reflectance spectroscopy has been widely used to obtain TFV-related soil properties (e.g., moisture, texture, crust, etc.), however, no studies have attempted to directly relate soil TFV to their spectral reflectance. The objective of this study was to investigate the relationship between soil TFV and soil reflectance in the visible and near infrared (VIS–NIR, 350–2500 nm) spectral region, and to identify the best range of wavelengths or combinations of wavelengths to predict TFV. Threshold friction velocity of 31 soils, along with their reflectance spectra and texture were measured in the Mojave Desert, California and Moab, Utah. A correlation analysis between TFV and soil reflectance identified a number of isolated, narrow spectral domains that largely fell into two spectral regions, the VIS area (400–700 nm) and the short-wavelength infrared (SWIR) area (1100–2500 nm). A partial least squares regression analysis (PLSR) confirmed the significant bands that were identified by correlation analysis. The PLSR further identified the strong relationship between the first-difference transformation and TFV at several narrow regions around 1400, 1900, and 2200 nm. The use of PLSR allowed us to identify a total of 17 key wavelengths in the investigated spectrum range, which may be used as the optimal spectral settings for estimating TFV in the laboratory and field, or mapping of TFV using airborne/satellite sensors.

  4. Using high-performance mathematical modelling tools to predict erosion and sediment fluxes in peri-urban catchments

    Science.gov (United States)

    Pereira, André; Conde, Daniel; Ferreira, Carla S. S.; Walsh, Rory; Ferreira, Rui M. L.

    2017-04-01

    Deforestation and urbanization generally lead to increased soil erosion andthrough the indirect effect of increased overland flow and peak flood discharges. Mathematical modelling tools can be helpful for predicting the spatial distribution of erosion and the morphological changes on the channel network. This is especially useful to predict the impacts of land-use changes in parts of the watershed, namely due to urbanization. However, given the size of the computational domain (normally the watershed itself), the need for high spatial resolution data to model accurately sediment transport processes and possible need to model transcritical flows, the computational cost is high and requires high-performance computing techniques. The aim of this work is to present the latest developments of the hydrodynamic and morphological model STAV2D and its applicability to predict runoff and erosion at watershed scale. STAV2D was developed at CEris - Instituto Superior Técnico, Universidade de Lisboa - as a tool particularly appropriated to model strong transient flows in complex and dynamic geometries. It is based on an explicit, first-order 2DH finite-volume discretization scheme for unstructured triangular meshes, in which a flux-splitting technique is paired with a reviewed Roe-Riemann solver, yielding a model applicable to discontinuous flows over time-evolving geometries. STAV2D features solid transport in both Euleran and Lagrangian forms, with the aim of describing the transport of fine natural sediments and then the large individual debris. The model has been validated with theoretical solutions and laboratory experiments (Canelas et al., 2013 & Conde et al., 2015). STAV-2D now supports fully distributed and heterogeneous simulations where multiple different hardware devices can be used to accelerate computation time within a unified Object-Oriented approach: the source code for CPU and GPU has the same compilation units and requires no device specific branches, like

  5. Saliva and dental erosion

    Directory of Open Access Journals (Sweden)

    Marília Afonso Rabelo Buzalaf

    2012-10-01

    Full Text Available Dental erosion is a multifactorial condition. The consideration of chemical, biological and behavioral factors is fundamental for its prevention and therapy. Among the biological factors, saliva is one of the most important parameters in the protection against erosive wear. Objective: This review discusses the role of salivary factors on the development of dental erosion. Material and Methods: A search was undertaken on MeDLINe website for papers from 1969 to 2010. The keywords used in the research were "saliva", "acquired pellicle", "salivary flow", "salivary buffering capacity" and "dental erosion". Inclusion of studies, data extraction and quality assessment were undertaken independently and in duplicate by two members of the review team. Disagreements were solved by discussion and consensus or by a third party. Results: Several characteristics and properties of saliva play an important role in dental erosion. Salivary clearance gradually eliminates the acids through swallowing and saliva presents buffering capacity causing neutralization and buffering of dietary acids. Salivary flow allows dilution of the acids. In addition, saliva is supersaturated with respect to tooth mineral, providing calcium, phosphate and fluoride necessary for remineralization after an erosive challenge. Furthermore, many proteins present in saliva and acquired pellicle play an important role in dental erosion. Conclusions: Saliva is the most important biological factor affecting the progression of dental erosion. Knowledge of its components and properties involved in this protective role can drive the development of preventive measures targeting to enhance its known beneficial effects.

  6. Saliva and dental erosion.

    Science.gov (United States)

    Buzalaf, Marília Afonso Rabelo; Hannas, Angélicas Reis; Kato, Melissa Thiemi

    2012-01-01

    Dental erosion is a multifactorial condition. The consideration of chemical, biological and behavioral factors is fundamental for its prevention and therapy. Among the biological factors, saliva is one of the most important parameters in the protection against erosive wear. This review discusses the role of salivary factors on the development of dental erosion. A search was undertaken on MeDLINe website for papers from 1969 to 2010. The keywords used in the research were "saliva", "acquired pellicle", "salivary flow", "salivary buffering capacity" and "dental erosion". Inclusion of studies, data extraction and quality assessment were undertaken independently and in duplicate by two members of the review team. Disagreements were solved by discussion and consensus or by a third party. Several characteristics and properties of saliva play an important role in dental erosion. Salivary clearance gradually eliminates the acids through swallowing and saliva presents buffering capacity causing neutralization and buffering of dietary acids. Salivary flow allows dilution of the acids. In addition, saliva is supersaturated with respect to tooth mineral, providing calcium, phosphate and fluoride necessary for remineralization after an erosive challenge. Furthermore, many proteins present in saliva and acquired pellicle play an important role in dental erosion. Saliva is the most important biological factor affecting the progression of dental erosion. Knowledge of its components and properties involved in this protective role can drive the development of preventive measures targeting to enhance its known beneficial effects.

  7. Predicting the effectiveness of different mulching techniques in reducing post-fire runoff and erosion at plot scale with the RUSLE, MMF and PESERA models.

    Science.gov (United States)

    Vieira, D C S; Serpa, D; Nunes, J P C; Prats, S A; Neves, R; Keizer, J J

    2018-08-01

    Wildfires have become a recurrent threat for many Mediterranean forest ecosystems. The characteristics of the Mediterranean climate, with its warm and dry summers and mild and wet winters, make this a region prone to wildfire occurrence as well as to post-fire soil erosion. This threat is expected to be aggravated in the future due to climate change and land management practices and planning. The wide recognition of wildfires as a driver for runoff and erosion in burnt forest areas has created a strong demand for model-based tools for predicting the post-fire hydrological and erosion response and, in particular, for predicting the effectiveness of post-fire management operations to mitigate these responses. In this study, the effectiveness of two post-fire treatments (hydromulch and natural pine needle mulch) in reducing post-fire runoff and soil erosion was evaluated against control conditions (i.e. untreated conditions), at different spatial scales. The main objective of this study was to use field data to evaluate the ability of different erosion models: (i) empirical (RUSLE), (ii) semi-empirical (MMF), and (iii) physically-based (PESERA), to predict the hydrological and erosive response as well as the effectiveness of different mulching techniques in fire-affected areas. The results of this study showed that all three models were reasonably able to reproduce the hydrological and erosive processes occurring in burned forest areas. In addition, it was demonstrated that the models can be calibrated at a small spatial scale (0.5 m 2 ) but provide accurate results at greater spatial scales (10 m 2 ). From this work, the RUSLE model seems to be ideal for fast and simple applications (i.e. prioritization of areas-at-risk) mainly due to its simplicity and reduced data requirements. On the other hand, the more complex MMF and PESERA models would be valuable as a base of a possible tool for assessing the risk of water contamination in fire-affected water bodies and

  8. Can control of soil erosion mitigate water pollution by sediments?

    Science.gov (United States)

    Rickson, R J

    2014-01-15

    The detrimental impact of sediment and associated pollutants on water quality is widely acknowledged, with many watercourses in the UK failing to meet the standard of 'good ecological status'. Catchment sediment budgets show that hill slope erosion processes can be significant sources of waterborne sediment, with rates of erosion likely to increase given predicted future weather patterns. However, linking on-site erosion rates with off-site impacts is complicated because of the limited data on soil erosion rates in the UK and the dynamic nature of the source-pathway-receptor continuum over space and time. Even so, soil erosion control measures are designed to reduce sediment production (source) and mobilisation/transport (pathway) on hill slopes, with consequent mitigation of pollution incidents in watercourses (receptors). The purpose of this paper is to review the scientific evidence of the effectiveness of erosion control measures used in the UK to reduce sediment loads of hill slope origin in watercourses. Although over 73 soil erosion mitigation measures have been identified from the literature, empirical data on erosion control effectiveness are limited. Baseline comparisons for the 18 measures where data do exist reveal erosion control effectiveness is highly variable over time and between study locations. Given the limitations of the evidence base in terms of geographical coverage and duration of monitoring, performance of the different measures cannot be extrapolated to other areas. This uncertainty in effectiveness has implications for implementing erosion/sediment risk reduction policies, where quantified targets are stipulated, as is the case in the EU Freshwater Fish and draft Soil Framework Directives. Also, demonstrating technical effectiveness of erosion control measures alone will not encourage uptake by land managers: quantifying the costs and benefits of adopting erosion mitigation is equally important, but these are uncertain and difficult to

  9. Predicting the effectiveness of different mulching techniques to reduce post-fire runoff and erosion in Mediterranean pine stands - does cover matter?

    Science.gov (United States)

    Vieira, Diana; Nunes, João; Prats, Sergio; Serpa, Dalila; Keizer, Jan

    2016-04-01

    Wildfires have become a recurrent threat for many forest ecosystems of the Mediterranean. The characteristics of the Mediterranean climate with its warm and dry summers and mild and wet winters make it prone to wildfire occurrence as well as to post-fire soil erosion. Furthermore, climate change and continuation of current land management practices and planning are generally expected to further increase this threat. The wide recognition of the effects of wildfires to enhance runoff and erosion has created a strong demand for model-based tools for predicting the post-fire hydrological and erosion response and, in particular, for predicting the effectiveness of post-fire forestry operations to mitigate these responses. Such a tool should allow to identify areas with elevated risks of soil erosion and to evaluate which measures should be applied and when to minimize these risks. A key element in evaluating these measures is also their costs, in order to optimize the use of the limited resources that are typically available for post-fire land management. In this study, two "treatments" are compared with control conditions (i.e. doing nothing) after a wildfire with a moderate soil burn severity: (i) 4 erosion plots were treated with hydro-mulch, (ii) 4 erosion plots were untreated but had a high pine needle cover quickly after the fire, due to needle cast from scorched pine crowns (often referred to as "natural mulching") (iii) 4 plots were untreated and had a very reduced protective litter cover . The main objective of this study was to asses if the revised MMF model could effectively predict the impacts of hydro-mulching and natural mulching with pine needle on runoff generation and the associated soil losses. If MMF could predict well the impact of natural mulching, it could be very useful in limiting the areas that should be considered for specific soil mitigation measures, especially in the case of wildfires that affect large areas with moderate severity. The

  10. Two-dimensional numerical study of ELMs-induced erosion of tungsten divertor target tiles with different edge shapes

    International Nuclear Information System (INIS)

    Huang, Yan; Sun, Jizhong; Hu, Wanpeng; Sang, Chaofeng; Wang, Dezhen

    2016-01-01

    Highlights: • Thermal performance of three edge-shaped divertor tiles was assessed numerically. • All the divertor tiles exposed to type-I ELMs like ITER's will melt. • The rounded edge tile thermally performs the best in all tiles of interest. • The incident energy flux density was evaluated with structural effects considered. - Abstract: Thermal performance of the divertor tile with different edge shapes was assessed numerically along the poloidal direction by a two-dimensional heat conduction model with considering the geometrical effects of castellated divertor tiles on the properties of its adjacent plasma. The energy flux density distribution arriving at the castellated divertor tile surface was evaluated by a two-dimension-in-space and three-dimension-in-velocity particle-in-cell plus Monte Carlo Collisions code and then the obtained energy flux distribution was used as input for the heat conduction model. The simulation results showed that the divertor tiles with any edge shape of interest (rectangular edge, slanted edge, and rounded edge) would melt, especially, in the edge surface region of facing plasma poloidally under typical heat flux density of a transient event of type-I ELMs for ITER, deposition energy of 1 MJ/m"2 in a duration of 600 μs. In comparison with uniform energy deposition, the vaporizing erosion was reduced greatly but the melting erosion was aggravated noticeably in the edge area of plasma facing diveror tile. Of three studied edge shapes, the simulation results indicated that the divertor plate with rounded edge was the most resistant to the thermal erosion.

  11. Observations and predictions of wave runup, extreme water levels, and medium-term dune erosion during storm conditions

    OpenAIRE

    Suanez , Serge ,; Cancouët , Romain; Floc'h , France; Blaise , Emmanuel; Ardhuin , Fabrice; Filipot , Jean-François; Cariolet , Jean-Marie; Delacourt , Christophe

    2015-01-01

    Monitoring of dune erosion and accretion on the high-energy macrotidal Vougot beach in North Brittany (France) over the past decade (2004–2014) has revealed significant morphological changes. Dune toe erosion/accretion records have been compared with extreme water level measurements, defined as the sum of (i) astronomic tide; (ii) storm surge; and (iii) vertical wave runup. Runup parameterization was conducted using swash limits, beach profiles, and hydrodynamic (Hm0, Tm0,–1, and high tide wa...

  12. Prediction of Human Drug Targets and Their Interactions Using Machine Learning Methods: Current and Future Perspectives.

    Science.gov (United States)

    Nath, Abhigyan; Kumari, Priyanka; Chaube, Radha

    2018-01-01

    Identification of drug targets and drug target interactions are important steps in the drug-discovery pipeline. Successful computational prediction methods can reduce the cost and time demanded by the experimental methods. Knowledge of putative drug targets and their interactions can be very useful for drug repurposing. Supervised machine learning methods have been very useful in drug target prediction and in prediction of drug target interactions. Here, we describe the details for developing prediction models using supervised learning techniques for human drug target prediction and their interactions.

  13. Predicting the impact of logging activities on soil erosion and water quality in steep, forested tropical islands

    Science.gov (United States)

    Wenger, Amelia S.; Atkinson, Scott; Santini, Talitha; Falinski, Kim; Hutley, Nicholas; Albert, Simon; Horning, Ned; Watson, James E. M.; Mumby, Peter J.; Jupiter, Stacy D.

    2018-04-01

    Increasing development in tropical regions provides new economic opportunities that can improve livelihoods, but it threatens the functional integrity and ecosystem services provided by terrestrial and aquatic ecosystems when conducted unsustainably. Given the small size of many islands, communities may have limited opportunities to replace loss and damage to the natural resources upon which they depend for ecosystem service provisioning, thus heightening the need for proactive, integrated management. This study quantifies the effectiveness of management strategies, stipulated in logging codes-of-practice, at minimizing soil erosion and sediment runoff as clearing extent increases, using Kolombangara Island, Solomon Islands as a case study. Further, we examine the ability of erosion reduction strategies to maintain sustainable soil erosion rates and reduce potential downstream impacts to drinking water and environmental water quality. We found that increasing land clearing—even with best management strategies in place—led to unsustainable levels of soil erosion and significant impacts to downstream water quality, compromising the integrity of the land for future agricultural uses, consistent access to clean drinking water, and important downstream ecosystems. Our results demonstrate that in order to facilitate sustainable development, logging codes of practice must explicitly link their soil erosion reduction strategies to soil erosion and downstream water quality thresholds, otherwise they will be ineffective at minimizing the impacts of logging activities. The approach taken here to explicitly examine soil erosion rates and downstream water quality in relation to best management practices and increasing land clearing should be applied more broadly across a range of ecosystems to inform decision-making about the socioeconomic and environmental trade-offs associated with logging, and other types of land use change.

  14. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

    Directory of Open Access Journals (Sweden)

    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  15. Erosive gastritis

    International Nuclear Information System (INIS)

    Mohammed, S.H.; Conrad, C.; Kjoergaad, J.

    1982-01-01

    Erosive gastritis is a well-defined radiologic and endoscopic entity. It is one of the common causes of upper gastrointestinal bleeding, yet it is seldom diagnosed and often confused with a number of other diseases. This communication re-emphasizes the characteristic endoscopic and radiologic features of erosive gastritis and its differential diagnosis. Two representative cases are reported. (orig.)

  16. Erosive gastritis

    Energy Technology Data Exchange (ETDEWEB)

    Mohammed, S.H.; Conrad, C.; Kjoergaad, J.

    1982-08-01

    Erosive gastritis is a well-defined radiologic and endoscopic entity. It is one of the common causes of upper gastrointestinal bleeding, yet it is seldom diagnosed and often confused with a number of other diseases. This communication re-emphasizes the characteristic endoscopic and radiologic features of erosive gastritis and its differential diagnosis. Two representative cases are reported.

  17. Creep life prediction of super heater coils used in coal based thermal power plants subjected to fly ash erosion and oxide scale formation

    Science.gov (United States)

    Srinivasan, P.; Kushwaha, Shashank

    2018-04-01

    Super heater coils of the coal based thermal power plants and subjected to severe operating conditions from both steam side and gas side. Formation of oxide scale due to prolonged service lead to temperature raise of the tube and erosion due to fly ash present in the combusted gases leads to tube thinning. Both these factors lead to creep rupture of the coils much before the designed service life. Failure of super heater coils during service of the boiler leads to power loss and huge monitory loss to the power plants. An attempt is made to model the creep damage caused to the super heater coils using heat transfer analysis tube thinning due to erosive wear of the tubes. Combined effects of these parameters are taken into consideration to predict the life of the super heater coils. This model may be used to estimate the life of the coils operating under the severe operating conditions to prevent the unexpected failure of the coils.

  18. Predicting Effects of Corrosion Erosion of High Strength Steel Pipelines Elbow on CO2-Acetic Acid (HAc) Solution

    International Nuclear Information System (INIS)

    Asmara, Y. P.; Ismail, M. F.; Chui, L. Giok; Halimi, Jamiludin

    2016-01-01

    Simultaneously effect of erosion combined with corrosion becomes the most concern in oil and gas industries. It is due to the fast deterioration of metal as effects of solid particles mixed with corrosive environment. There are many corrosion software to investigate possible degradation mechanisms developed by researchers. They are using many combination factors of chemical reactions and physical process. However effects of CO 2 and acid on pipelines orientations are still remain uncovered in their simulation. This research will investigate combination effects of CO 2 and HAc on corrosion and erosion artificial environmental containing sands particles in 45°, 90° and 180° elbow pipelines. The research used theoretical calculations combined with experiments for verification. The main concerns are to investigate the maximum erosion corrosion rate and maximum shear stress at the surface. Methodology used to calculate corrosion rate are Linear Polarization Resistance (LPR) and weight loss. The results showed that at 45°, erosion rate is the more significant effects in contributing degradation of the metal. The effects of CO 2 and HAc gave significant effects when flow rate of the solution are high which reflect synergism effects of solid particles and those chemical compositions. (paper)

  19. Observations and Predictions of Wave Runup, Extreme Water Levels, and Medium-Term Dune Erosion during Storm Conditions

    Directory of Open Access Journals (Sweden)

    Serge Suanez

    2015-07-01

    Full Text Available Monitoring of dune erosion and accretion on the high-energy macrotidal Vougot beach in North Brittany (France over the past decade (2004–2014 has revealed significant morphological changes. Dune toe erosion/accretion records have been compared with extreme water level measurements, defined as the sum of (i astronomic tide; (ii storm surge; and (iii vertical wave runup. Runup parameterization was conducted using swash limits, beach profiles, and hydrodynamic (Hm0, Tm0,–1, and high tide water level—HTWL data sets obtained from high frequency field surveys. The aim was to quantify in-situ environmental conditions and dimensional swash parameters for the best calibration of Battjes [1] runup formula. In addition, an empirical equation based on observed tidal water level and offshore wave height was produced to estimate extreme water levels over the whole period of dune morphological change monitoring. A good correlation between this empirical equation (1.01Hmoξo and field runup measurements (Rmax was obtained (R2 85%. The goodness of fit given by the RMSE was about 0.29 m. A good relationship was noticed between dune erosion and high water levels when the water levels exceeded the dune foot elevation. In contrast, when extreme water levels were below the height of the toe of the dune sediment budget increased, inducing foredune recovery. These erosion and accretion phases may be related to the North Atlantic Oscillation Index.

  20. Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling.

    Science.gov (United States)

    Vlot, Anna H C; de Witte, Wilhelmus E A; Danhof, Meindert; van der Graaf, Piet H; van Westen, Gerard J P; de Lange, Elizabeth C M

    2017-12-04

    Selectivity is an important attribute of effective and safe drugs, and prediction of in vivo target and tissue selectivity would likely improve drug development success rates. However, a lack of understanding of the underlying (pharmacological) mechanisms and availability of directly applicable predictive methods complicates the prediction of selectivity. We explore the value of combining physiologically based pharmacokinetic (PBPK) modeling with quantitative structure-activity relationship (QSAR) modeling to predict the influence of the target dissociation constant (K D ) and the target dissociation rate constant on target and tissue selectivity. The K D values of CB1 ligands in the ChEMBL database are predicted by QSAR random forest (RF) modeling for the CB1 receptor and known off-targets (TRPV1, mGlu5, 5-HT1a). Of these CB1 ligands, rimonabant, CP-55940, and Δ 8 -tetrahydrocanabinol, one of the active ingredients of cannabis, were selected for simulations of target occupancy for CB1, TRPV1, mGlu5, and 5-HT1a in three brain regions, to illustrate the principles of the combined PBPK-QSAR modeling. Our combined PBPK and target binding modeling demonstrated that the optimal values of the K D and k off for target and tissue selectivity were dependent on target concentration and tissue distribution kinetics. Interestingly, if the target concentration is high and the perfusion of the target site is low, the optimal K D value is often not the lowest K D value, suggesting that optimization towards high drug-target affinity can decrease the benefit-risk ratio. The presented integrative structure-pharmacokinetic-pharmacodynamic modeling provides an improved understanding of tissue and target selectivity.

  1. Prediction methodologies for target scene generation in the aerothermal targets analysis program (ATAP)

    Science.gov (United States)

    Hudson, Douglas J.; Torres, Manuel; Dougherty, Catherine; Rajendran, Natesan; Thompson, Rhoe A.

    2003-09-01

    The Air Force Research Laboratory (AFRL) Aerothermal Targets Analysis Program (ATAP) is a user-friendly, engineering-level computational tool that features integrated aerodynamics, six-degree-of-freedom (6-DoF) trajectory/motion, convective and radiative heat transfer, and thermal/material response to provide an optimal blend of accuracy and speed for design and analysis applications. ATAP is sponsored by the Kinetic Kill Vehicle Hardware-in-the-Loop Simulator (KHILS) facility at Eglin AFB, where it is used with the CHAMP (Composite Hardbody and Missile Plume) technique for rapid infrared (IR) signature and imagery predictions. ATAP capabilities include an integrated 1-D conduction model for up to 5 in-depth material layers (with options for gaps/voids with radiative heat transfer), fin modeling, several surface ablation modeling options, a materials library with over 250 materials, options for user-defined materials, selectable/definable atmosphere and earth models, multiple trajectory options, and an array of aerodynamic prediction methods. All major code modeling features have been validated with ground-test data from wind tunnels, shock tubes, and ballistics ranges, and flight-test data for both U.S. and foreign strategic and theater systems. Numerous applications include the design and analysis of interceptors, booster and shroud configurations, window environments, tactical missiles, and reentry vehicles.

  2. Early Antenatal Prediction of Gestational Diabetes in Obese Women: Development of Prediction Tools for Targeted Intervention.

    Directory of Open Access Journals (Sweden)

    Sara L White

    Full Text Available All obese women are categorised as being of equally high risk of gestational diabetes (GDM whereas the majority do not develop the disorder. Lifestyle and pharmacological interventions in unselected obese pregnant women have been unsuccessful in preventing GDM. Our aim was to develop a prediction tool for early identification of obese women at high risk of GDM to facilitate targeted interventions in those most likely to benefit. Clinical and anthropometric data and non-fasting blood samples were obtained at 15+0-18+6 weeks' gestation in 1303 obese pregnant women from UPBEAT, a randomised controlled trial of a behavioural intervention. Twenty one candidate biomarkers associated with insulin resistance, and a targeted nuclear magnetic resonance (NMR metabolome were measured. Prediction models were constructed using stepwise logistic regression. Twenty six percent of women (n = 337 developed GDM (International Association of Diabetes and Pregnancy Study Groups criteria. A model based on clinical and anthropometric variables (age, previous GDM, family history of type 2 diabetes, systolic blood pressure, sum of skinfold thicknesses, waist:height and neck:thigh ratios provided an area under the curve of 0.71 (95%CI 0.68-0.74. This increased to 0.77 (95%CI 0.73-0.80 with addition of candidate biomarkers (random glucose, haemoglobin A1c (HbA1c, fructosamine, adiponectin, sex hormone binding globulin, triglycerides, but was not improved by addition of NMR metabolites (0.77; 95%CI 0.74-0.81. Clinically translatable models for GDM prediction including readily measurable variables e.g. mid-arm circumference, age, systolic blood pressure, HbA1c and adiponectin are described. Using a ≥35% risk threshold, all models identified a group of high risk obese women of whom approximately 50% (positive predictive value later developed GDM, with a negative predictive value of 80%. Tools for early pregnancy identification of obese women at risk of GDM are described

  3. Ability of One-Dimensional Hairsine-Rose Erosion Model to Predict Sediment Transport over a Soil with Significant Surface Stones

    Science.gov (United States)

    Jomaa, S.; Barry, D. A.; Sander, G. C.; Parlange, J.-Y.; Heng, B. C. P.; Tromp-van Meerveld, H. J.

    2010-05-01

    Surface stones affect erosion rates by reducing raindrop-driven detachment and protecting the original soil against overland flow induced-hydraulic stress. Numerous studies have shown that the effect of surface stones on erosion depends on both the stone characteristics (e.g., size, distribution) and the soil properties. The aim of this study was (i) to quantify how the stone characteristics can affect the total sediment concentration and the concentrations of the individual size classes, (ii) to test if stones affect preferentially a particular size class within the eroded sediment and (iii) to determine whether the 1D Hairsine-Rose (H-R) erosion model can represent the experimental data. A series of laboratory experiments were conducted using the 2 m × 6 m EPFL erosion flume for a high rainfall intensity (60 mm/h) event on a gentle slope (2.2%). The flume was divided into two identical 1-m wide flumes. This separation was done to allow simultaneous replicate experiments. Experiments were conducted with different configurations and scenarios (stone coverage, size and emplacement). Three coverage proportions (20%, 40%, and 70%), two stone diameters (3-4 and 6-7 cm) and two emplacement types (topsoil and partially embedded) were tested. For each experiment, the total sediment concentration, the concentration for the individual size classes, and the flume discharge were measured. Infiltration rates were measured at different depths and locations. A high resolution laser scanner provided details of the surface change due to erosion during the experiments. This technique allowed us to quantify the spatial distribution of eroded soil and to understand better if sediment transport is 1D or rather 2D over the flumes. The one-dimensional Hairsine-Rose (H-R) erosion model was used to fit the integrated data and to provide estimates of the parameters. The ability of the 1D H-R model to predict the measured sediment concentrations in the presence of stones in the soil matrix

  4. Upper Gastrointestinal Symptoms Predictive of Candida Esophagitis and Erosive Esophagitis in HIV and Non-HIV Patients: An Endoscopy-Based Cross-Sectional Study of 6011 Patients.

    Science.gov (United States)

    Takahashi, Yuta; Nagata, Naoyoshi; Shimbo, Takuro; Nishijima, Takeshi; Watanabe, Koji; Aoki, Tomonori; Sekine, Katsunori; Okubo, Hidetaka; Watanabe, Kazuhiro; Sakurai, Toshiyuki; Yokoi, Chizu; Mimori, Akio; Oka, Shinichi; Uemura, Naomi; Akiyama, Junichi

    2015-11-01

    Upper gastrointestinal (GI) symptoms are common in both HIV and non-HIV-infected patients, but the difference of GI symptom severity between 2 groups remains unknown. Candida esophagitis and erosive esophagitis, 2 major types of esophagitis, are seen in both HIV and non-HIV-infected patients, but differences in GI symptoms that are predictive of esophagitis between 2 groups remain unknown. We aimed to determine whether GI symptoms differ between HIV-infected and non-HIV-infected patients, and identify specific symptoms of candida esophagitis and erosive esophagitis between 2 groups.We prospectively enrolled 6011 patients (HIV, 430; non-HIV, 5581) who underwent endoscopy and completed questionnaires. Nine upper GI symptoms (epigastric pain, heartburn, acid regurgitation, hunger cramps, nausea, early satiety, belching, dysphagia, and odynophagia) were evaluated using a 7-point Likert scale. Associations between esophagitis and symptoms were analyzed by the multivariate logistic regression model adjusted for age, sex, and proton pump inhibitors.Endoscopy revealed GI-organic diseases in 33.4% (2010/6.011) of patients. The prevalence of candida esophagitis and erosive esophagitis was 11.2% and 12.1% in HIV-infected patients, respectively, whereas it was 2.9% and 10.7 % in non-HIV-infected patients, respectively. After excluding GI-organic diseases, HIV-infected patients had significantly (P symptom scores for heartburn, hunger cramps, nausea, early satiety, belching, dysphagia, and odynophagia than non-HIV-infected patients. In HIV-infected patients, any symptom was not significantly associated with CD4 cell count. In multivariate analysis, none of the 9 GI symptoms were associated with candida esophagitis in HIV-infected patients, whereas dysphagia and odynophagia were independently (P HIV-infected patients. However, heartburn and acid regurgitation were independently (P symptom scores were reliable in both HIV (α, 0.86) and non-HIV-infected patients (α, 0.85).This

  5. DIANA-microT web server: elucidating microRNA functions through target prediction.

    Science.gov (United States)

    Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

    2009-07-01

    Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

  6. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets

    NARCIS (Netherlands)

    Biswas, A.; Gagnon, J.N.; Brouns, S.J.J.; Fineran, P.C.; Brown, C.M.

    2013-01-01

    The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are

  7. Statistical model based gender prediction for targeted NGS clinical panels

    Directory of Open Access Journals (Sweden)

    Palani Kannan Kandavel

    2017-12-01

    The reference test dataset are being used to test the model. The sensitivity on predicting the gender has been increased from the current “genotype composition in ChrX” based approach. In addition, the prediction score given by the model can be used to evaluate the quality of clinical dataset. The higher prediction score towards its respective gender indicates the higher quality of sequenced data.

  8. Predictive Models of target organ and Systemic toxicities (BOSC)

    Science.gov (United States)

    The objective of this work is to predict the hazard classification and point of departure (PoD) of untested chemicals in repeat-dose animal testing studies. We used supervised machine learning to objectively evaluate the predictive accuracy of different classification and regress...

  9. Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

    International Nuclear Information System (INIS)

    Nigsch, Florian; Mitchell, John B.O.

    2008-01-01

    The combination of models for protein target prediction with large databases containing toxicological information for individual molecules allows the derivation of 'toxiclogical' profiles, i.e., to what extent are molecules of known toxicity predicted to interact with a set of protein targets. To predict protein targets of drug-like and toxic molecules, we built a computational multiclass model using the Winnow algorithm based on a dataset of protein targets derived from the MDL Drug Data Report. A 15-fold Monte Carlo cross-validation using 50% of each class for training, and the remaining 50% for testing, provided an assessment of the accuracy of that model. We retained the 3 top-ranking predictions and found that in 82% of all cases the correct target was predicted within these three predictions. The first prediction was the correct one in almost 70% of cases. A model built on the whole protein target dataset was then used to predict the protein targets for 150 000 molecules from the MDL Toxicity Database. We analysed the frequency of the predictions across the panel of protein targets for experimentally determined toxicity classes of all molecules. This allowed us to identify clusters of proteins related by their toxicological profiles, as well as toxicities that are related. Literature-based evidence is provided for some specific clusters to show the relevance of the relationships identified

  10. TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds

    Directory of Open Access Journals (Sweden)

    Shihua Zhang

    2018-02-01

    Full Text Available Tea is one of the most popular non-alcoholic beverages consumed worldwide. Numerous bioactive constituents of tea were confirmed to possess healthy benefits via the mechanisms of regulating gene expressions or protein activities. However, a complete interacting profile between tea bioactive compounds (TBCs and their target genes is lacking, which put an obstacle in the study of healthy function of tea. To fill this gap, we developed a database of target genes of TBCs (TBC2target, http://camellia.ahau.edu.cn/TBC2target based on a pharmacophore mapping approach. In TBC2target, 6,226 interactions between 240 TBCs and 673 target genes were documented. TBC2target contains detailed information about each interacting entry, such as TBC, CAS number, PubChem CID, source of compound (e.g., green, black, compound type, target gene(s of TBC, gene symbol, gene ID, ENSEMBL ID, PDB ID, TBC bioactivity and the reference. Using the TBC-target associations, we constructed a bipartite network and provided users the global network and local sub-network visualization and topological analyses. The entire database is free for online browsing, searching and downloading. In addition, TBC2target provides a BLAST search function to facilitate use of the database. The particular strengths of TBC2target are the inclusion of the comprehensive TBC-target interactions, and the capacity to visualize and analyze the interacting networks, which may help uncovering the beneficial effects of tea on human health as a central resource in tea health community.

  11. TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds.

    Science.gov (United States)

    Zhang, Shihua; Zhang, Liang; Wang, Yijun; Yang, Jian; Liao, Mingzhi; Bi, Shoudong; Xie, Zhongwen; Ho, Chi-Tang; Wan, Xiaochun

    2018-01-01

    Tea is one of the most popular non-alcoholic beverages consumed worldwide. Numerous bioactive constituents of tea were confirmed to possess healthy benefits via the mechanisms of regulating gene expressions or protein activities. However, a complete interacting profile between tea bioactive compounds (TBCs) and their target genes is lacking, which put an obstacle in the study of healthy function of tea. To fill this gap, we developed a database of target genes of TBCs (TBC2target, http://camellia.ahau.edu.cn/TBC2target) based on a pharmacophore mapping approach. In TBC2target, 6,226 interactions between 240 TBCs and 673 target genes were documented. TBC2target contains detailed information about each interacting entry, such as TBC, CAS number, PubChem CID, source of compound (e.g., green, black), compound type, target gene(s) of TBC, gene symbol, gene ID, ENSEMBL ID, PDB ID, TBC bioactivity and the reference. Using the TBC-target associations, we constructed a bipartite network and provided users the global network and local sub-network visualization and topological analyses. The entire database is free for online browsing, searching and downloading. In addition, TBC2target provides a BLAST search function to facilitate use of the database. The particular strengths of TBC2target are the inclusion of the comprehensive TBC-target interactions, and the capacity to visualize and analyze the interacting networks, which may help uncovering the beneficial effects of tea on human health as a central resource in tea health community.

  12. Modeling the fluid/soil interface erosion in the Hole Erosion Test

    Directory of Open Access Journals (Sweden)

    Kissi B.

    2012-07-01

    Full Text Available Soil erosion is a complex phenomenon which yields at its final stage to insidious fluid leakages under the hydraulic infrastructures known as piping and which are the main cause of their rupture. The Hole Erosion Test is commonly used to quantify the rate of piping erosion. In this work, The Hole Erosion Test is modelled by using Fluent software package. The aim is to predict the erosion rate of soil during the hole erosion test. The renormalization group theory – based k–ε turbulence model equations are used. This modelling makes it possible describing the effect of the clay concentration in flowing water on erosion. Unlike the usual one dimensional models, the proposed modelling shows that erosion is not uniform erosion along the hole length. In particular, the concentration of clay is found to increase noticeably the erosion rate.

  13. Predicting drug-target interaction for new drugs using enhanced similarity measures and super-target clustering.

    Science.gov (United States)

    Shi, Jian-Yu; Yiu, Siu-Ming; Li, Yiming; Leung, Henry C M; Chin, Francis Y L

    2015-07-15

    Predicting drug-target interaction using computational approaches is an important step in drug discovery and repositioning. To predict whether there will be an interaction between a drug and a target, most existing methods identify similar drugs and targets in the database. The prediction is then made based on the known interactions of these drugs and targets. This idea is promising. However, there are two shortcomings that have not yet been addressed appropriately. Firstly, most of the methods only use 2D chemical structures and protein sequences to measure the similarity of drugs and targets respectively. However, this information may not fully capture the characteristics determining whether a drug will interact with a target. Secondly, there are very few known interactions, i.e. many interactions are "missing" in the database. Existing approaches are biased towards known interactions and have no good solutions to handle possibly missing interactions which affect the accuracy of the prediction. In this paper, we enhance the similarity measures to include non-structural (and non-sequence-based) information and introduce the concept of a "super-target" to handle the problem of possibly missing interactions. Based on evaluations on real data, we show that our similarity measure is better than the existing measures and our approach is able to achieve higher accuracy than the two best existing algorithms, WNN-GIP and KBMF2K. Our approach is available at http://web.hku.hk/∼liym1018/projects/drug/drug.html or http://www.bmlnwpu.org/us/tools/PredictingDTI_S2/METHODS.html. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Postural control of elderly: moving to predictable and unpredictable targets.

    NARCIS (Netherlands)

    Jongman, Vera; Lamoth, Claudine J C; van Keeken, Helco; Caljouw, Simone R

    2012-01-01

    Impaired postural control with muscle weakness is an important predictor of falls within the elderly population.Particular daily activities that require weight shifting in order to be able to reach a specific target (a cup on a table) require continuous adjustments to keep the body's center of mass

  15. In silico prediction of novel therapeutic targets using gene-disease association data.

    Science.gov (United States)

    Ferrero, Enrico; Dunham, Ian; Sanseau, Philippe

    2017-08-29

    Target identification and validation is a pressing challenge in the pharmaceutical industry, with many of the programmes that fail for efficacy reasons showing poor association between the drug target and the disease. Computational prediction of successful targets could have a considerable impact on attrition rates in the drug discovery pipeline by significantly reducing the initial search space. Here, we explore whether gene-disease association data from the Open Targets platform is sufficient to predict therapeutic targets that are actively being pursued by pharmaceutical companies or are already on the market. To test our hypothesis, we train four different classifiers (a random forest, a support vector machine, a neural network and a gradient boosting machine) on partially labelled data and evaluate their performance using nested cross-validation and testing on an independent set. We then select the best performing model and use it to make predictions on more than 15,000 genes. Finally, we validate our predictions by mining the scientific literature for proposed therapeutic targets. We observe that the data types with the best predictive power are animal models showing a disease-relevant phenotype, differential expression in diseased tissue and genetic association with the disease under investigation. On a test set, the neural network classifier achieves over 71% accuracy with an AUC of 0.76 when predicting therapeutic targets in a semi-supervised learning setting. We use this model to gain insights into current and failed programmes and to predict 1431 novel targets, of which a highly significant proportion has been independently proposed in the literature. Our in silico approach shows that data linking genes and diseases is sufficient to predict novel therapeutic targets effectively and confirms that this type of evidence is essential for formulating or strengthening hypotheses in the target discovery process. Ultimately, more rapid and automated target

  16. Predicted allowable doses to normal organs for biologically targeted radiotherapy

    International Nuclear Information System (INIS)

    O'Donoghue, J.A.; Wheldon, T.E.; Western Regional Hospital Board, Glasgow

    1988-01-01

    The authors have used Dale's extension to the ''linear quadratic'' (LQ) model (Dale, 1985) to evaluate ''equivalent doses'' in cases involving exponentially decaying dose rates. This analysis indicates that the dose-rate effect will be a significant determinant of allowable doses to organs such as liver, kidney and lung. These organ tolerance doses constitute independent constraints on the therapeutic intensity of biologically targeted radiotherapy in exactly the same way as for conventional external beam radiotherapy. In the context of marrow rescue they will in all likelihood constitute the dose-limiting side-effects and thus be especially important. (author)

  17. Contextual remapping in visual search after predictable target-location changes.

    Science.gov (United States)

    Conci, Markus; Sun, Luning; Müller, Hermann J

    2011-07-01

    Invariant spatial context can facilitate visual search. For instance, detection of a target is faster if it is presented within a repeatedly encountered, as compared to a novel, layout of nontargets, demonstrating a role of contextual learning for attentional guidance ('contextual cueing'). Here, we investigated how context-based learning adapts to target location (and identity) changes. Three experiments were performed in which, in an initial learning phase, observers learned to associate a given context with a given target location. A subsequent test phase then introduced identity and/or location changes to the target. The results showed that contextual cueing could not compensate for target changes that were not 'predictable' (i.e. learnable). However, for predictable changes, contextual cueing remained effective even immediately after the change. These findings demonstrate that contextual cueing is adaptive to predictable target location changes. Under these conditions, learned contextual associations can be effectively 'remapped' to accommodate new task requirements.

  18. An ensemble method to predict target genes and pathways in uveal melanoma

    Directory of Open Access Journals (Sweden)

    Wei Chao

    2018-04-01

    Full Text Available This work proposes to predict target genes and pathways for uveal melanoma (UM based on an ensemble method and pathway analyses. Methods: The ensemble method integrated a correlation method (Pearson correlation coefficient, PCC, a causal inference method (IDA and a regression method (Lasso utilizing the Borda count election method. Subsequently, to validate the performance of PIL method, comparisons between confirmed database and predicted miRNA targets were performed. Ultimately, pathway enrichment analysis was conducted on target genes in top 1000 miRNA-mRNA interactions to identify target pathways for UM patients. Results: Thirty eight of the predicted interactions were matched with the confirmed interactions, indicating that the ensemble method was a suitable and feasible approach to predict miRNA targets. We obtained 50 seed miRNA-mRNA interactions of UM patients and extracted target genes from these interactions, such as ASPG, BSDC1 and C4BP. The 601 target genes in top 1,000 miRNA-mRNA interactions were enriched in 12 target pathways, of which Phototransduction was the most significant one. Conclusion: The target genes and pathways might provide a new way to reveal the molecular mechanism of UM and give hand for target treatments and preventions of this malignant tumor.

  19. Erhversbetinget erosion?

    DEFF Research Database (Denmark)

    Dige, Irene; Gjørup, Hans; Nyvad, Bente

    2012-01-01

    Baggrund – I forbindelse med dental erosion er en grundig udredning af patienten vigtig, således at årsagen til erosionernes opståen findes, og der kan iværksættes adækvat forebyggende indsats. En sådan udredning er ikke mindst vigtig, når arbejdsmiljøet mistænkes. Patienttilfælde – En 30-årig...... arbejdsskade, men ikke anerkendt, da erosioner ikke er optaget på Arbejdsskadestyrelsens liste over erhvervssygdomme. En systematisk registrering af lignende tilfælde kunne imidlertid på sigt ændre retspraksis for fremtidige patienter med arbejdsbetinget erosion....... patient, der arbejder som pladesmed, blev henvist til Landsdels- og Videnscenter, Århus Sygehus, med henblik på udredning af patientens kraftige slid. Patienten udviste ikke-alderssvarende tandslid af emalje og dentin svarende til erosion forårsaget af syredampe i arbejdsmiljøet, muligvis forstærket af...

  20. Literature-based condition-specific miRNA-mRNA target prediction.

    Directory of Open Access Journals (Sweden)

    Minsik Oh

    Full Text Available miRNAs are small non-coding RNAs that regulate gene expression by binding to the 3'-UTR of genes. Many recent studies have reported that miRNAs play important biological roles by regulating specific mRNAs or genes. Many sequence-based target prediction algorithms have been developed to predict miRNA targets. However, these methods are not designed for condition-specific target predictions and produce many false positives; thus, expression-based target prediction algorithms have been developed for condition-specific target predictions. A typical strategy to utilize expression data is to leverage the negative control roles of miRNAs on genes. To control false positives, a stringent cutoff value is typically set, but in this case, these methods tend to reject many true target relationships, i.e., false negatives. To overcome these limitations, additional information should be utilized. The literature is probably the best resource that we can utilize. Recent literature mining systems compile millions of articles with experiments designed for specific biological questions, and the systems provide a function to search for specific information. To utilize the literature information, we used a literature mining system, BEST, that automatically extracts information from the literature in PubMed and that allows the user to perform searches of the literature with any English words. By integrating omics data analysis methods and BEST, we developed Context-MMIA, a miRNA-mRNA target prediction method that combines expression data analysis results and the literature information extracted based on the user-specified context. In the pathway enrichment analysis using genes included in the top 200 miRNA-targets, Context-MMIA outperformed the four existing target prediction methods that we tested. In another test on whether prediction methods can re-produce experimentally validated target relationships, Context-MMIA outperformed the four existing target prediction

  1. Impact assessment of rainfall-vegetation on sedimentation and predicting erosion-prone region by GIS and RS

    Directory of Open Access Journals (Sweden)

    Mahboob Alam

    2016-03-01

    Full Text Available Water reservoirs are facing universal sedimentation problems worldwide. Land covers, whether natural or manmade, eventually change, and the vegetation cover and rainfall have a great effect on the sediment load. Traditional techniques for analysing this problem are time-consuming and spatially limited. Remote sensing (RS provides a convenient way to observe land cover changes, and geographic information system (GIS provides tools for geographic analysis. This study demonstrates a GIS-based methodology for calculating the impact of vegetation and rainfall on the sediment load using remotely sensed data. Moderate resolution imaging spectroradiometer data were used to observe temporal changes in the vegetation-cover area of the watershed surface. The total drainage area for the reservoir was calculated from shuttle radar topographic mission data. The annual rainfall amount was used to compute the annual available rainwater for the watershed, and the impact of the annual available rainwater on the vegetation-covered area was determined. In addition, areas that were adding sedimentation to the reservoir were identified. An inverse relationship between the rainfall and vegetation cover was observed, clearly showing the triggering of erosion.

  2. Statistical learning for predictive targeting in online advertising

    DEFF Research Database (Denmark)

    Fruergaard, Bjarne Ørum

    The focus in this thesis is investigation of machine learning methods with applications in computational advertising. Computational advertising is the broad discipline of building systems which can reach audiences browsing the Internet with targeted advertisements. At the core of such systems......, an international online advertising technology partner. This also means that the analyses and methods in this work are developed with particular use-cases within Adform in mind and thus need also to be applicable in Adform’s technology stack. This implies extra thought on scalability and performance...... application in real-time bidding ad exchanges, where each advertiser is given a chance to place bids for showing their ad while the page loads, and the winning bid gets to display their banner. The contributions of this thesis entail application of a hybrid model of explicit and latent features for learning...

  3. Design of a tripartite network for the prediction of drug targets

    Science.gov (United States)

    Kunimoto, Ryo; Bajorath, Jürgen

    2018-02-01

    Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred. The tripartite network was found to have a stable structure and simulated network growth was accompanied by a steady increase in assortativity, reflecting increasing correlation between degrees of connected nodes leading to even network connectivity. Local drug environments in the tripartite network typically contained neighbor targets and revealed interesting drug-compound-target relationships for further analysis. Candidate targets were prioritized. The tripartite network design extends standard drug-target networks and provides additional opportunities for drug target prediction.

  4. Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

    Science.gov (United States)

    Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

    2014-08-01

    Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. DeepMirTar: a deep-learning approach for predicting human miRNA targets.

    Science.gov (United States)

    Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

    2018-06-01

    MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

  6. Drug-Target Interaction Prediction through Label Propagation with Linear Neighborhood Information.

    Science.gov (United States)

    Zhang, Wen; Chen, Yanlin; Li, Dingfang

    2017-11-25

    Interactions between drugs and target proteins provide important information for the drug discovery. Currently, experiments identified only a small number of drug-target interactions. Therefore, the development of computational methods for drug-target interaction prediction is an urgent task of theoretical interest and practical significance. In this paper, we propose a label propagation method with linear neighborhood information (LPLNI) for predicting unobserved drug-target interactions. Firstly, we calculate drug-drug linear neighborhood similarity in the feature spaces, by considering how to reconstruct data points from neighbors. Then, we take similarities as the manifold of drugs, and assume the manifold unchanged in the interaction space. At last, we predict unobserved interactions between known drugs and targets by using drug-drug linear neighborhood similarity and known drug-target interactions. The experiments show that LPLNI can utilize only known drug-target interactions to make high-accuracy predictions on four benchmark datasets. Furthermore, we consider incorporating chemical structures into LPLNI models. Experimental results demonstrate that the model with integrated information (LPLNI-II) can produce improved performances, better than other state-of-the-art methods. The known drug-target interactions are an important information source for computational predictions. The usefulness of the proposed method is demonstrated by cross validation and the case study.

  7. Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

    International Nuclear Information System (INIS)

    Cao Dongsheng; Liu Shao; Xu Qingsong; Lu Hongmei; Huang Jianhua; Hu Qiannan; Liang Yizeng

    2012-01-01

    Highlights: ► Drug–target interactions are predicted using an extended SAR methodology. ► A drug–target interaction is regarded as an event triggered by many factors. ► Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. ► Our approach shows compatibility between the new scheme and current SAR methodology. - Abstract: The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug–target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug–target interactions in a timely manner. In this article, we aim at extending current structure–activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug–target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug–target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug–target interactions, and show a general compatibility between the new scheme and current SAR

  8. TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.

    Science.gov (United States)

    Bandyopadhyay, Sanghamitra; Mitra, Ramkrishna

    2009-10-15

    Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an important area of research. However, most of the methods suffer from either high false positive or false negative rates. One reason for this is the marked deficiency of negative examples or miRNA non-target pairs. Systematic identification of non-target mRNAs is still not addressed properly, and therefore, current machine learning approaches are compelled to rely on artificially generated negative examples for training. In this article, we have identified approximately 300 tissue-specific negative examples using a novel approach that involves expression profiling of both miRNAs and mRNAs, miRNA-mRNA structural interactions and seed-site conservation. The newly generated negative examples are validated with pSILAC dataset, which elucidate the fact that the identified non-targets are indeed non-targets.These high-throughput tissue-specific negative examples and a set of experimentally verified positive examples are then used to build a system called TargetMiner, a support vector machine (SVM)-based classifier. In addition to assessing the prediction accuracy on cross-validation experiments, TargetMiner has been validated with a completely independent experimental test dataset. Our method outperforms 10 existing target prediction algorithms and provides a good balance between sensitivity and specificity that is not reflected in the existing methods. We achieve a significantly higher sensitivity and specificity of 69% and 67.8% based on a pool of 90 feature set and 76.5% and 66.1% using a set of 30 selected feature set on the completely independent test dataset. In order to establish the effectiveness of the systematically generated negative examples, the SVM is trained using a different set of negative data generated using the method in Yousef et al. A significantly higher false positive rate (70.6%) is observed when tested on the independent set, while all other factors are kept the

  9. Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.

    Science.gov (United States)

    Liu, Yong; Wu, Min; Miao, Chunyan; Zhao, Peilin; Li, Xiao-Li

    2016-02-01

    In pharmaceutical sciences, a crucial step of the drug discovery process is the identification of drug-target interactions. However, only a small portion of the drug-target interactions have been experimentally validated, as the experimental validation is laborious and costly. To improve the drug discovery efficiency, there is a great need for the development of accurate computational approaches that can predict potential drug-target interactions to direct the experimental verification. In this paper, we propose a novel drug-target interaction prediction algorithm, namely neighborhood regularized logistic matrix factorization (NRLMF). Specifically, the proposed NRLMF method focuses on modeling the probability that a drug would interact with a target by logistic matrix factorization, where the properties of drugs and targets are represented by drug-specific and target-specific latent vectors, respectively. Moreover, NRLMF assigns higher importance levels to positive observations (i.e., the observed interacting drug-target pairs) than negative observations (i.e., the unknown pairs). Because the positive observations are already experimentally verified, they are usually more trustworthy. Furthermore, the local structure of the drug-target interaction data has also been exploited via neighborhood regularization to achieve better prediction accuracy. We conducted extensive experiments over four benchmark datasets, and NRLMF demonstrated its effectiveness compared with five state-of-the-art approaches.

  10. Target motion predictions for pre-operative planning during needle-based interventions

    NARCIS (Netherlands)

    op den Buijs, J.; Abayazid, Momen; de Korte, Chris L.; Misra, Sarthak

    During biopsies, breast tissue is subjected to displacement upon needle indentation, puncture, and penetration. Thus, accurate needle placement requires pre-operative predictions of the target motions. In this paper, we used ultrasound elastography measurements to non-invasively predict elastic

  11. An efficient numerical target strength prediction model: Validation against analysis solutions

    NARCIS (Netherlands)

    Fillinger, L.; Nijhof, M.J.J.; Jong, C.A.F. de

    2014-01-01

    A decade ago, TNO developed RASP (Rapid Acoustic Signature Prediction), a numerical model for the prediction of the target strength of immersed underwater objects. The model is based on Kirchhoff diffraction theory. It is currently being improved to model refraction, angle dependent reflection and

  12. Accurate microRNA target prediction correlates with protein repression levels

    Directory of Open Access Journals (Sweden)

    Simossis Victor A

    2009-09-01

    Full Text Available Abstract Background MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease. Results DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction. Conclusion Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at http://www.microrna.gr/microT

  13. Drug-target interaction prediction via class imbalance-aware ensemble learning.

    Science.gov (United States)

    Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2016-12-22

    Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was

  14. Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations.

    Science.gov (United States)

    Zong, Nansu; Kim, Hyeoneui; Ngo, Victoria; Harismendy, Olivier

    2017-08-01

    A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure. DeepWalk, a deep learning method, is adopted in this study to calculate the similarities within Linked Tripartite Network (LTN), a heterogeneous network generated from biomedical linked datasets. This proposed method shows promising results for drug-target association prediction: 98.96% AUC ROC score with a 10-fold cross-validation and 99.25% AUC ROC score with a Monte Carlo cross-validation with LTN. By utilizing DeepWalk, we demonstrate that: (i) this method outperforms other existing topology-based similarity computation methods, (ii) the performance is better for tripartite than with bipartite networks and (iii) the measure of similarity using network topology outperforms the ones derived from chemical structure (drugs) or genomic sequence (targets). Our proposed methodology proves to be capable of providing a promising solution for drug-target prediction based on topological similarity with a heterogeneous network, and may be readily re-purposed and adapted in the existing of similarity-based methodologies. The proposed method has been developed in JAVA and it is available, along with the data at the following URL: https://github.com/zongnansu1982/drug-target-prediction . nazong@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  15. Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses

    Directory of Open Access Journals (Sweden)

    Arthur C. Oliveira

    2017-05-01

    Full Text Available Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature—TargetScan (TS, miRanda-mirSVR (MR, Pita, and RNA22 (R22, and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection. For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p and 1,400 genes (700 validated and 700 non-validated as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions.

  16. Supplementary Material for: DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-01-01

    Abstract Background Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient computational methods for the accurate prediction of potential DTIs. To-date, many computational methods have been proposed for this purpose, but they suffer the drawback of a high rate of false positive predictions. Results Here, we developed a novel computational DTI prediction method, DASPfind. DASPfind uses simple paths of particular lengths inferred from a graph that describes DTIs, similarities between drugs, and similarities between the protein targets of drugs. We show that on average, over the four gold standard DTI datasets, DASPfind significantly outperforms other existing methods when the single top-ranked predictions are considered, resulting in 46.17 % of these predictions being correct, and it achieves 49.22 % correct single top ranked predictions when the set of all DTIs for a single drug is tested. Furthermore, we demonstrate that our method is best suited for predicting DTIs in cases of drugs with no known targets or with few known targets. We also show the practical use of DASPfind by generating novel predictions for the Ion Channel dataset and validating them manually. Conclusions DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery

  17. Synergistic target combination prediction from curated signaling networks: Machine learning meets systems biology and pharmacology.

    Science.gov (United States)

    Chua, Huey Eng; Bhowmick, Sourav S; Tucker-Kellogg, Lisa

    2017-10-01

    Given a signaling network, the target combination prediction problem aims to predict efficacious and safe target combinations for combination therapy. State-of-the-art in silico methods use Monte Carlo simulated annealing (mcsa) to modify a candidate solution stochastically, and use the Metropolis criterion to accept or reject the proposed modifications. However, such stochastic modifications ignore the impact of the choice of targets and their activities on the combination's therapeutic effect and off-target effects, which directly affect the solution quality. In this paper, we present mascot, a method that addresses this limitation by leveraging two additional heuristic criteria to minimize off-target effects and achieve synergy for candidate modification. Specifically, off-target effects measure the unintended response of a signaling network to the target combination and is often associated with toxicity. Synergy occurs when a pair of targets exerts effects that are greater than the sum of their individual effects, and is generally a beneficial strategy for maximizing effect while minimizing toxicity. mascot leverages on a machine learning-based target prioritization method which prioritizes potential targets in a given disease-associated network to select more effective targets (better therapeutic effect and/or lower off-target effects); and on Loewe additivity theory from pharmacology which assesses the non-additive effects in a combination drug treatment to select synergistic target activities. Our experimental study on two disease-related signaling networks demonstrates the superiority of mascot in comparison to existing approaches. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. A mathematical model of reservoir sediment quality prediction based on land-use and erosion processes in watershed

    Science.gov (United States)

    Junakova, N.; Balintova, M.; Junak, J.

    2017-10-01

    The aim of this paper is to propose a mathematical model for determining of total nitrogen (N) and phosphorus (P) content in eroded soil particles with emphasis on prediction of bottom sediment quality in reservoirs. The adsorbed nutrient concentrations are calculated using the Universal Soil Loss Equation (USLE) extended by the determination of the average soil nutrient concentration in top soils. The average annual vegetation and management factor is divided into five periods of the cropping cycle. For selected plants, the average plant nutrient uptake divided into five cropping periods is also proposed. The average nutrient concentrations in eroded soil particles in adsorbed form are modified by sediment enrichment ratio to obtain the total nutrient content in transported soil particles. The model was designed for the conditions of north-eastern Slovakia. The study was carried out in the agricultural basin of the small water reservoir Klusov.

  19. Predictive distractor context facilitates attentional selection of high, but not intermediate and low, salience targets.

    Science.gov (United States)

    Töllner, Thomas; Conci, Markus; Müller, Hermann J

    2015-03-01

    It is well established that we can focally attend to a specific region in visual space without shifting our eyes, so as to extract action-relevant sensory information from covertly attended locations. The underlying mechanisms that determine how fast we engage our attentional spotlight in visual-search scenarios, however, remain controversial. One dominant view advocated by perceptual decision-making models holds that the times taken for focal-attentional selection are mediated by an internal template that biases perceptual coding and selection decisions exclusively through target-defining feature coding. This notion directly predicts that search times remain unaffected whether or not participants can anticipate the upcoming distractor context. Here we tested this hypothesis by employing an illusory-figure localization task that required participants to search for an invariant target amongst a variable distractor context, which gradually changed--either randomly or predictably--as a function of distractor-target similarity. We observed a graded decrease in internal focal-attentional selection times--correlated with external behavioral latencies--for distractor contexts of higher relative to lower similarity to the target. Critically, for low but not intermediate and high distractor-target similarity, these context-driven effects were cortically and behaviorally amplified when participants could reliably predict the type of distractors. This interactive pattern demonstrates that search guidance signals can integrate information about distractor, in addition to target, identities to optimize distractor-target competition for focal-attentional selection. © 2014 Wiley Periodicals, Inc.

  20. Novel computational methods to predict drug–target interactions using graph mining and machine learning approaches

    KAUST Repository

    Olayan, Rawan S.

    2017-12-01

    Computational drug repurposing aims at finding new medical uses for existing drugs. The identification of novel drug-target interactions (DTIs) can be a useful part of such a task. Computational determination of DTIs is a convenient strategy for systematic screening of a large number of drugs in the attempt to identify new DTIs at low cost and with reasonable accuracy. This necessitates development of accurate computational methods that can help focus on the follow-up experimental validation on a smaller number of highly likely targets for a drug. Although many methods have been proposed for computational DTI prediction, they suffer the high false positive prediction rate or they do not predict the effect that drugs exert on targets in DTIs. In this report, first, we present a comprehensive review of the recent progress in the field of DTI prediction from data-centric and algorithm-centric perspectives. The aim is to provide a comprehensive review of computational methods for identifying DTIs, which could help in constructing more reliable methods. Then, we present DDR, an efficient method to predict the existence of DTIs. DDR achieves significantly more accurate results compared to the other state-of-theart methods. As supported by independent evidences, we verified as correct 22 out of the top 25 DDR DTIs predictions. This validation proves the practical utility of DDR, suggesting that DDR can be used as an efficient method to identify 5 correct DTIs. Finally, we present DDR-FE method that predicts the effect types of a drug on its target. On different representative datasets, under various test setups, and using different performance measures, we show that DDR-FE achieves extremely good performance. Using blind test data, we verified as correct 2,300 out of 3,076 DTIs effects predicted by DDR-FE. This suggests that DDR-FE can be used as an efficient method to identify correct effects of a drug on its target.

  1. Validation of a probabilistic post-fire erosion model

    Science.gov (United States)

    Pete Robichaud; William J. Elliot; Sarah A. Lewis; Mary Ellen Miller

    2016-01-01

    Post-fire increases of runoff and erosion often occur and land managers need tools to be able to project the increased risk. The Erosion Risk Management Tool (ERMiT) uses the Water Erosion Prediction Project (WEPP) model as the underlying processor. ERMiT predicts the probability of a given amount of hillslope sediment delivery from a single rainfall or...

  2. Spherical and cylindrical cavity expansion models based prediction of penetration depths of concrete targets.

    Directory of Open Access Journals (Sweden)

    Xiaochao Jin

    Full Text Available The cavity expansion theory is most widely used to predict the depth of penetration of concrete targets. The main purpose of this work is to clarify the differences between the spherical and cylindrical cavity expansion models and their scope of application in predicting the penetration depths of concrete targets. The factors that influence the dynamic cavity expansion process of concrete materials were first examined. Based on numerical results, the relationship between expansion pressure and velocity was established. Then the parameters in the Forrestal's formula were fitted to have a convenient and effective prediction of the penetration depth. Results showed that both the spherical and cylindrical cavity expansion models can accurately predict the depth of penetration when the initial velocity is lower than 800 m/s. However, the prediction accuracy decreases with the increasing of the initial velocity and diameters of the projectiles. Based on our results, it can be concluded that when the initial velocity is higher than the critical velocity, the cylindrical cavity expansion model performs better than the spherical cavity expansion model in predicting the penetration depth, while when the initial velocity is lower than the critical velocity the conclusion is quite the contrary. This work provides a basic principle for selecting the spherical or cylindrical cavity expansion model to predict the penetration depth of concrete targets.

  3. Application of PCARES in locating the soil erosion Hotspots in the Manupali River Watershed

    OpenAIRE

    Paningbatan, E.

    2004-01-01

    In this presentation the author covers: GIS mapping of land attributes, dynamic modeling of soil erosion at watershed scale using PCARES (Predicting Catchment Runoff and Soil Erosion for Sustainability), identifying soil erosion "hotspots" in the Manupali River watershed

  4. Buffer erosion in dilute groundwater

    International Nuclear Information System (INIS)

    Schatz, T.; Kanerva, N.; Martikainen, J.; Sane, P.; Olin, M.; Seppaelae, A.; Koskinen, K.

    2013-08-01

    One scenario of interest for repository safety assessment involves the loss of bentonite buffer material in contact with dilute groundwater flowing through a transmissive fracture interface. In order to examine the extrusion/erosion behavior of bentonite buffer material under such circumstances, a series of experiments were performed in a flow-through, 1 mm aperture, artificial fracture system. These experiments covered a range of solution chemistry (salt concentration and composition), material composition (sodium montmorillonite and admixtures with calcium montmorillonite), and flow velocity conditions. No erosion was observed for sodium montmorillonite against solution compositions from 0.5 g/L to 10 g/L NaCl. No erosion was observed for 50/50 calcium/sodium montmorillonite against 0.5 g/L NaCl. Erosion was observed for both sodium montmorillonite and 50/50 calcium/sodium montmorillonite against solution compositions ≤ 0.25 g/L NaCl. The calculated erosion rates for the tests with the highest levels of measured erosion, i.e., the tests run under the most dilute conditions (ionic strength (IS) < ∼1 mM), were well-correlated to flow velocity, whereas the calculated erosion rates for the tests with lower levels of measured erosion, i.e., the tests run under somewhat less dilute conditions (∼1 mM < IS < ∼4 mM), were not similarly correlated indicating that material and solution composition can significantly affect erosion rates. In every experiment, both erosive and non-erosive, emplaced buffer material extruded into the fracture and was observed to be impermeable to water flowing in the fracture effectively forming an extended diffusive barrier around the intersecting fracture/buffer interface. Additionally, a model which was developed previously to predict the rate of erosion of bentonite buffer material in low ionic strength water in rock fracture environments was applied to three different cases: sodium montmorillonite expansion in a vertical tube, a

  5. The effects of incidentally learned temporal and spatial predictability on response times and visual fixations during target detection and discrimination.

    Directory of Open Access Journals (Sweden)

    Melissa R Beck

    Full Text Available Responses are quicker to predictable stimuli than if the time and place of appearance is uncertain. Studies that manipulate target predictability often involve overt cues to speed up response times. However, less is known about whether individuals will exhibit faster response times when target predictability is embedded within the inter-trial relationships. The current research examined the combined effects of spatial and temporal target predictability on reaction time (RT and allocation of overt attention in a sustained attention task. Participants responded as quickly as possible to stimuli while their RT and eye movements were measured. Target temporal and spatial predictability were manipulated by altering the number of: 1 different time intervals between a response and the next target; and 2 possible spatial locations of the target. The effects of target predictability on target detection (Experiment 1 and target discrimination (Experiment 2 were tested. For both experiments, shorter RTs as target predictability increased across both space and time were found. In addition, the influences of spatial and temporal target predictability on RT and the overt allocation of attention were task dependent; suggesting that effective orienting of attention relies on both spatial and temporal predictability. These results indicate that stimulus predictability can be increased without overt cues and detected purely through inter-trial relationships over the course of repeated stimulus presentations.

  6. Large-scale prediction of drug-target interactions using protein sequences and drug topological structures

    Energy Technology Data Exchange (ETDEWEB)

    Cao Dongsheng [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Liu Shao [Xiangya Hospital, Central South University, Changsha 410008 (China); Xu Qingsong [School of Mathematical Sciences and Computing Technology, Central South University, Changsha 410083 (China); Lu Hongmei; Huang Jianhua [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Hu Qiannan [Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071 (China); Liang Yizeng, E-mail: yizeng_liang@263.net [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China)

    2012-11-08

    Highlights: Black-Right-Pointing-Pointer Drug-target interactions are predicted using an extended SAR methodology. Black-Right-Pointing-Pointer A drug-target interaction is regarded as an event triggered by many factors. Black-Right-Pointing-Pointer Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. Black-Right-Pointing-Pointer Our approach shows compatibility between the new scheme and current SAR methodology. - Abstract: The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug-target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug-target interactions in a timely manner. In this article, we aim at extending current structure-activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug-target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug-target

  7. Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Ming; Wang, Yanli, E-mail: ywang@ncbi.nlm.nih.gov; Bryant, Stephen H., E-mail: bryant@ncbi.nlm.nih.gov

    2016-02-25

    Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI predictions. Using benchmark DTI datasets, our proposed algorithm achieves the state-of-the-art results with area under precision–recall curve (AUPR) of 0.915, 0.925, 0.853 and 0.909 for enzymes, ion channels (IC), G protein-coupled receptors (GPCR) and nuclear receptors (NR) based on 10 fold cross-validation. The performance can further be improved by using a recalculated kernel matrix, especially for the small set of nuclear receptors with AUPR of 0.945. Importantly, most of the top ranked interaction predictions can be validated by experimental data reported in the literature, bioassay results in the PubChem BioAssay database, as well as other previous studies. Our analysis suggests that the proposed RLS-KF is helpful for studying DTI, drug repositioning as well as polypharmacology, and may help to accelerate drug discovery by identifying novel drug targets. - Graphical abstract: Flowchart of the proposed RLS-KF algorithm for drug-target interaction predictions. - Highlights: • A nonlinear kernel fusion algorithm is proposed to perform drug-target interaction predictions. • Performance can further be improved by using the recalculated kernel. • Top predictions can be validated by experimental data.

  8. Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique

    International Nuclear Information System (INIS)

    Hao, Ming; Wang, Yanli; Bryant, Stephen H.

    2016-01-01

    Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI predictions. Using benchmark DTI datasets, our proposed algorithm achieves the state-of-the-art results with area under precision–recall curve (AUPR) of 0.915, 0.925, 0.853 and 0.909 for enzymes, ion channels (IC), G protein-coupled receptors (GPCR) and nuclear receptors (NR) based on 10 fold cross-validation. The performance can further be improved by using a recalculated kernel matrix, especially for the small set of nuclear receptors with AUPR of 0.945. Importantly, most of the top ranked interaction predictions can be validated by experimental data reported in the literature, bioassay results in the PubChem BioAssay database, as well as other previous studies. Our analysis suggests that the proposed RLS-KF is helpful for studying DTI, drug repositioning as well as polypharmacology, and may help to accelerate drug discovery by identifying novel drug targets. - Graphical abstract: Flowchart of the proposed RLS-KF algorithm for drug-target interaction predictions. - Highlights: • A nonlinear kernel fusion algorithm is proposed to perform drug-target interaction predictions. • Performance can further be improved by using the recalculated kernel. • Top predictions can be validated by experimental data.

  9. A Meta-Path-Based Prediction Method for Human miRNA-Target Association

    Directory of Open Access Journals (Sweden)

    Jiawei Luo

    2016-01-01

    Full Text Available MicroRNAs (miRNAs are short noncoding RNAs that play important roles in regulating gene expressing, and the perturbed miRNAs are often associated with development and tumorigenesis as they have effects on their target mRNA. Predicting potential miRNA-target associations from multiple types of genomic data is a considerable problem in the bioinformatics research. However, most of the existing methods did not fully use the experimentally validated miRNA-mRNA interactions. Here, we developed RMLM and RMLMSe to predict the relationship between miRNAs and their targets. RMLM and RMLMSe are global approaches as they can reconstruct the missing associations for all the miRNA-target simultaneously and RMLMSe demonstrates that the integration of sequence information can improve the performance of RMLM. In RMLM, we use RM measure to evaluate different relatedness between miRNA and its target based on different meta-paths; logistic regression and MLE method are employed to estimate the weight of different meta-paths. In RMLMSe, sequence information is utilized to improve the performance of RMLM. Here, we carry on fivefold cross validation and pathway enrichment analysis to prove the performance of our methods. The fivefold experiments show that our methods have higher AUC scores compared with other methods and the integration of sequence information can improve the performance of miRNA-target association prediction.

  10. Net-erosion profile model and simulation experiments

    International Nuclear Information System (INIS)

    Sagara, Akio

    2001-01-01

    Estimation of net-erosion profile is requisite for evaluating the lifetime of divertor plates under high heat and particle fluxes of fusion plasmas. As a reference in benchmark tests of numerical calculation codes, a self-consistent analytical solution is presented for a simplified divertor condition, wherein the magnetic field line is normal to the target plate and the ionization mean free path of sputtered particles is assumed constant. The primary flux profile of hydrogen and impurities are externally given as well as the return ratio of sputtered atoms to the target. In the direction along the divertor trace, all conditions are uniform. The analytical solution is compared with net-erosion experiments carried out using the Compact Helical System (CHS). The deposition profiles of Ti and O impurities are in very good agreement with the analytical predictions. Recent preliminary results observed on divertor plates in the Large Helical Device (LHD) are briefly presented. (author)

  11. Application of a catchment evolution model to the prediction of long-term erosion on the spoil heap at Ranger uranium mine. Supervising Scientist report 132

    International Nuclear Information System (INIS)

    Willgoose, G.

    1998-01-01

    There is a need to assess the long-term stability of engineered landforms associated with the rehabilitation of Ranger Uranium Mine, Northern Territory, Australia, as it is a requirement that mill tailings must be contained for periods in excess of 1000 years. The geomorphic model, SIBERIA, is calibrated on hydrology and erosion data collected by a combination of monitoring and rainfall simulation experiments on the waste rock dumps of Ranger. Preliminary analysis of Ranger's preferred above-grade and below-grade rehabilitation options suggests that erosion of the order of 7-8 m will occur on the structure in a period of 1000 years. This depth of erosion may be sufficient to compromise the integrity of the containment. It is shown that SIBERIA has significant advantages over steady-state erosion models. Suggestions are made for the design that will enhance the stability of the structure and extend the structural life of the containment

  12. Wind erosion modelling in a Sahelian environment

    NARCIS (Netherlands)

    Faye-Visser, S.M.; Sterk, G.; Karssenberg, D.

    2005-01-01

    In the Sahel field observations of wind-blown mass transport often show considerable spatial variation related to the spatial variation of the wind erosion controlling parameters, e.g. soil crust and vegetation cover. A model, used to predict spatial variation in wind erosion and deposition is a

  13. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

    Directory of Open Access Journals (Sweden)

    Huthmacher Carola

    2010-08-01

    Full Text Available Abstract Background Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed. Results Here, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicted life cycle stage specific metabolism with the help of a flux balance approach that integrates gene expression data. Predicted metabolite exchanges between parasite and host were found to be in good accordance with experimental findings when the parasite's metabolic network was embedded into that of its host (erythrocyte. Knock-out simulations identified 307 indispensable metabolic reactions within the parasite. 35 out of 57 experimentally demonstrated essential enzymes were recovered and another 16 enzymes, if additionally the assumption was made that nutrient uptake from the host cell is limited and all reactions catalyzed by the inhibited enzyme are blocked. This predicted set of putative drug targets, shown to be enriched with true targets by a factor of at least 2.75, was further analyzed with respect to homology to human enzymes, functional similarity to therapeutic targets in other organisms and their predicted potency for prophylaxis and disease treatment. Conclusions The results suggest that the set of essential enzymes predicted by our flux balance approach represents a promising starting point for further drug development.

  14. Modified linear predictive coding approach for moving target tracking by Doppler radar

    Science.gov (United States)

    Ding, Yipeng; Lin, Xiaoyi; Sun, Ke-Hui; Xu, Xue-Mei; Liu, Xi-Yao

    2016-07-01

    Doppler radar is a cost-effective tool for moving target tracking, which can support a large range of civilian and military applications. A modified linear predictive coding (LPC) approach is proposed to increase the target localization accuracy of the Doppler radar. Based on the time-frequency analysis of the received echo, the proposed approach first real-time estimates the noise statistical parameters and constructs an adaptive filter to intelligently suppress the noise interference. Then, a linear predictive model is applied to extend the available data, which can help improve the resolution of the target localization result. Compared with the traditional LPC method, which empirically decides the extension data length, the proposed approach develops an error array to evaluate the prediction accuracy and thus, adjust the optimum extension data length intelligently. Finally, the prediction error array is superimposed with the predictor output to correct the prediction error. A series of experiments are conducted to illustrate the validity and performance of the proposed techniques.

  15. Some Remarks on Prediction of Drug-Target Interaction with Network Models.

    Science.gov (United States)

    Zhang, Shao-Wu; Yan, Xiao-Ying

    2017-01-01

    System-level understanding of the relationships between drugs and targets is very important for enhancing drug research, especially for drug function repositioning. The experimental methods used to determine drug-target interactions are usually time-consuming, tedious and expensive, and sometimes lack reproducibility. Thus, it is highly desired to develop computational methods for efficiently and effectively analyzing and detecting new drug-target interaction pairs. With the explosive growth of different types of omics data, such as genome, pharmacology, phenotypic, and other kinds of molecular networks, numerous computational approaches have been developed to predict Drug-Target Interactions (DTI). In this review, we make a survey on the recent advances in predicting drug-target interaction with network-based models from the following aspects: i) Available public data sources and benchmark datasets; ii) Drug/target similarity metrics; iii) Network construction; iv) Common network algorithms; v) Performance comparison of existing network-based DTI predictors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  16. Asymptotically Constant-Risk Predictive Densities When the Distributions of Data and Target Variables Are Different

    Directory of Open Access Journals (Sweden)

    Keisuke Yano

    2014-05-01

    Full Text Available We investigate the asymptotic construction of constant-risk Bayesian predictive densities under the Kullback–Leibler risk when the distributions of data and target variables are different and have a common unknown parameter. It is known that the Kullback–Leibler risk is asymptotically equal to a trace of the product of two matrices: the inverse of the Fisher information matrix for the data and the Fisher information matrix for the target variables. We assume that the trace has a unique maximum point with respect to the parameter. We construct asymptotically constant-risk Bayesian predictive densities using a prior depending on the sample size. Further, we apply the theory to the subminimax estimator problem and the prediction based on the binary regression model.

  17. Ranking of microRNA target prediction scores by Pareto front analysis.

    Science.gov (United States)

    Sahoo, Sudhakar; Albrecht, Andreas A

    2010-12-01

    Over the past ten years, a variety of microRNA target prediction methods has been developed, and many of the methods are constantly improved and adapted to recent insights into miRNA-mRNA interactions. In a typical scenario, different methods return different rankings of putative targets, even if the ranking is reduced to selected mRNAs that are related to a specific disease or cell type. For the experimental validation it is then difficult to decide in which order to process the predicted miRNA-mRNA bindings, since each validation is a laborious task and therefore only a limited number of mRNAs can be analysed. We propose a new ranking scheme that combines ranked predictions from several methods and - unlike standard thresholding methods - utilises the concept of Pareto fronts as defined in multi-objective optimisation. In the present study, we attempt a proof of concept by applying the new ranking scheme to hsa-miR-21, hsa-miR-125b, and hsa-miR-373 and prediction scores supplied by PITA and RNAhybrid. The scores are interpreted as a two-objective optimisation problem, and the elements of the Pareto front are ranked by the STarMir score with a subsequent re-calculation of the Pareto front after removal of the top-ranked mRNA from the basic set of prediction scores. The method is evaluated on validated targets of the three miRNA, and the ranking is compared to scores from DIANA-microT and TargetScan. We observed that the new ranking method performs well and consistent, and the first validated targets are elements of Pareto fronts at a relatively early stage of the recurrent procedure, which encourages further research towards a higher-dimensional analysis of Pareto fronts. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. Role of retinal slip in the prediction of target motion during smooth and saccadic pursuit.

    Science.gov (United States)

    de Brouwer, S; Missal, M; Lefèvre, P

    2001-08-01

    Visual tracking of moving targets requires the combination of smooth pursuit eye movements with catch-up saccades. In primates, catch-up saccades usually take place only during pursuit initiation because pursuit gain is close to unity. This contrasts with the lower and more variable gain of smooth pursuit in cats, where smooth eye movements are intermingled with catch-up saccades during steady-state pursuit. In this paper, we studied in detail the role of retinal slip in the prediction of target motion during smooth and saccadic pursuit in the cat. We found that the typical pattern of pursuit in the cat was a combination of smooth eye movements with saccades. During smooth pursuit initiation, there was a correlation between peak eye acceleration and target velocity. During pursuit maintenance, eye velocity oscillated at approximately 3 Hz around a steady-state value. The average gain of smooth pursuit was approximately 0.5. Trained cats were able to continue pursuing in the absence of a visible target, suggesting a role of the prediction of future target motion in this species. The analysis of catch-up saccades showed that the smooth-pursuit motor command is added to the saccadic command during catch-up saccades and that both position error and retinal slip are taken into account in their programming. The influence of retinal slip on catch-up saccades showed that prediction about future target motion is used in the programming of catch-up saccades. Altogether, these results suggest that pursuit systems in primates and cats are qualitatively similar, with a lower average gain in the cat and that prediction affects both saccades and smooth eye movements during pursuit.

  19. Mapping monthly rainfall erosivity in Europe

    DEFF Research Database (Denmark)

    Ballabio, C; Meusburger, K; Klik, A

    2017-01-01

    to Eastern Europe. The maps also show a clear delineation of areas with different erosivity seasonal patterns, whose spatial outline was evidenced by cluster analysis. The monthly erosivity maps can be used to develop composite indicators that map both intra-annual variability and concentration of erosive...... and seasonal R-factor maps and assess rainfall erosivity both spatially and temporally. During winter months, significant rainfall erosivity is present only in part of the Mediterranean countries. A sudden increase of erosivity occurs in major part of European Union (except Mediterranean basin, western part...... selected among various statistical models to perform the spatial interpolation due to its excellent performance, ability to model non-linearity and interpretability. The monthly prediction is an order more difficult than the annual one as it is limited by the number of covariates and, for consistency...

  20. Novel Methods for Drug-Target Interaction Prediction using Graph Mining

    KAUST Repository

    Ba Alawi, Wail

    2016-08-31

    The problem of developing drugs that can be used to cure diseases is important and requires a careful approach. Since pursuing the wrong candidate drug for a particular disease could be very costly in terms of time and money, there is a strong interest in minimizing such risks. Drug repositioning has become a hot topic of research, as it helps reduce these risks significantly at the early stages of drug development by reusing an approved drug for the treatment of a different disease. Still, finding new usage for a drug is non-trivial, as it is necessary to find out strong supporting evidence that the proposed new uses of drugs are plausible. Many computational approaches were developed to narrow the list of possible candidate drug-target interactions (DTIs) before any experiments are done. However, many of these approaches suffer from unacceptable levels of false positives. We developed two novel methods based on graph mining networks of drugs and targets. The first method (DASPfind) finds all non-cyclic paths that connect a drug and a target, and using a function that we define, calculates a score from all the paths. This score describes our confidence that DTI is correct. We show that DASPfind significantly outperforms other state-of-the-art methods in predicting the top ranked target for each drug. We demonstrate the utility of DASPfind by predicting 15 novel DTIs over a set of ion channel proteins, and confirming 12 out of these 15 DTIs through experimental evidence reported in literature and online drug databases. The second method (DASPfind+) modifies DASPfind in order to increase the confidence and reliability of the resultant predictions. Based on the structure of the drug-target interaction (DTI) networks, we introduced an optimization scheme that incrementally alters the network structure locally for each drug to achieve more robust top 1 ranked predictions. Moreover, we explored effects of several similarity measures between the targets on the prediction

  1. Modelling sewer sediment deposition, erosion, and transport processes to predict acute influent and reduce combined sewer overflows and CO(2) emissions.

    Science.gov (United States)

    Mouri, Goro; Oki, Taikan

    2010-01-01

    Understanding of solids deposition, erosion, and transport processes in sewer systems has improved considerably in the past decade. This has provided guidance for controlling sewer solids and associated acute pollutants to protect the environment and improve the operation of wastewater systems. Although measures to decrease combined sewer overflow (CSO) events have reduced the amount of discharged pollution, overflows continue to occur during rainy weather in combined sewer systems. The solution lies in the amount of water allotted to various processes in an effluent treatment system, in impact evaluation of water quality and prediction technology, and in stressing the importance of developing a control technology. Extremely contaminated inflow has been a serious research subject, especially in connection with the influence of rainy weather on nitrogen and organic matter removal efficiency in wastewater treatment plants (WWTP). An intensive investigation of an extremely polluted inflow load to WWTP during rainy weather was conducted in the city of Matsuyama, the region used for the present research on total suspended solid (TSS) concentration. Since the inflow during rainy weather can be as much as 400 times that in dry weather, almost all sewers are unsettled and overflowing when a rain event is more than moderate. Another concern is the energy consumed by wastewater treatment; this problem has become important from the viewpoint of reducing CO(2) emissions and overall costs. Therefore, while establishing a prediction technology for the inflow water quality characteristics of a sewage disposal plant is an important priority, the development of a management/control method for an effluent treatment system that minimises energy consumption and CO(2) emissions due to water disposal is also a pressing research topic with regards to the quality of treated water. The procedure to improve water quality must make use of not only water quality and biotic criteria, but also

  2. Performance of a Predictive Model for Calculating Ascent Time to a Target Temperature

    Directory of Open Access Journals (Sweden)

    Jin Woo Moon

    2016-12-01

    Full Text Available The aim of this study was to develop an artificial neural network (ANN prediction model for controlling building heating systems. This model was used to calculate the ascent time of indoor temperature from the setback period (when a building was not occupied to a target setpoint temperature (when a building was occupied. The calculated ascent time was applied to determine the proper moment to start increasing the temperature from the setback temperature to reach the target temperature at an appropriate time. Three major steps were conducted: (1 model development; (2 model optimization; and (3 performance evaluation. Two software programs—Matrix Laboratory (MATLAB and Transient Systems Simulation (TRNSYS—were used for model development, performance tests, and numerical simulation methods. Correlation analysis between input variables and the output variable of the ANN model revealed that two input variables (current indoor air temperature and temperature difference from the target setpoint temperature, presented relatively strong relationships with the ascent time to the target setpoint temperature. These two variables were used as input neurons. Analyzing the difference between the simulated and predicted values from the ANN model provided the optimal number of hidden neurons (9, hidden layers (3, moment (0.9, and learning rate (0.9. At the study’s conclusion, the optimized model proved its prediction accuracy with acceptable errors.

  3. Predicting the Types of Ion Channel-Targeted Conotoxins Based on AVC-SVM Model.

    Science.gov (United States)

    Xianfang, Wang; Junmei, Wang; Xiaolei, Wang; Yue, Zhang

    2017-01-01

    The conotoxin proteins are disulfide-rich small peptides. Predicting the types of ion channel-targeted conotoxins has great value in the treatment of chronic diseases, epilepsy, and cardiovascular diseases. To solve the problem of information redundancy existing when using current methods, a new model is presented to predict the types of ion channel-targeted conotoxins based on AVC (Analysis of Variance and Correlation) and SVM (Support Vector Machine). First, the F value is used to measure the significance level of the feature for the result, and the attribute with smaller F value is filtered by rough selection. Secondly, redundancy degree is calculated by Pearson Correlation Coefficient. And the threshold is set to filter attributes with weak independence to get the result of the refinement. Finally, SVM is used to predict the types of ion channel-targeted conotoxins. The experimental results show the proposed AVC-SVM model reaches an overall accuracy of 91.98%, an average accuracy of 92.17%, and the total number of parameters of 68. The proposed model provides highly useful information for further experimental research. The prediction model will be accessed free of charge at our web server.

  4. Rainfall Erosivity in Europe

    DEFF Research Database (Denmark)

    Panagos, Panos; Ballabio, Cristiano; Borrelli, Pasquale

    2015-01-01

    Rainfall is one the main drivers of soil erosion. The erosive force of rainfall is expressed as rainfall erosivity. Rainfall erosivity considers the rainfall amount and intensity, and is most commonly expressed as the Rfactor in the USLE model and its revised version, RUSLE. At national...... and continental levels, the scarce availability of data obliges soil erosion modellers to estimate this factor based on rainfall data with only low temporal resolution (daily, monthly, annual averages). The purpose of this study is to assess rainfall erosivity in Europe in the form of the RUSLE R-factor, based...

  5. Soil erosion assessment on hillslope of GCE using RUSLE model

    Indian Academy of Sciences (India)

    Md. Rabiul Islam

    2018-05-22

    May 22, 2018 ... A vegetation density available on these plots is measured ... Finally, erosion prediction is computed based on the RUSLE model in ... which is lower compared to the C value from the soil erosion ..... Comparison of rainfall erosivity factor (R) value. ...... Vorovencii I and Muntean D 2012 Evaluation of super-.

  6. Assessing soil erosion risk in the Tillabery landscape, Niger ...

    African Journals Online (AJOL)

    The results show that soil erosion output scenarios predict greater soil erosion in the study area from 2070 onwards. They suggest that human disturbance and topographic factors are the main impact factors in the affected areas. Key words: Tillabéry landscape (Niger), sheet and rill erosion modelling, data mining.

  7. Tracking Maneuvering Group Target with Extension Predicted and Best Model Augmentation Method Adapted

    Directory of Open Access Journals (Sweden)

    Linhai Gan

    2017-01-01

    Full Text Available The random matrix (RM method is widely applied for group target tracking. The assumption that the group extension keeps invariant in conventional RM method is not yet valid, as the orientation of the group varies rapidly while it is maneuvering; thus, a new approach with group extension predicted is derived here. To match the group maneuvering, a best model augmentation (BMA method is introduced. The existing BMA method uses a fixed basic model set, which may lead to a poor performance when it could not ensure basic coverage of true motion modes. Here, a maneuvering group target tracking algorithm is proposed, where the group extension prediction and the BMA adaption are exploited. The performance of the proposed algorithm will be illustrated by simulation.

  8. Recommendation Techniques for Drug-Target Interaction Prediction and Drug Repositioning.

    Science.gov (United States)

    Alaimo, Salvatore; Giugno, Rosalba; Pulvirenti, Alfredo

    2016-01-01

    The usage of computational methods in drug discovery is a common practice. More recently, by exploiting the wealth of biological knowledge bases, a novel approach called drug repositioning has raised. Several computational methods are available, and these try to make a high-level integration of all the knowledge in order to discover unknown mechanisms. In this chapter, we review drug-target interaction prediction methods based on a recommendation system. We also give some extensions which go beyond the bipartite network case.

  9. Automatically detect and track infrared small targets with kernel Fukunaga-Koontz transform and Kalman prediction

    Science.gov (United States)

    Liu, Ruiming; Liu, Erqi; Yang, Jie; Zeng, Yong; Wang, Fanglin; Cao, Yuan

    2007-11-01

    Fukunaga-Koontz transform (FKT), stemming from principal component analysis (PCA), is used in many pattern recognition and image-processing fields. It cannot capture the higher-order statistical property of natural images, so its detection performance is not satisfying. PCA has been extended into kernel PCA in order to capture the higher-order statistics. However, thus far there have been no researchers who have definitely proposed kernel FKT (KFKT) and researched its detection performance. For accurately detecting potential small targets from infrared images, we first extend FKT into KFKT to capture the higher-order statistical properties of images. Then a framework based on Kalman prediction and KFKT, which can automatically detect and track small targets, is developed. Results of experiments show that KFKT outperforms FKT and the proposed framework is competent to automatically detect and track infrared point targets.

  10. Soil loss prediction in Guaraíra river experimental basin, Paraíba, Brazil based on two erosion simulation models

    Directory of Open Access Journals (Sweden)

    Jorge Flávio Cazé B. da Costa Silva

    2007-12-01

    Full Text Available In this study, two hydrological models to estimate soil losses and sediment yield due to sheet and channel erosion, at the basin outlet, are applied to Guaraíra River Experimental Basin, located in Paraíba State, northeastern Brazil. The soil erosion models are (a the classical Universal Soil Loss Equation (USLE, which is used to simulate annual and monthly soil losses; and (b Kineros model, which is used to simulate the sediment yield within the basin. Kineros model is a physically-based distributed model that uses a cascade of planes and channels to represent the basin and to describe the processes of interception, infiltration, surface runoff and erosion within the basin. The USLE is computed using land use, soil erodibility, topographic digital maps, as well as observed rainfall data. It was found that Guaraíra river experimental basin has a low potential for soil losses; however, specific areas which are susceptible to the erosion process in the basin could be detected by the modeling techniques coupled to a GIS (Geographic Information System.

  11. Ensemble Sensitivity Analysis of a Severe Downslope Windstorm in Complex Terrain: Implications for Forecast Predictability Scales and Targeted Observing Networks

    Science.gov (United States)

    2013-09-01

    observations, linear regression finds the straight line that explains the linear relationship of the sample. This line is given by the equation y = mx + b...SENSITIVITY ANALYSIS OF A SEVERE DOWNSLOPE WINDSTORM IN COMPLEX TERRAIN: IMPLICATIONS FOR FORECAST PREDICTABILITY SCALES AND TARGETED OBSERVING...SENSITIVITY ANALYSIS OF A SEVERE DOWNSLOPE WINDSTORM IN COMPLEX TERRAIN: IMPLICATIONS FOR FORECAST PREDICTABILITY SCALES AND TARGETED OBSERVING NETWORKS

  12. Prediction problem for target events based on the inter-event waiting time

    Science.gov (United States)

    Shapoval, A.

    2010-11-01

    In this paper we address the problem of forecasting the target events of a time series given the distribution ξ of time gaps between target events. Strong earthquakes and stock market crashes are the two types of such events that we are focusing on. In the series of earthquakes, as McCann et al. show [W.R. Mc Cann, S.P. Nishenko, L.R. Sykes, J. Krause, Seismic gaps and plate tectonics: seismic potential for major boundaries, Pure and Applied Geophysics 117 (1979) 1082-1147], there are well-defined gaps (called seismic gaps) between strong earthquakes. On the other hand, usually there are no regular gaps in the series of stock market crashes [M. Raberto, E. Scalas, F. Mainardi, Waiting-times and returns in high-frequency financial data: an empirical study, Physica A 314 (2002) 749-755]. For the case of seismic gaps, we analytically derive an upper bound of prediction efficiency given the coefficient of variation of the distribution ξ. For the case of stock market crashes, we develop an algorithm that predicts the next crash within a certain time interval after the previous one. We show that this algorithm outperforms random prediction. The efficiency of our algorithm sets up a lower bound of efficiency for effective prediction of stock market crashes.

  13. Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies

    Directory of Open Access Journals (Sweden)

    Jennifer D. Atkins

    2015-08-01

    Full Text Available The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.

  14. Mapping erosion from space

    NARCIS (Netherlands)

    Vrieling, A.

    2007-01-01

    Soil erosion by water is the most important land degradation problem worldwide. Spatial information on erosion is required for defining effective soil and water conservation strategies. Satellite remote sensing can provide relevant input to regional erosion assessment. This thesis comprises a review

  15. Erosion-corrosion

    International Nuclear Information System (INIS)

    Aghili, B.

    1999-05-01

    A literature study on erosion-corrosion of pipings in the nuclear industry was performed. Occurred incidents are reviewed, and the mechanism driving the erosion-corrosion is described. Factors that influence the effect in negative or positive direction are treated, as well as programs for control and inspection. Finally, examples of failures from databases on erosion-corrosion are given in an attachment

  16. Assessing storm erosion hazards

    NARCIS (Netherlands)

    Ranasinghe, Ranasinghe W M R J B; Callaghan, D.; Ciavola, Paolo; Coco, Giovanni

    2017-01-01

    The storm erosion hazard on coasts is usually expressed as an erosion volume and/or associated episodic coastline retreat. The accurate assessment of present-day and future storm erosion volumes is a key task for coastal zone managers, planners and engineers. There are four main approaches that can

  17. Predictive markers of efficacy for an angiopoietin-2 targeting therapeutic in xenograft models.

    Directory of Open Access Journals (Sweden)

    Gallen Triana-Baltzer

    Full Text Available The clinical efficacy of anti-angiogenic therapies has been difficult to predict, and biomarkers that can predict responsiveness are sorely needed in this era of personalized medicine. CVX-060 is an angiopoietin-2 (Ang2 targeting therapeutic, consisting of two peptides that bind Ang2 with high affinity and specificity, covalently fused to a scaffold antibody. In order to optimize the use of this compound in the clinic the construction of a predictive model is described, based on the efficacy of CVX-060 in 13 cell line and 2 patient-derived xenograft models. Pretreatment size tumors from each of the models were profiled for the levels of 27 protein markers of angiogenesis, SNP haplotype in 5 angiogenesis genes, and somatic mutation status for 11 genes implicated in tumor growth and/or vascularization. CVX-060 efficacy was determined as tumor growth inhibition (TGI% at termination of each study. A predictive statistical model was constructed based on the correlation of these efficacy data with the marker profiles, and the model was subsequently tested by prospective analysis in 11 additional models. The results reveal a range of CVX-060 efficacy in xenograft models of diverse tissue types (0-64% TGI, median = 27% and define a subset of 3 proteins (Ang1, EGF, Emmprin, the levels of which may be predictive of TGI by Ang2 blockade. The direction of the associations is such that better efficacy correlates with high levels of target and low levels of compensatory/antagonizing molecules. This effort has revealed a set of candidate predictive markers for CVX-060 efficacy that will be further evaluated in ongoing clinical trials.

  18. Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets.

    Science.gov (United States)

    Prakash, Pravin; Rajakani, Raja; Gupta, Vikrant

    2016-04-01

    MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Mining predicted essential genes of Brugia malayi for nematode drug targets.

    Directory of Open Access Journals (Sweden)

    Sanjay Kumar

    Full Text Available We report results from the first genome-wide application of a rational drug target selection methodology to a metazoan pathogen genome, the completed draft sequence of Brugia malayi, a parasitic nematode responsible for human lymphatic filariasis. More than 1.5 billion people worldwide are at risk of contracting lymphatic filariasis and onchocerciasis, a related filarial disease. Drug treatments for filariasis have not changed significantly in over 20 years, and with the risk of resistance rising, there is an urgent need for the development of new anti-filarial drug therapies. The recent publication of the draft genomic sequence for B. malayi enables a genome-wide search for new drug targets. However, there is no functional genomics data in B. malayi to guide the selection of potential drug targets. To circumvent this problem, we have utilized the free-living model nematode Caenorhabditis elegans as a surrogate for B. malayi. Sequence comparisons between the two genomes allow us to map C. elegans orthologs to B. malayi genes. Using these orthology mappings and by incorporating the extensive genomic and functional genomic data, including genome-wide RNAi screens, that already exist for C. elegans, we identify potentially essential genes in B. malayi. Further incorporation of human host genome sequence data and a custom algorithm for prioritization enables us to collect and rank nearly 600 drug target candidates. Previously identified potential drug targets cluster near the top of our prioritized list, lending credibility to our methodology. Over-represented Gene Ontology terms, predicted InterPro domains, and RNAi phenotypes of C. elegans orthologs associated with the potential target pool are identified. By virtue of the selection procedure, the potential B. malayi drug targets highlight components of key processes in nematode biology such as central metabolism, molting and regulation of gene expression.

  20. Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy.

    Science.gov (United States)

    Jung, Jinmyung; Kwon, Mijin; Bae, Sunghwa; Yim, Soorin; Lee, Doheon

    2018-03-05

    Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value net. We generated a list of the potential therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards

  1. Modelling rainfall erosion resulting from climate change

    Science.gov (United States)

    Kinnell, Peter

    2016-04-01

    It is well known that soil erosion leads to agricultural productivity decline and contributes to water quality decline. The current widely used models for determining soil erosion for management purposes in agriculture focus on long term (~20 years) average annual soil loss and are not well suited to determining variations that occur over short timespans and as a result of climate change. Soil loss resulting from rainfall erosion is directly dependent on the product of runoff and sediment concentration both of which are likely to be influenced by climate change. This presentation demonstrates the capacity of models like the USLE, USLE-M and WEPP to predict variations in runoff and erosion associated with rainfall events eroding bare fallow plots in the USA with a view to modelling rainfall erosion in areas subject to climate change.

  2. Identification of the feedforward component in manual control with predictable target signals.

    Science.gov (United States)

    Drop, Frank M; Pool, Daan M; Damveld, Herman J; van Paassen, Marinus M; Mulder, Max

    2013-12-01

    In the manual control of a dynamic system, the human controller (HC) often follows a visible and predictable reference path. Compared with a purely feedback control strategy, performance can be improved by making use of this knowledge of the reference. The operator could effectively introduce feedforward control in conjunction with a feedback path to compensate for errors, as hypothesized in literature. However, feedforward behavior has never been identified from experimental data, nor have the hypothesized models been validated. This paper investigates human control behavior in pursuit tracking of a predictable reference signal while being perturbed by a quasi-random multisine disturbance signal. An experiment was done in which the relative strength of the target and disturbance signals were systematically varied. The anticipated changes in control behavior were studied by means of an ARX model analysis and by fitting three parametric HC models: two different feedback models and a combined feedforward and feedback model. The ARX analysis shows that the experiment participants employed control action on both the error and the target signal. The control action on the target was similar to the inverse of the system dynamics. Model fits show that this behavior can be modeled best by the combined feedforward and feedback model.

  3. Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene.

    Directory of Open Access Journals (Sweden)

    Marinus F van Batenburg

    2010-01-01

    Full Text Available Glucocorticoids act in part via glucocorticoid receptor binding to hormone response elements (HREs, but their direct target genes in vivo are still largely unknown. We developed the criterion that genomic occurrence of paired HREs at an inter-HRE distance less than 200 bp predicts hormone responsiveness, based on synergy of multiple HREs, and HRE information from known target genes. This criterion predicts a substantial number of novel responsive genes, when applied to genomic regions 10 kb upstream of genes. Multiple-tissue in situ hybridization showed that mRNA expression of 6 out of 10 selected genes was induced in a tissue-specific manner in mice treated with a single dose of corticosterone, with the spleen being the most responsive organ. Caveolin-1 was strongly responsive in several organs, and the HRE pair in its upstream region showed increased occupancy by glucocorticoid receptor in response to corticosterone. Our approach allowed for discovery of novel tissue specific glucocorticoid target genes, which may exemplify responses underlying the permissive actions of glucocorticoids.

  4. Mathematical modeling of antibody drug conjugates with the target and tubulin dynamics to predict AUC.

    Science.gov (United States)

    Byun, Jong Hyuk; Jung, Il Hyo

    2018-04-14

    Antibody drug conjugates (ADCs)are one of the most recently developed chemotherapeutics to treat some types of tumor cells. They consist of monoclonal antibodies (mAbs), linkers, and potent cytotoxic drugs. Unlike common chemotherapies, ADCs combine selectively with a target at the surface of the tumor cell, and a potent cytotoxic drug (payload) effectively prevents microtubule polymerization. In this work, we construct an ADC model that considers both the target of antibodies and the receptor (tubulin) of the cytotoxic payloads. The model is simulated with brentuximab vedotin, one of ADCs, and used to investigate the pharmacokinetic (PK) characteristics of ADCs in vivo. It also predicts area under the curve (AUC) of ADCs and the payloads by identifying the half-life. The results show that dynamical behaviors fairly coincide with the observed data and half-life and capture AUC. Thus, the model can be used for estimating some parameters, fitting experimental observations, predicting AUC, and exploring various dynamical behaviors of the target and the receptor. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. MirZ: an integrated microRNA expression atlas and target prediction resource.

    Science.gov (United States)

    Hausser, Jean; Berninger, Philipp; Rodak, Christoph; Jantscher, Yvonne; Wirth, Stefan; Zavolan, Mihaela

    2009-07-01

    MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens.

  6. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

    Science.gov (United States)

    Hu, Ruifeng; Sun, Xiaobo

    2016-08-01

    Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

  7. Managing dental erosion.

    Science.gov (United States)

    Curtis, Donald A; Jayanetti, Jay; Chu, Raymond; Staninec, Michal

    2012-01-01

    The clinical signs of dental erosion are initially subtle, yet often progress because the patient remains asymptomatic, unaware and uninformed. Erosion typically works synergistically with abrasion and attrition to cause loss of tooth structure, making diagnosis and management complex. The purpose of this article is to outline clinical examples of patients with dental erosion that highlight the strategy of early identification, patient education and conservative restorative management. Dental erosion is defined as the pathologic chronic loss of dental hard tissues as a result of the chemical influence of exogenous or endogenous acids without bacterial involvement. Like caries or periodontal disease, erosion has a multifactorial etiology and requires a thorough history and examination for diagnosis. It also requires patient understanding and compliance for improved outcomes. Erosion can affect the loss of tooth structure in isolation of other cofactors, but most often works in synergy with abrasion and attrition in the loss of tooth structure (Table 1). Although erosion is thought to be an underlying etiology of dentin sensitivity, erosion and loss of tooth structure often occurs with few symptoms. The purpose of this article is threefold: first, to outline existing barriers that may limit early management of dental erosion. Second, to review the clinical assessment required to establish a diagnosis of erosion. And third, to outline clinical examples that review options to restore lost tooth structure. The authors have included illustrations they hope will be used to improve patient understanding and motivation in the early management of dental erosion.

  8. Numerical study of impact erosion of multiple solid particle

    Science.gov (United States)

    Zheng, Chao; Liu, Yonghong; Chen, Cheng; Qin, Jie; Ji, Renjie; Cai, Baoping

    2017-11-01

    Material erosion caused by continuous particle impingement during hydraulic fracturing results in significant economic loss and increased production risks. The erosion process is complex and has not been clearly explained through physical experiments. To address this problem, a multiple particle model in a 3D configuration was proposed to investigate the dynamic erosion process. This approach can significantly reduce experiment costs. The numerical model considered material damping and elastic-plastic material behavior of target material. The effects of impact parameters on erosion characteristics, such as plastic deformation, contact time, and energy loss rate, were investigated. Based on comprehensive studies, the dynamic erosion mechanism and geometry evolution of eroded crater was obtained. These findings can provide a detailed erosion process of target material and insights into the material erosion caused by multiple particle impingement.

  9. Prediction of Effective Drug Combinations by Chemical Interaction, Protein Interaction and Target Enrichment of KEGG Pathways

    Directory of Open Access Journals (Sweden)

    Lei Chen

    2013-01-01

    Full Text Available Drug combinatorial therapy could be more effective in treating some complex diseases than single agents due to better efficacy and reduced side effects. Although some drug combinations are being used, their underlying molecular mechanisms are still poorly understood. Therefore, it is of great interest to deduce a novel drug combination by their molecular mechanisms in a robust and rigorous way. This paper attempts to predict effective drug combinations by a combined consideration of: (1 chemical interaction between drugs, (2 protein interactions between drugs’ targets, and (3 target enrichment of KEGG pathways. A benchmark dataset was constructed, consisting of 121 confirmed effective combinations and 605 random combinations. Each drug combination was represented by 465 features derived from the aforementioned three properties. Some feature selection techniques, including Minimum Redundancy Maximum Relevance and Incremental Feature Selection, were adopted to extract the key features. Random forest model was built with its performance evaluated by 5-fold cross-validation. As a result, 55 key features providing the best prediction result were selected. These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations.

  10. Molybdenum erosion measurements in Alcator C-Mod

    Energy Technology Data Exchange (ETDEWEB)

    Wampler, W.R. [Sandia National Labs., Albuquerque, NM (United States); LaBombard, B.; Lipshultz, B.; Pappas, D.; Pitcher, C.S. [Massachusetts Inst. of Tech., Cambridge, MA (United States); McCracken, G.M. [JET Joint Undertaking, Abingdon (United Kingdom)

    1998-05-01

    Erosion of molybdenum was measured on a set of 21 tiles after a run campaign of 1,090 shots in the Alcator C-Mod tokamak. The net erosion of molybdenum, was determined from changes in the depth of a thin chromium marker layer measured by Rutherford backscattering. Net Mo erosion was found to be approximately 150 nm near the outer divertor strike point, and much less everywhere else. Gross erosion rates by sputtering were estimated using ion energies and fluxes obtained from Langmuir probe measurements of edge-plasma conditions. Predicted net erosion using calculated gross erosion with prompt redeposition and measured net erosion agree within a factor of 3. Sputtering by boron and molybdenum impurities dominates erosion.

  11. Three procedures for estimating erosion from construction areas

    International Nuclear Information System (INIS)

    Abt, S.R.; Ruff, J.F.

    1978-01-01

    Erosion from many mining and construction sites can lead to serious environmental pollution problems. Therefore, erosion management plans must be developed in order that the engineer may implement measures to control or eliminate excessive soil losses. To properly implement a management program, it is necessary to estimate potential soil losses from the time the project begins to beyond project completion. Three methodologies are presented which project the estimated soil losses due to sheet or rill erosion of water and are applicable to mining and construction areas. Furthermore, the three methods described are intended as indicators of the state-of-the-art in water erosion prediction. The procedures herein do not account for gully erosion, snowmelt erosion, wind erosion, freeze-thaw erosion or extensive flooding

  12. Open-source chemogenomic data-driven algorithms for predicting drug-target interactions.

    Science.gov (United States)

    Hao, Ming; Bryant, Stephen H; Wang, Yanli

    2018-02-06

    While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug-target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.

  13. Predictive Biomarkers in Colorectal Cancer: From the Single Therapeutic Target to a Plethora of Options

    Directory of Open Access Journals (Sweden)

    Daniela Rodrigues

    2016-01-01

    Full Text Available Colorectal cancer (CRC is one of the most frequent cancers and is a leading cause of cancer death worldwide. Treatments used for CRC may include some combination of surgery, radiation therapy, chemotherapy, and targeted therapy. The current standard drugs used in chemotherapy are 5-fluorouracil and leucovorin in combination with irinotecan and/or oxaliplatin. Most recently, biologic agents have been proven to have therapeutic benefits in metastatic CRC alone or in association with standard chemotherapy. However, patients present different treatment responses, in terms of efficacy and toxicity; therefore, it is important to identify biological markers that can predict the response to therapy and help select patients that would benefit from specific regimens. In this paper, authors review CRC genetic markers that could be useful in predicting the sensitivity/resistance to chemotherapy.

  14. Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics

    Science.gov (United States)

    Greulich, Philip; Doležal, Jakub; Scott, Matthew; Evans, Martin R.; Allen, Rosalind J.

    2017-12-01

    Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance—yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment regimen. In particular, in the clinic, antibiotic treatment is time-dependent. Here, we use a theoretical model, previously applied to steady-state bacterial growth, to predict the dynamical response of a bacterial cell to a time-dependent dose of ribosome-targeting antibiotic. Our results depend strongly on whether the antibiotic shows reversible transport and/or low-affinity ribosome binding (‘low-affinity antibiotic’) or, in contrast, irreversible transport and/or high affinity ribosome binding (‘high-affinity antibiotic’). For low-affinity antibiotics, our model predicts that growth inhibition depends on the duration of the antibiotic pulse, and can show a transient period of very fast growth following removal of the antibiotic. For high-affinity antibiotics, growth inhibition depends on peak dosage rather than dose duration, and the model predicts a pronounced post-antibiotic effect, due to hysteresis, in which growth can be suppressed for long times after the antibiotic dose has ended. These predictions are experimentally testable and may be of clinical significance.

  15. A field method for soil erosion measurements in agricultural and natural lands

    Science.gov (United States)

    Y.P. Hsieh; K.T. Grant; G.C. Bugna

    2009-01-01

    Soil erosion is one of the most important watershed processes in nature, yet quantifying it under field conditions remains a challenge. The lack of soil erosion field data is a major factor hindering our ability to predict soil erosion in a watershed. We present here the development of a simple and sensitive field method that quantifies soil erosion and the resulting...

  16. Soil erosion assessment - Mind the gap

    Science.gov (United States)

    Kim, Jongho; Ivanov, Valeriy Y.; Fatichi, Simone

    2016-12-01

    Accurate assessment of erosion rates remains an elusive problem because soil loss is strongly nonunique with respect to the main drivers. In addressing the mechanistic causes of erosion responses, we discriminate between macroscale effects of external factors - long studied and referred to as "geomorphic external variability", and microscale effects, introduced as "geomorphic internal variability." The latter source of erosion variations represents the knowledge gap, an overlooked but vital element of geomorphic response, significantly impacting the low predictability skill of deterministic models at field-catchment scales. This is corroborated with experiments using a comprehensive physical model that dynamically updates the soil mass and particle composition. As complete knowledge of microscale conditions for arbitrary location and time is infeasible, we propose that new predictive frameworks of soil erosion should embed stochastic components in deterministic assessments of external and internal types of geomorphic variability.

  17. Numerical and experimental investigations on cavitation erosion

    Science.gov (United States)

    Fortes Patella, R.; Archer, A.; Flageul, C.

    2012-11-01

    A method is proposed to predict cavitation damage from cavitating flow simulations. For this purpose, a numerical process coupling cavitating flow simulations and erosion models was developed and applied to a two-dimensional (2D) hydrofoil tested at TUD (Darmstadt University of Technology, Germany) [1] and to a NACA 65012 tested at LMH-EPFL (Lausanne Polytechnic School) [2]. Cavitation erosion tests (pitting tests) were carried out and a 3D laser profilometry was used to analyze surfaces damaged by cavitation [3]. The method allows evaluating the pit characteristics, and mainly the volume damage rates. The paper describes the developed erosion model, the technique of cavitation damage measurement and presents some comparisons between experimental results and numerical damage predictions. The extent of cavitation erosion was correctly estimated in both hydrofoil geometries. The simulated qualitative influence of flow velocity, sigma value and gas content on cavitation damage agreed well with experimental observations.

  18. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

    Science.gov (United States)

    Yu, Haoyu S; Deng, Yuqing; Wu, Yujie; Sindhikara, Dan; Rask, Amy R; Kimura, Takayuki; Abel, Robert; Wang, Lingle

    2017-12-12

    Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.

  19. Airphoto analysis of erosion control practices

    Science.gov (United States)

    Morgan, K. M.; Morris-Jones, D. R.; Lee, G. B.; Kiefer, R. W.

    1980-01-01

    The Universal Soil Loss Equation (USLE) is a widely accepted tool for erosion prediction and conservation planning. In this study, airphoto analysis of color and color infrared 70 mm photography at a scale of 1:60,000 was used to determine the erosion control practice factor in the USLE. Information about contour tillage, contour strip cropping, and grass waterways was obtained from aerial photography for Pheasant Branch Creek watershed in Dane County, Wisconsin.

  20. The Arctic Coastal Erosion Problem

    Energy Technology Data Exchange (ETDEWEB)

    Frederick, Jennifer M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thomas, Matthew Anthony [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bull, Diana L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jones, Craig A. [Integral Consulting Inc., San Francisco, CA (United States); Roberts, Jesse D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-09-01

    Permafrost-dominated coastlines in the Arctic are rapidly disappearing. Arctic coastal erosion rates in the United States have doubled since the middle of the twentieth century and appear to be accelerating. Positive erosion trends have been observed for highly-variable geomorphic conditions across the entire Arctic, suggesting a major (human-timescale) shift in coastal landscape evolution. Unfortunately, irreversible coastal land loss in this region poses a threat to native, industrial, scientific, and military communities. The Arctic coastline is vast, spanning more than 100,000 km across eight nations, ten percent of which is overseen by the United States. Much of area is inaccessible by all-season roads. People and infrastructure, therefore, are commonly located near the coast. The impact of the Arctic coastal erosion problem is widespread. Homes are being lost. Residents are being dispersed and their villages relocated. Shoreline fuel storage and delivery systems are at greater risk. The U.S. Department of Energy (DOE) and Sandia National Laboratories (SNL) operate research facilities along some of the most rapidly eroding sections of coast in the world. The U.S. Department of Defense (DOD) is struggling to fortify coastal radar sites, operated to ensure national sovereignty in the air, against the erosion problem. Rapid alterations to the Arctic coastline are facilitated by oceanographic and geomorphic perturbations associated with climate change. Sea ice extent is declining, sea level is rising, sea water temperature is increasing, and permafrost state is changing. The polar orientation of the Arctic exacerbates the magnitude and rate of the environmental forcings that facilitate coastal land area loss. The fundamental mechanics of these processes are understood; their non-linear combination poses an extreme hazard. Tools to accurately predict Arctic coastal erosion do not exist. To obtain an accurate predictive model, a coupling of the influences of

  1. Predicting human miRNA target genes using a novel evolutionary methodology

    KAUST Repository

    Aigli, Korfiati; Kleftogiannis, Dimitrios A.; Konstantinos, Theofilatos; Spiros, Likothanassis; Athanasios, Tsakalidis; Seferina, Mavroudi

    2012-01-01

    The discovery of miRNAs had great impacts on traditional biology. Typically, miRNAs have the potential to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. The experimental identification of their targets has many drawbacks including cost, time and low specificity and these are the reasons why many computational approaches have been developed so far. However, existing computational approaches do not include any advanced feature selection technique and they are facing problems concerning their classification performance and their interpretability. In the present paper, we propose a novel hybrid methodology which combines genetic algorithms and support vector machines in order to locate the optimal feature subset while achieving high classification performance. The proposed methodology was compared with two of the most promising existing methodologies in the problem of predicting human miRNA targets. Our approach outperforms existing methodologies in terms of classification performances while selecting a much smaller feature subset. © 2012 Springer-Verlag.

  2. Predicting human miRNA target genes using a novel evolutionary methodology

    KAUST Repository

    Aigli, Korfiati

    2012-01-01

    The discovery of miRNAs had great impacts on traditional biology. Typically, miRNAs have the potential to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. The experimental identification of their targets has many drawbacks including cost, time and low specificity and these are the reasons why many computational approaches have been developed so far. However, existing computational approaches do not include any advanced feature selection technique and they are facing problems concerning their classification performance and their interpretability. In the present paper, we propose a novel hybrid methodology which combines genetic algorithms and support vector machines in order to locate the optimal feature subset while achieving high classification performance. The proposed methodology was compared with two of the most promising existing methodologies in the problem of predicting human miRNA targets. Our approach outperforms existing methodologies in terms of classification performances while selecting a much smaller feature subset. © 2012 Springer-Verlag.

  3. Soil erosion predictions from a landscape evolution model - An assessment of a post-mining landform using spatial climate change analogues.

    Science.gov (United States)

    Hancock, G R; Verdon-Kidd, D; Lowry, J B C

    2017-12-01

    Landscape Evolution Modelling (LEM) technologies provide a means by which it is possible to simulate the long-term geomorphic stability of a conceptual rehabilitated landform. However, simulations rarely consider the potential effects of anthropogenic climate change and consequently risk not accounting for the range of rainfall variability that might be expected in both the near and far future. One issue is that high resolution (both spatial and temporal) rainfall projections incorporating the potential effects of greenhouse forcing are required as input. However, projections of rainfall change are still highly uncertain for many regions, particularly at sub annual/seasonal scales. This is the case for northern Australia, where a decrease or an increase in rainfall post 2030 is considered equally likely based on climate model simulations. The aim of this study is therefore to investigate a spatial analogue approach to develop point scale hourly rainfall scenarios to be used as input to the CAESAR - Lisflood LEM to test the sensitivity of the geomorphic stability of a conceptual rehabilitated landform to potential changes in climate. Importantly, the scenarios incorporate the range of projected potential increase/decrease in rainfall for northern Australia and capture the expected envelope of erosion rates and erosion patterns (i.e. where erosion and deposition occurs) over a 100year modelled period. We show that all rainfall scenarios produce sediment output and gullying greater than that of the surrounding natural system, however a 'wetter' future climate produces the highest output. Importantly, incorporating analogue rainfall scenarios into LEM has the capacity to both improve landform design and enhance the modelling software. Further, the method can be easily transferred to other sites (both nationally and internationally) where rainfall variability is significant and climate change impacts are uncertain. Crown Copyright © 2017. Published by Elsevier B.V. All

  4. Finite element method for one-dimensional rill erosion simulation on a curved slope

    Directory of Open Access Journals (Sweden)

    Lijuan Yan

    2015-03-01

    Full Text Available Rill erosion models are important to hillslope soil erosion prediction and to land use planning. The development of rill erosion models and their use has become increasingly of great concern. The purpose of this research was to develop mathematic models with computer simulation procedures to simulate and predict rill erosion. The finite element method is known as an efficient tool in many other applications than in rill soil erosion. In this study, the hydrodynamic and sediment continuity model equations for a rill erosion system were solved by the Galerkin finite element method and Visual C++ procedures. The simulated results are compared with the data for spatially and temporally measured processes for rill erosion under different conditions. The results indicate that the one-dimensional linear finite element method produced excellent predictions of rill erosion processes. Therefore, this study supplies a tool for further development of a dynamic soil erosion prediction model.

  5. Regionalization of monthly rainfall erosivity patternsin Switzerland

    Science.gov (United States)

    Schmidt, Simon; Alewell, Christine; Panagos, Panos; Meusburger, Katrin

    2016-10-01

    One major controlling factor of water erosion is rainfall erosivity, which is quantified as the product of total storm energy and a maximum 30 min intensity (I30). Rainfall erosivity is often expressed as R-factor in soil erosion risk models like the Universal Soil Loss Equation (USLE) and its revised version (RUSLE). As rainfall erosivity is closely correlated with rainfall amount and intensity, the rainfall erosivity of Switzerland can be expected to have a regional characteristic and seasonal dynamic throughout the year. This intra-annual variability was mapped by a monthly modeling approach to assess simultaneously spatial and monthly patterns of rainfall erosivity. So far only national seasonal means and regional annual means exist for Switzerland. We used a network of 87 precipitation gauging stations with a 10 min temporal resolution to calculate long-term monthly mean R-factors. Stepwise generalized linear regression (GLM) and leave-one-out cross-validation (LOOCV) were used to select spatial covariates which explain the spatial and temporal patterns of the R-factor for each month across Switzerland. The monthly R-factor is mapped by summarizing the predicted R-factor of the regression equation and the corresponding residues of the regression, which are interpolated by ordinary kriging (regression-kriging). As spatial covariates, a variety of precipitation indicator data has been included such as snow depths, a combination product of hourly precipitation measurements and radar observations (CombiPrecip), daily Alpine precipitation (EURO4M-APGD), and monthly precipitation sums (RhiresM). Topographic parameters (elevation, slope) were also significant explanatory variables for single months. The comparison of the 12 monthly rainfall erosivity maps showed a distinct seasonality with the highest rainfall erosivity in summer (June, July, and August) influenced by intense rainfall events. Winter months have the lowest rainfall erosivity. A proportion of 62 % of

  6. Linking removal targets to the ecological effects of invaders: a predictive model and field test.

    Science.gov (United States)

    Green, Stephanie J; Dulvy, Nicholas K; Brooks, Annabelle M L; Akins, John L; Cooper, Andrew B; Miller, Skylar; Côté, Isabelle M

    Species invasions have a range of negative effects on recipient ecosystems, and many occur at a scale and magnitude that preclude complete eradication. When complete extirpation is unlikely with available management resources, an effective strategy may be to suppress invasive populations below levels predicted to cause undesirable ecological change. We illustrated this approach by developing and testing targets for the control of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) on Western Atlantic coral reefs. We first developed a size-structured simulation model of predation by lionfish on native fish communities, which we used to predict threshold densities of lionfish beyond which native fish biomass should decline. We then tested our predictions by experimentally manipulating lionfish densities above or below reef-specific thresholds, and monitoring the consequences for native fish populations on 24 Bahamian patch reefs over 18 months. We found that reducing lionfish below predicted threshold densities effectively protected native fish community biomass from predation-induced declines. Reductions in density of 25–92%, depending on the reef, were required to suppress lionfish below levels predicted to overconsume prey. On reefs where lionfish were kept below threshold densities, native prey fish biomass increased by 50–70%. Gains in small (15 cm total length), including ecologically important grazers and economically important fisheries species, had increased by 10–65% by the end of the experiment. Crucially, similar gains in prey fish biomass were realized on reefs subjected to partial and full removal of lionfish, but partial removals took 30% less time to implement. By contrast, the biomass of small native fishes declined by >50% on all reefs with lionfish densities exceeding reef-specific thresholds. Large inter-reef variation in the biomass of prey fishes at the outset of the study, which influences the threshold density of lionfish

  7. Advances in modeling soil erosion after disturbance on rangelands

    Science.gov (United States)

    Research has been undertaken to develop process based models that predict soil erosion rate after disturbance on rangelands. In these models soil detachment is predicted as a combination of multiple erosion processes, rain splash and thin sheet flow (splash and sheet) detachment and concentrated flo...

  8. Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications.

    Science.gov (United States)

    Kobayashi, Hiroki; Harada, Hiroko; Nakamura, Masaomi; Futamura, Yushi; Ito, Akihiro; Yoshida, Minoru; Iemura, Shun-Ichiro; Shin-Ya, Kazuo; Doi, Takayuki; Takahashi, Takashi; Natsume, Tohru; Imoto, Masaya; Sakakibara, Yasubumi

    2012-04-05

    Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system.As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.

  9. Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications

    Directory of Open Access Journals (Sweden)

    Kobayashi Hiroki

    2012-04-01

    Full Text Available Abstract Background Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. Results We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system. As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. Conclusions This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.

  10. An analytical erosion model for divertor plates and limiter experiments in CHS

    International Nuclear Information System (INIS)

    Sagara, A.; Noda, N.; Akiyama, R.; Arimoto, H.; Idei, H.; Iguchi, H.; Kaneko, O.; Kohmoto, T.; Kubo, S.; Matsuoka, K.; Morita, S.; Motojima, O.; Nishimura, K.; Okamura, S.; Takahasi, C.; Takita, Y.; Yamada, I.; Matsunami, N.; Rice, J.; Yamada, H.; Shoji, T.; Ueda, M.

    1992-01-01

    A self-consistent analytical solution for net erosion of a divertor plate which is set perpendicular to magnetic field lines is presented. The primary flux profile of hydrogen and impurities except redepositing particles is externally given as well as the return ratio of sputtered atoms to the plate. In the direction along the divertor trace, all conditions are uniform. The ionization mean free path is assumed constant to simplify equations. The analytical solution is compared with net erosion experiments carried out in compact helical system (CHS) by exposing a graphite target to a neutral beam heated plasma column introduced perpendicularly to the target along the magnetic field lines through a 2 cm slit opend on a graphite limiter. After exposure to 98 discharges, the target surface is analyzed with Rutherford backscattering method. Deposition profiles of Ti and O impurities are very well explained with the analytical predictions. (orig.)

  11. Protection from erosion following wildfire

    Science.gov (United States)

    Peter R. Robichaud; William J. Elliot

    2006-01-01

    Erosion in the first year after a wildfire can be up to three orders of magnitude greater than the erosion from undisturbed forests. To mitigate potential postfire erosion, various erosion control treatments are applied on highly erodible areas with downstream resources in need of protection. Because postfire erosion rates generally decline by an order of magnitude for...

  12. Deriving a clinical prediction rule to target sexual healthcare to women attending British General Practices.

    Science.gov (United States)

    Edelman, N L; Cassell, J A; Mercer, C H; Bremner, S A; Jones, C I; Gersten, A; deVisser, R O

    2018-07-01

    Some women attending General Practices (GPs) are at higher risk of unintended pregnancy (RUIP) and sexually transmitted infections (STI) than others. A clinical prediction rule (CPR) may help target resources using psychosocial questions as an acceptable, effective means of assessment. The aim was to derive a CPR that discriminates women who would benefit from sexual health discussion and intervention. Participants were recruited to a cross-sectional survey from six GPs in a city in South-East England in 2016. On arrival, female patients aged 16-44 years were invited to complete a questionnaire that addressed psychosocial factors, and the following self-reported outcomes: 2+ sexual partners in the last year (2PP) and RUIP. For each sexual risk, psychosocial questions were retained from logistic regression modelling which best discriminated women at risk using the C-statistic. Sensitivity and specificity were established in consultation with GP staff. The final sample comprised N = 1238 women. 2PP was predicted by 11 questions including age, binge-drinking weekly, ever having a partner who insulted you often, current smoking, and not cohabiting (C-statistic = 0.83, sensitivity = 73% and specificity = 77%). RUIP was predicted by 5 questions including sexual debut years, and emergency contraception use in the last 6 months (C-statistic = 0.70, sensitivity = 69% and specificity = 57%). 2PP was better discriminated than RUIP but neither to a clinically-useful degree. The finding that different psychosocial factors predicted each outcome has implications for prevention strategies. Further research should investigate causal links between psychosocial factors and sexual risk. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Predictive modeling of EEG time series for evaluating surgery targets in epilepsy patients.

    Science.gov (United States)

    Steimer, Andreas; Müller, Michael; Schindler, Kaspar

    2017-05-01

    During the last 20 years, predictive modeling in epilepsy research has largely been concerned with the prediction of seizure events, whereas the inference of effective brain targets for resective surgery has received surprisingly little attention. In this exploratory pilot study, we describe a distributional clustering framework for the modeling of multivariate time series and use it to predict the effects of brain surgery in epilepsy patients. By analyzing the intracranial EEG, we demonstrate how patients who became seizure free after surgery are clearly distinguished from those who did not. More specifically, for 5 out of 7 patients who obtained seizure freedom (= Engel class I) our method predicts the specific collection of brain areas that got actually resected during surgery to yield a markedly lower posterior probability for the seizure related clusters, when compared to the resection of random or empty collections. Conversely, for 4 out of 5 Engel class III/IV patients who still suffer from postsurgical seizures, performance of the actually resected collection is not significantly better than performances displayed by random or empty collections. As the number of possible collections ranges into billions and more, this is a substantial contribution to a problem that today is still solved by visual EEG inspection. Apart from epilepsy research, our clustering methodology is also of general interest for the analysis of multivariate time series and as a generative model for temporally evolving functional networks in the neurosciences and beyond. Hum Brain Mapp 38:2509-2531, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Conception de couches minces tribologiques pour augmenter la resistance a l'erosion par impacts de particules

    Science.gov (United States)

    Hassani, Salim

    calculation variables include impact velocity (in the range of 50--300 m/s), particle size and the mechanical properties of both the target and the impacting particle. Specifically, we investigate the impact response of coatings fabricated by physical vapor deposition (PVD) and plasma enhanced chemical vapor deposition (PECVD). This includes single and multilayer TiN and nanocomposite nc-TiN/a-SiN1.3 and nc-TiCN/a-SiCN systems on titanium alloy and stainless steel substrates. In particular, we correlate the thickness and the coating macroscopic properties, such as hardness, Young's modulus, and toughness with the erosion. The calculations confirmed earlier findings that for a single layer coating, a combination of low modulus and a high thickness lead to local stress reduction and hence possible erosion resistance enhancement. The FE simulations have further shown that a tensile stress exceeding a critical stress sigmacrit = 3.95 GPa can be easily produced by a single particle impact. For each combination of particle velocity and size, a map of tensile stresses in the TiN coating, corresponding to the predicted erosion performance, was produced. The FE model has then been extended to multilayer coating systems containing superhard nanocomposite materials. These coatings configurations, when combined with tailored mechanical properties have shown to provide an improvement of the performance over comparable single layer configurations. The development of high performance erosion-resistant coatings also requires understanding of stress propagation upon particle impact. In the second part of this work, we apply a finite element methodology to enhance and optimize the resistance of protective coatings to erosion by solid particles with appropriate stress management. A controlled distribution of the initial residual stress in the coating was used to counteract impact stress, while a Young's modulus distribution was applied to optimize impact energy spreading throughout the coating

  15. Erosion and stability of a mine soil

    International Nuclear Information System (INIS)

    Wu, T.H.; Stadler, A.T.; Low, C.

    1996-01-01

    Mine soils developed from mine spoils commonly have a wide range of particle size. The slopes of old spoil piles usually are marked by gullies due to years of uncontrolled erosion. These characteristics raise questions about applicability of available theories and models for estimating runoff and erosion. An investigation was made to determine whether available erosion models can work for mine soils and can account for gully erosion. The investigation at an abandoned surface mine consisted of measurement of soil and sediment properties, measurement of runoff and erosion, observations of armor by rock fragments on gully floor, and calculations with available theories of sediment transport and slope stability. The results at this site suggest that (1) predictions with the ANSWERS model have about the same accuracy as those made for agricultural lands; (2) armor provided by rock fragments are temporary as they are periodically removed by debris flows; (3) detachment by rainfall impact is the primary cause of erosion on short steep slopes; and (4) a simplified method can be used for estimating erosion on such slopes

  16. A Generic Multi-Compartmental CNS Distribution Model Structure for 9 Drugs Allows Prediction of Human Brain Target Site Concentrations

    NARCIS (Netherlands)

    Yamamoto, Yumi; Valitalo, Pyry A.; van den Berg, Dirk-Jan; Hartman, Robin; van den Brink, Willem; Wong, Yin Cheong; Huntjens, Dymphy R.; Proost, Johannes H.; Vermeulen, An; Krauwinkel, Walter; Bakshi, Suruchi; Aranzana-Climent, Vincent; Marchand, Sandrine; Dahyot-Fizelier, Claire; Couet, William; Danhof, Meindert; van Hasselt, Johan G. C.; de lange, Elizabeth C. M.

    Purpose Predicting target site drug concentration in the brain is of key importance for the successful development of drugs acting on the central nervous system. We propose a generic mathematical model to describe the pharmacokinetics in brain compartments, and apply this model to predict human

  17. A program to evaluate the erosion on the CFC tiles of the ITER divertor

    Energy Technology Data Exchange (ETDEWEB)

    D' Agata, E. [ITER International Team, ITER Joint Work Site, Boltzmannstr 2, 85748 Garching (Germany)], E-mail: elio.dagata@iter.org; Ogorodnikova, O.V. [Association Euratom-CEA, CEA/DSM/DRFC, CEA/Cadarache, F-13108 Saint-Paul-Lez-Durance (France); Tivey, R. [ITER International Team, ITER Joint Work Site, Boltzmannstr 2, 85748 Garching (Germany); Lowry, C.; Schlosser, J. [Association Euratom-CEA, CEA/DSM/DRFC, CEA/Cadarache, F-13108 Saint-Paul-Lez-Durance (France)

    2007-10-15

    The plasma-facing surfaces of the ITER divertor are armoured with tungsten in the upper part of the inner and outer vertical targets, and carbon fibre composite (CFC) in the lower part, the region where the scrape-off layer intercepts the divertor. The CFC in the form of a monoblock in the vertical target is the most loaded part of the plasma-facing surfaces, and hence it is subjected to high erosion and has a significant risk of failure. A program has been developed with the aim of understanding the impact on the erosion lifetime due to a combination of two main effects: the material property variations (particularly pronounced in CFC) and the presence of joining defects. The software allows the evolution of the surface profile of the armour to be predicted and the margin on critical heat flux at the heat-sink-to-coolant interface to be estimated for a range of postulated defects, from start-of-life through to end-of-life of the component. In assessing erosion, the code takes account of geometry and sublimation, and physical and chemical erosion of the CFC armour. The incident angle (a glancing angle of a few degrees) of the particle and heat flux onto the target is taken into account. The program has been validated by comparison with analytical approximations very well validated against experimental data. The code has been developed in the APDL language to operate inside a commercial and certificated finite element program such as ANSYS.

  18. A program to evaluate the erosion on the CFC tiles of the ITER divertor

    International Nuclear Information System (INIS)

    D'Agata, E.; Ogorodnikova, O.V.; Tivey, R.; Lowry, C.; Schlosser, J.

    2007-01-01

    The plasma-facing surfaces of the ITER divertor are armoured with tungsten in the upper part of the inner and outer vertical targets, and carbon fibre composite (CFC) in the lower part, the region where the scrape-off layer intercepts the divertor. The CFC in the form of a monoblock in the vertical target is the most loaded part of the plasma-facing surfaces, and hence it is subjected to high erosion and has a significant risk of failure. A program has been developed with the aim of understanding the impact on the erosion lifetime due to a combination of two main effects: the material property variations (particularly pronounced in CFC) and the presence of joining defects. The software allows the evolution of the surface profile of the armour to be predicted and the margin on critical heat flux at the heat-sink-to-coolant interface to be estimated for a range of postulated defects, from start-of-life through to end-of-life of the component. In assessing erosion, the code takes account of geometry and sublimation, and physical and chemical erosion of the CFC armour. The incident angle (a glancing angle of a few degrees) of the particle and heat flux onto the target is taken into account. The program has been validated by comparison with analytical approximations very well validated against experimental data. The code has been developed in the APDL language to operate inside a commercial and certificated finite element program such as ANSYS

  19. Predicting 2D target velocity cannot help 2D motion integration for smooth pursuit initiation.

    Science.gov (United States)

    Montagnini, Anna; Spering, Miriam; Masson, Guillaume S

    2006-12-01

    Smooth pursuit eye movements reflect the temporal dynamics of bidimensional (2D) visual motion integration. When tracking a single, tilted line, initial pursuit direction is biased toward unidimensional (1D) edge motion signals, which are orthogonal to the line orientation. Over 200 ms, tracking direction is slowly corrected to finally match the 2D object motion during steady-state pursuit. We now show that repetition of line orientation and/or motion direction does not eliminate the transient tracking direction error nor change the time course of pursuit correction. Nonetheless, multiple successive presentations of a single orientation/direction condition elicit robust anticipatory pursuit eye movements that always go in the 2D object motion direction not the 1D edge motion direction. These results demonstrate that predictive signals about target motion cannot be used for an efficient integration of ambiguous velocity signals at pursuit initiation.

  20. Scales and erosion

    Science.gov (United States)

    There is a need to develop scale explicit understanding of erosion to overcome existing conceptual and methodological flaws in our modelling methods currently applied to understand the process of erosion, transport and deposition at the catchment scale. These models need to be based on a sound under...

  1. Mapping monthly rainfall erosivity in Europe.

    Science.gov (United States)

    Ballabio, Cristiano; Borrelli, Pasquale; Spinoni, Jonathan; Meusburger, Katrin; Michaelides, Silas; Beguería, Santiago; Klik, Andreas; Petan, Sašo; Janeček, Miloslav; Olsen, Preben; Aalto, Juha; Lakatos, Mónika; Rymszewicz, Anna; Dumitrescu, Alexandru; Tadić, Melita Perčec; Diodato, Nazzareno; Kostalova, Julia; Rousseva, Svetla; Banasik, Kazimierz; Alewell, Christine; Panagos, Panos

    2017-02-01

    Rainfall erosivity as a dynamic factor of soil loss by water erosion is modelled intra-annually for the first time at European scale. The development of Rainfall Erosivity Database at European Scale (REDES) and its 2015 update with the extension to monthly component allowed to develop monthly and seasonal R-factor maps and assess rainfall erosivity both spatially and temporally. During winter months, significant rainfall erosivity is present only in part of the Mediterranean countries. A sudden increase of erosivity occurs in major part of European Union (except Mediterranean basin, western part of Britain and Ireland) in May and the highest values are registered during summer months. Starting from September, R-factor has a decreasing trend. The mean rainfall erosivity in summer is almost 4 times higher (315MJmmha -1 h -1 ) compared to winter (87MJmmha -1 h -1 ). The Cubist model has been selected among various statistical models to perform the spatial interpolation due to its excellent performance, ability to model non-linearity and interpretability. The monthly prediction is an order more difficult than the annual one as it is limited by the number of covariates and, for consistency, the sum of all months has to be close to annual erosivity. The performance of the Cubist models proved to be generally high, resulting in R 2 values between 0.40 and 0.64 in cross-validation. The obtained months show an increasing trend of erosivity occurring from winter to summer starting from western to Eastern Europe. The maps also show a clear delineation of areas with different erosivity seasonal patterns, whose spatial outline was evidenced by cluster analysis. The monthly erosivity maps can be used to develop composite indicators that map both intra-annual variability and concentration of erosive events. Consequently, spatio-temporal mapping of rainfall erosivity permits to identify the months and the areas with highest risk of soil loss where conservation measures should be

  2. Ignition condition and gain prediction for perturbed inertial confinement fusion targets

    International Nuclear Information System (INIS)

    Kishony, Roy; Shvarts, Dov

    2001-01-01

    The effect of perturbations on hot spot ignition is studied using full two-dimensional (2D) numerical simulations of the National Ignition Facility [J. D. Lindl, Phys. Plasmas 2, 3933 (1995)] direct drive Laboratory for Laser Energetics target design and newly derived 2D self-similar solutions for a perturbed burn wave propagation. It is shown that the required implosion velocity needed for ignition increases with the perturbation mode number and final amplitude, reaching an asymptotic value for high enough perturbation mode numbers, when the entire mixing zone no longer contributes to the ignition of the hot spot. Using the new self-similar solutions, ignition conditions for various perturbation mode numbers and amplitudes are obtained. These ignition conditions, which correspond to areal densities higher than needed for ignition in the symmetric case, are translated to a required increase in the implosion velocity needed for ignition, using the 1D Levendahl-Lindl scaling, in good agreement with the full 2D numerical simulation results. Finally, using the above results, a model for predicting the gain of a perturbed targets as a function of the perturbation spectra (single-mode and multi-mode) is presented, in good agreement with full numerical simulations

  3. Multi-Source Multi-Target Dictionary Learning for Prediction of Cognitive Decline.

    Science.gov (United States)

    Zhang, Jie; Li, Qingyang; Caselli, Richard J; Thompson, Paul M; Ye, Jieping; Wang, Yalin

    2017-06-01

    Alzheimer's Disease (AD) is the most common type of dementia. Identifying correct biomarkers may determine pre-symptomatic AD subjects and enable early intervention. Recently, Multi-task sparse feature learning has been successfully applied to many computer vision and biomedical informatics researches. It aims to improve the generalization performance by exploiting the shared features among different tasks. However, most of the existing algorithms are formulated as a supervised learning scheme. Its drawback is with either insufficient feature numbers or missing label information. To address these challenges, we formulate an unsupervised framework for multi-task sparse feature learning based on a novel dictionary learning algorithm. To solve the unsupervised learning problem, we propose a two-stage Multi-Source Multi-Target Dictionary Learning (MMDL) algorithm. In stage 1, we propose a multi-source dictionary learning method to utilize the common and individual sparse features in different time slots. In stage 2, supported by a rigorous theoretical analysis, we develop a multi-task learning method to solve the missing label problem. Empirical studies on an N = 3970 longitudinal brain image data set, which involves 2 sources and 5 targets, demonstrate the improved prediction accuracy and speed efficiency of MMDL in comparison with other state-of-the-art algorithms.

  4. Boolean network model for cancer pathways: predicting carcinogenesis and targeted therapy outcomes.

    Directory of Open Access Journals (Sweden)

    Herman F Fumiã

    Full Text Available A Boolean dynamical system integrating the main signaling pathways involved in cancer is constructed based on the currently known protein-protein interaction network. This system exhibits stationary protein activation patterns--attractors--dependent on the cell's microenvironment. These dynamical attractors were determined through simulations and their stabilities against mutations were tested. In a higher hierarchical level, it was possible to group the network attractors into distinct cell phenotypes and determine driver mutations that promote phenotypic transitions. We find that driver nodes are not necessarily central in the network topology, but at least they are direct regulators of central components towards which converge or through which crosstalk distinct cancer signaling pathways. The predicted drivers are in agreement with those pointed out by diverse census of cancer genes recently performed for several human cancers. Furthermore, our results demonstrate that cell phenotypes can evolve towards full malignancy through distinct sequences of accumulated mutations. In particular, the network model supports routes of carcinogenesis known for some tumor types. Finally, the Boolean network model is employed to evaluate the outcome of molecularly targeted cancer therapies. The major find is that monotherapies were additive in their effects and that the association of targeted drugs is necessary for cancer eradication.

  5. Discovery of a Novel Inhibitor of the Hedgehog Signaling Pathway through Cell-based Compound Discovery and Target Prediction.

    Science.gov (United States)

    Kremer, Lea; Schultz-Fademrecht, Carsten; Baumann, Matthias; Habenberger, Peter; Choidas, Axel; Klebl, Bert; Kordes, Susanne; Schöler, Hans R; Sterneckert, Jared; Ziegler, Slava; Schneider, Gisbert; Waldmann, Herbert

    2017-10-09

    Cell-based assays enable monitoring of small-molecule bioactivity in a target-agnostic manner and help uncover new biological mechanisms. Subsequent identification and validation of the small-molecule targets, typically employing proteomics techniques, is very challenging and limited, in particular if the targets are membrane proteins. Herein, we demonstrate that the combination of cell-based bioactive-compound discovery with cheminformatic target prediction may provide an efficient approach to accelerate the process and render target identification and validation more efficient. Using a cell-based assay, we identified the pyrazolo-imidazole smoothib as a new inhibitor of hedgehog (Hh) signaling and an antagonist of the protein smoothened (SMO) with a novel chemotype. Smoothib targets the heptahelical bundle of SMO, prevents its ciliary localization, reduces the expression of Hh target genes, and suppresses the growth of Ptch +/- medulloblastoma cells. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. In Silico Prediction and Validation of Gfap as an miR-3099 Target in Mouse Brain.

    Science.gov (United States)

    Abidin, Shahidee Zainal; Leong, Jia-Wen; Mahmoudi, Marzieh; Nordin, Norshariza; Abdullah, Syahril; Cheah, Pike-See; Ling, King-Hwa

    2017-08-01

    MicroRNAs are small non-coding RNAs that play crucial roles in the regulation of gene expression and protein synthesis during brain development. MiR-3099 is highly expressed throughout embryogenesis, especially in the developing central nervous system. Moreover, miR-3099 is also expressed at a higher level in differentiating neurons in vitro, suggesting that it is a potential regulator during neuronal cell development. This study aimed to predict the target genes of miR-3099 via in-silico analysis using four independent prediction algorithms (miRDB, miRanda, TargetScan, and DIANA-micro-T-CDS) with emphasis on target genes related to brain development and function. Based on the analysis, a total of 3,174 miR-3099 target genes were predicted. Those predicted by at least three algorithms (324 genes) were subjected to DAVID bioinformatics analysis to understand their overall functional themes and representation. The analysis revealed that nearly 70% of the target genes were expressed in the nervous system and a significant proportion were associated with transcriptional regulation and protein ubiquitination mechanisms. Comparison of in situ hybridization (ISH) expression patterns of miR-3099 in both published and in-house-generated ISH sections with the ISH sections of target genes from the Allen Brain Atlas identified 7 target genes (Dnmt3a, Gabpa, Gfap, Itga4, Lxn, Smad7, and Tbx18) having expression patterns complementary to miR-3099 in the developing and adult mouse brain samples. Of these, we validated Gfap as a direct downstream target of miR-3099 using the luciferase reporter gene system. In conclusion, we report the successful prediction and validation of Gfap as an miR-3099 target gene using a combination of bioinformatics resources with enrichment of annotations based on functional ontologies and a spatio-temporal expression dataset.

  7. In Vitro Drug Sensitivity Tests to Predict Molecular Target Drug Responses in Surgically Resected Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Ryohei Miyazaki

    Full Text Available Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs and anaplastic lymphoma kinase (ALK inhibitors have dramatically changed the strategy of medical treatment of lung cancer. Patients should be screened for the presence of the EGFR mutation or echinoderm microtubule-associated protein-like 4 (EML4-ALK fusion gene prior to chemotherapy to predict their clinical response. The succinate dehydrogenase inhibition (SDI test and collagen gel droplet embedded culture drug sensitivity test (CD-DST are established in vitro drug sensitivity tests, which may predict the sensitivity of patients to cytotoxic anticancer drugs. We applied in vitro drug sensitivity tests for cyclopedic prediction of clinical responses to different molecular targeting drugs.The growth inhibitory effects of erlotinib and crizotinib were confirmed for lung cancer cell lines using SDI and CD-DST. The sensitivity of 35 cases of surgically resected lung cancer to erlotinib was examined using SDI or CD-DST, and compared with EGFR mutation status.HCC827 (Exon19: E746-A750 del and H3122 (EML4-ALK cells were inhibited by lower concentrations of erlotinib and crizotinib, respectively than A549, H460, and H1975 (L858R+T790M cells were. The viability of the surgically resected lung cancer was 60.0 ± 9.8 and 86.8 ± 13.9% in EGFR-mutants vs. wild types in the SDI (p = 0.0003. The cell viability was 33.5 ± 21.2 and 79.0 ± 18.6% in EGFR mutants vs. wild-type cases (p = 0.026 in CD-DST.In vitro drug sensitivity evaluated by either SDI or CD-DST correlated with EGFR gene status. Therefore, SDI and CD-DST may be useful predictors of potential clinical responses to the molecular anticancer drugs, cyclopedically.

  8. Limited-area short-range ensemble predictions targeted for heavy rain in Europe

    Directory of Open Access Journals (Sweden)

    K. Sattler

    2005-01-01

    Full Text Available Inherent uncertainties in short-range quantitative precipitation forecasts (QPF from the high-resolution, limited-area numerical weather prediction model DMI-HIRLAM (LAM are addressed using two different approaches to creating a small ensemble of LAM simulations, with focus on prediction of extreme rainfall events over European river basins. The first ensemble type is designed to represent uncertainty in the atmospheric state of the initial condition and at the lateral LAM boundaries. The global ensemble prediction system (EPS from ECMWF serves as host model to the LAM and provides the state perturbations, from which a small set of significant members is selected. The significance is estimated on the basis of accumulated precipitation over a target area of interest, which contains the river basin(s under consideration. The selected members provide the initial and boundary data for the ensemble integration in the LAM. A second ensemble approach tries to address a portion of the model-inherent uncertainty responsible for errors in the forecasted precipitation field by utilising different parameterisation schemes for condensation and convection in the LAM. Three periods around historical heavy rain events that caused or contributed to disastrous river flooding in Europe are used to study the performance of the LAM ensemble designs. The three cases exhibit different dynamic and synoptic characteristics and provide an indication of the ensemble qualities in different weather situations. Precipitation analyses from the Deutsche Wetterdienst (DWD are used as the verifying reference and a comparison of daily rainfall amounts is referred to the respective river basins of the historical cases.

  9. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information.

    Science.gov (United States)

    Luo, Yunan; Zhao, Xinbin; Zhou, Jingtian; Yang, Jinglin; Zhang, Yanqing; Kuang, Wenhua; Peng, Jian; Chen, Ligong; Zeng, Jianyang

    2017-09-18

    The emergence of large-scale genomic, chemical and pharmacological data provides new opportunities for drug discovery and repositioning. In this work, we develop a computational pipeline, called DTINet, to predict novel drug-target interactions from a constructed heterogeneous network, which integrates diverse drug-related information. DTINet focuses on learning a low-dimensional vector representation of features, which accurately explains the topological properties of individual nodes in the heterogeneous network, and then makes prediction based on these representations via a vector space projection scheme. DTINet achieves substantial performance improvement over other state-of-the-art methods for drug-target interaction prediction. Moreover, we experimentally validate the novel interactions between three drugs and the cyclooxygenase proteins predicted by DTINet, and demonstrate the new potential applications of these identified cyclooxygenase inhibitors in preventing inflammatory diseases. These results indicate that DTINet can provide a practically useful tool for integrating heterogeneous information to predict new drug-target interactions and repurpose existing drugs.Network-based data integration for drug-target prediction is a promising avenue for drug repositioning, but performance is wanting. Here, the authors introduce DTINet, whose performance is enhanced in the face of noisy, incomplete and high-dimensional biological data by learning low-dimensional vector representations.

  10. Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Precious Takondwa Makondi

    Full Text Available Acquired drug resistance to the chemotherapeutic drug irinotecan (the active metabolite of which is SN-38 is one of the significant obstacles in the treatment of advanced colorectal cancer (CRC. The molecular mechanism or targets mediating irinotecan resistance are still unclear. It is urgent to find the irinotecan response biomarkers to improve CRC patients' therapy.Genetic Omnibus Database GSE42387 which contained the gene expression profiles of parental and irinotecan-resistant HCT-116 cell lines was used. Differentially expressed genes (DEGs between parental and irinotecan-resistant cells, protein-protein interactions (PPIs, gene ontologies (GOs and pathway analysis were performed to identify the overall biological changes. The most common DEGs in the PPIs, GOs and pathways were identified and were validated clinically by their ability to predict overall survival and disease free survival. The gene-gene expression correlation and gene-resistance correlation was also evaluated in CRC patients using The Cancer Genomic Atlas data (TCGA.The 135 DEGs were identified of which 36 were upregulated and 99 were down regulated. After mapping the PPI networks, the GOs and the pathways, nine genes (GNAS, PRKACB, MECOM, PLA2G4C, BMP6, BDNF, DLG4, FGF2 and FGF9 were found to be commonly enriched. Signal transduction was the most significant GO and MAPK pathway was the most significant pathway. The five genes (FGF2, FGF9, PRKACB, MECOM and PLA2G4C in the MAPK pathway were all contained in the signal transduction and the levels of those genes were upregulated. The FGF2, FGF9 and MECOM expression were highly associated with CRC patients' survival rate but not PRKACB and PLA2G4C. In addition, FGF9 was also associated with irinotecan resistance and poor disease free survival. FGF2, FGF9 and PRKACB were positively correlated with each other while MECOM correlated positively with FGF9 and PLA2G4C, and correlated negatively with FGF2 and PRKACB after doing gene

  11. Divertor erosion in DIII-D

    International Nuclear Information System (INIS)

    Whyte, D.G.; Bastasz, R.; Wampler, W.R.; Brooks, J.N.; West, W.P.; Wong, C.P.C.; Buzhinskij, O.I.; Opimach, I.V.

    1998-08-01

    Net erosion rates of carbon target plates have been measured in situ for the DIII-D lower divertor. The principal method of obtaining this data is the DiMES sample probe. Recent experiments have focused on erosion at the outer strike-point (OSP) of two divertor plasma conditions: attached (T e > 40 eV) ELMing plasmas, and detached (T e 2 . In this case, measurements and modeling agree for both gross and net carbon erosion, showing the near-surface transport and redeposition of the carbon is well understood. In the attached cases, physical sputtering (with enhancement from self-sputtering and oblique incidence) is dominant, and the effective sputtering yield, Y, is greater than 10%. In ELM-free discharges, the total OSP net erosion rate is equal to the rate of carbon accumulation in the core plasma. For the detached divertor cases, the cold incident plasma eliminates physical sputtering. Attempts to measure chemically eroded hydrocarbon molecules spectroscopically indicate an upper limit of Y ≤ 0.1% for the chemical sputtering yield. Net erosion is suppressed at the outer strike-point, which becomes a region of net redeposition (∼ 4 cm/exposure-year). The private flux wall is measured to be a region of net redeposition with dense, high neutral pressure, attached divertor plasmas. Leading edges intercepting parallel heat flux (∼ 50 MW/m 2 ) have very high net erosion rates at the OSP of an attached plasma (∼ 10 microm/s > 1,000x erosion rate of aligned surfaces). Leading edge erosion, and subsequent carbon redeposition, caused by tile gaps can account for half of the deuterium codeposition in the DIII-D divertor

  12. Divertor erosion in DIII-D

    International Nuclear Information System (INIS)

    Whyte, D.G.; Bastasz, R.; Wampler, W.R.; Brooks, J.N.; West, W.P.; Wong, C.P.C.

    1998-05-01

    Net erosion rates of carbon target plates have been measured in situ for the DIII-D lower divertor. The principal method of obtaining this data is the DiMES sample probe. Recent experiments have focused on erosion at the outer strike-point of two divertor plasma conditions: (1) attached (Te > 40 eV) ELMing plasmas and (2) detached (Te 10 cm/year, even with incident heat flux 2 . In this case, measurements and modeling agree for both gross and net carbon erosion, showing the near-surface transport and redeposition of the carbon is well understood and that effective sputtering yields are > 10%. In ELM-free discharges, this erosion rate can account for the rate of carbon accumulation in the core plasma. Divertor plasma detachment eliminates physical sputtering, while spectroscopically measured chemical erosion yields are also found to be low (Y(C/D + ) ≤ 2.0 x 10 -3 ). This leads to suppression of net erosion at the outer strike-point, which becomes a region of net redeposition (∼ 4 cm/year). The private flux wall is measured to be a region of net redeposition with dense, high neutral pressure, attached divertor plasmas. Leading edges intercepting parallel heat flux (∼ 50 MW/m 2 ) have very high net erosion rates (∼ 10 microm/s) at the OSP of an attached plasma. Leading edge erosion, and subsequent carbon redeposition, caused by tile gaps can account for half of the deuterium codeposition in the DIII-D divertor

  13. Numerical modelling of concentrated leak erosion during Hole Erosion Tests

    OpenAIRE

    Mercier, F.; Bonelli, S.; Golay, F.; Anselmet, F.; Philippe, P.; Borghi, R.

    2015-01-01

    This study focuses on the numerical modelling of concentrated leak erosion of a cohesive soil by a turbulent flow in axisymmetrical geometry, with application to the Hole Erosion Test (HET). The numerical model is based on adaptive remeshing of the water/soil interface to ensure accurate description of the mechanical phenomena occurring near the soil/water interface. The erosion law governing the interface motion is based on two erosion parameters: the critical shear stress and the erosion co...

  14. An efficient hybrid technique in RCS predictions of complex targets at high frequencies

    Science.gov (United States)

    Algar, María-Jesús; Lozano, Lorena; Moreno, Javier; González, Iván; Cátedra, Felipe

    2017-09-01

    Most computer codes in Radar Cross Section (RCS) prediction use Physical Optics (PO) and Physical theory of Diffraction (PTD) combined with Geometrical Optics (GO) and Geometrical Theory of Diffraction (GTD). The latter approaches are computationally cheaper and much more accurate for curved surfaces, but not applicable for the computation of the RCS of all surfaces of a complex object due to the presence of caustic problems in the analysis of concave surfaces or flat surfaces in the far field. The main contribution of this paper is the development of a hybrid method based on a new combination of two asymptotic techniques: GTD and PO, considering the advantages and avoiding the disadvantages of each of them. A very efficient and accurate method to analyze the RCS of complex structures at high frequencies is obtained with the new combination. The proposed new method has been validated comparing RCS results obtained for some simple cases using the proposed approach and RCS using the rigorous technique of Method of Moments (MoM). Some complex cases have been examined at high frequencies contrasting the results with PO. This study shows the accuracy and the efficiency of the hybrid method and its suitability for the computation of the RCS at really large and complex targets at high frequencies.

  15. Prediction of buried mine-like target radar signatures using wideband electromagnetic modeling

    Energy Technology Data Exchange (ETDEWEB)

    Warrick, A.L.; Azevedo, S.G.; Mast, J.E.

    1998-04-06

    Current ground penetrating radars (GPR) have been tested for land mine detection, but they have generally been costly and have poor performance. Comprehensive modeling and experimentation must be done to predict the electromagnetic (EM) signatures of mines to access the effect of clutter on the EM signature of the mine, and to understand the merit and limitations of using radar for various mine detection scenarios. This modeling can provide a basis for advanced radar design and detection techniques leading to superior performance. Lawrence Livermore National Laboratory (LLNL) has developed a radar technology that when combined with comprehensive modeling and detection methodologies could be the basis of an advanced mine detection system. Micropower Impulse Radar (MIR) technology exhibits a combination of properties, including wideband operation, extremely low power consumption, extremely small size and low cost, array configurability, and noise encoded pulse generation. LLNL is in the process of developing an optimal processing algorithm to use with the MIR sensor. In this paper, we use classical numerical models to obtain the signature of mine-like targets and examine the effect of surface roughness on the reconstructed signals. These results are then qualitatively compared to experimental data.

  16. STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.

    Science.gov (United States)

    Shen, Judong; Song, Kijoung; Slater, Andrew J; Ferrero, Enrico; Nelson, Matthew R

    2017-09-01

    We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes. This database can be used for a multitude of investigations into the genes and genetic mechanisms underlying inter-individual variation in human traits, as well as supporting drug discovery applications. Shell, R, Perl and Python scripts and STOPGAP R data files (version 2.5.1 at publication) are available at https://github.com/StatGenPRD/STOPGAP . Some of the most useful STOPGAP fields can be queried through an R Shiny web application at http://stopgapwebapp.com . matthew.r.nelson@gsk.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  17. A Compact Methodology to Understand, Evaluate, and Predict the Performance of Automatic Target Recognition

    Science.gov (United States)

    Li, Yanpeng; Li, Xiang; Wang, Hongqiang; Chen, Yiping; Zhuang, Zhaowen; Cheng, Yongqiang; Deng, Bin; Wang, Liandong; Zeng, Yonghu; Gao, Lei

    2014-01-01

    This paper offers a compacted mechanism to carry out the performance evaluation work for an automatic target recognition (ATR) system: (a) a standard description of the ATR system's output is suggested, a quantity to indicate the operating condition is presented based on the principle of feature extraction in pattern recognition, and a series of indexes to assess the output in different aspects are developed with the application of statistics; (b) performance of the ATR system is interpreted by a quality factor based on knowledge of engineering mathematics; (c) through a novel utility called “context-probability” estimation proposed based on probability, performance prediction for an ATR system is realized. The simulation result shows that the performance of an ATR system can be accounted for and forecasted by the above-mentioned measures. Compared to existing technologies, the novel method can offer more objective performance conclusions for an ATR system. These conclusions may be helpful in knowing the practical capability of the tested ATR system. At the same time, the generalization performance of the proposed method is good. PMID:24967605

  18. Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics

    Directory of Open Access Journals (Sweden)

    Jaehee V. Shim

    2017-09-01

    Full Text Available Tyrosine kinase inhibitors (TKIs are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help to control critical processes such as survival signaling, energy homeostasis, and excitation–contraction coupling. However, mechanistic understanding is limited at present due to the complexities of tyrosine kinase signaling, and the wide range of targets inhibited by TKIs. Here, we review the use of TKIs in cancer and the cardiotoxicities that have been reported, discuss potential mechanisms underlying cardiotoxicity, and describe recent progress in achieving a more systematic understanding of cardiotoxicity via the use of mechanistic models. In particular, we argue that future advances are likely to be enabled by studies that combine large-scale experimental measurements with Quantitative Systems Pharmacology (QSP models describing biological mechanisms and dynamics. As such approaches have proven extremely valuable for understanding and predicting other drug toxicities, it is likely that QSP modeling can be successfully applied to cardiotoxicity induced by TKIs. We conclude by discussing a potential strategy for integrating genome-wide expression measurements with models, illustrate initial advances in applying this approach to cardiotoxicity, and describe challenges that must be overcome to truly develop a mechanistic and systematic understanding of cardiotoxicity caused by TKIs.

  19. DDR: Efficient computational method to predict drug–target interactions using graph mining and machine learning approaches

    KAUST Repository

    Olayan, Rawan S.

    2017-11-23

    Motivation Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. Results We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using five repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new, and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs.

  20. Prediction of target genes for miR-140-5p in pulmonary arterial hypertension using bioinformatics methods.

    Science.gov (United States)

    Li, Fangwei; Shi, Wenhua; Wan, Yixin; Wang, Qingting; Feng, Wei; Yan, Xin; Wang, Jian; Chai, Limin; Zhang, Qianqian; Li, Manxiang

    2017-12-01

    The expression of microRNA (miR)-140-5p is known to be reduced in both pulmonary arterial hypertension (PAH) patients and monocrotaline-induced PAH models in rat. Identification of target genes for miR-140-5p with bioinformatics analysis may reveal new pathways and connections in PAH. This study aimed to explore downstream target genes and relevant signaling pathways regulated by miR-140-5p to provide theoretical evidences for further researches on role of miR-140-5p in PAH. Multiple downstream target genes and upstream transcription factors (TFs) of miR-140-5p were predicted in the analysis. Gene ontology (GO) enrichment analysis indicated that downstream target genes of miR-140-5p were enriched in many biological processes, such as biological regulation, signal transduction, response to chemical stimulus, stem cell proliferation, cell surface receptor signaling pathways. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis found that downstream target genes were mainly located in Notch, TGF-beta, PI3K/Akt, and Hippo signaling pathway. According to TF-miRNA-mRNA network, the important downstream target genes of miR-140-5p were PPI, TGF-betaR1, smad4, JAG1, ADAM10, FGF9, PDGFRA, VEGFA, LAMC1, TLR4, and CREB. After thoroughly reviewing published literature, we found that 23 target genes and seven signaling pathways were truly inhibited by miR-140-5p in various tissues or cells; most of these verified targets were in accordance with our present prediction. Other predicted targets still need further verification in vivo and in vitro .

  1. Modeling soil erosion and transport on forest landscape

    Science.gov (United States)

    Ge Sun; Steven G McNulty

    1998-01-01

    Century-long studies on the impacts of forest management in North America suggest sediment can cause major reduction on stream water quality. Soil erosion patterns in forest watersheds are patchy and heterogeneous. Therefore, patterns of soil erosion are difficult to model and predict. The objective of this study is to develop a user friendly management tool for land...

  2. Rainfall erosivity in Europe.

    Science.gov (United States)

    Panagos, Panos; Ballabio, Cristiano; Borrelli, Pasquale; Meusburger, Katrin; Klik, Andreas; Rousseva, Svetla; Tadić, Melita Perčec; Michaelides, Silas; Hrabalíková, Michaela; Olsen, Preben; Aalto, Juha; Lakatos, Mónika; Rymszewicz, Anna; Dumitrescu, Alexandru; Beguería, Santiago; Alewell, Christine

    2015-04-01

    Rainfall is one the main drivers of soil erosion. The erosive force of rainfall is expressed as rainfall erosivity. Rainfall erosivity considers the rainfall amount and intensity, and is most commonly expressed as the R-factor in the USLE model and its revised version, RUSLE. At national and continental levels, the scarce availability of data obliges soil erosion modellers to estimate this factor based on rainfall data with only low temporal resolution (daily, monthly, annual averages). The purpose of this study is to assess rainfall erosivity in Europe in the form of the RUSLE R-factor, based on the best available datasets. Data have been collected from 1541 precipitation stations in all European Union (EU) Member States and Switzerland, with temporal resolutions of 5 to 60 min. The R-factor values calculated from precipitation data of different temporal resolutions were normalised to R-factor values with temporal resolutions of 30 min using linear regression functions. Precipitation time series ranged from a minimum of 5 years to a maximum of 40 years. The average time series per precipitation station is around 17.1 years, the most datasets including the first decade of the 21st century. Gaussian Process Regression (GPR) has been used to interpolate the R-factor station values to a European rainfall erosivity map at 1 km resolution. The covariates used for the R-factor interpolation were climatic data (total precipitation, seasonal precipitation, precipitation of driest/wettest months, average temperature), elevation and latitude/longitude. The mean R-factor for the EU plus Switzerland is 722 MJ mm ha(-1) h(-1) yr(-1), with the highest values (>1000 MJ mm ha(-1) h(-1) yr(-1)) in the Mediterranean and alpine regions and the lowest (<500 MJ mm ha(-1) h(-1) yr(-1)) in the Nordic countries. The erosivity density (erosivity normalised to annual precipitation amounts) was also the highest in Mediterranean regions which implies high risk for erosive events and floods

  3. An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer

    Directory of Open Access Journals (Sweden)

    Liang Yu

    2008-12-01

    Full Text Available Abstract Background Patients diagnosed with lung adenocarcinoma (AD and squamous cell carcinoma (SCC, two major histologic subtypes of lung cancer, currently receive similar standard treatments, but resistance to adjuvant chemotherapy is prevalent. Identification of differentially expressed genes marking AD and SCC may prove to be of diagnostic value and help unravel molecular basis of their histogenesis and biologies, and deliver more effective and specific systemic therapy. Methods MiRNA target genes were predicted by union of miRanda, TargetScan, and PicTar, followed by screening for matched gene symbols in NCBI human sequences and Gene Ontology (GO terms using the PANTHER database that was also used for analyzing the significance of biological processes and pathways within each ontology term. Microarray data were extracted from Gene Expression Omnibus repository, and tumor subtype prediction by gene expression used Prediction Analysis of Microarrays. Results Computationally predicted target genes of three microRNAs, miR-34b/34c/449, that were detected in human lung, testis, and fallopian tubes but not in other normal tissues, were filtered by representation of GO terms and their ability to classify lung cancer subtypes, followed by a meta-analysis of microarray data to classify AD and SCC. Expression of a minimal set of 17 predicted miR-34b/34c/449 target genes derived from the developmental process GO category was identified from a training set to classify 41 AD and 17 SCC, and correctly predicted in average 87% of 354 AD and 82% of 282 SCC specimens from total 9 independent published datasets. The accuracy of prediction still remains comparable when classifying 103 AD and 79 SCC samples from another 4 published datasets that have only 14 to 16 of the 17 genes available for prediction (84% and 85% for AD and SCC, respectively. Expression of this signature in two published datasets of epithelial cells obtained at bronchoscopy from cigarette

  4. Novel Methods for Drug-Target Interaction Prediction using Graph Mining

    KAUST Repository

    Ba Alawi, Wail

    2016-01-01

    -target interactions (DTIs) before any experiments are done. However, many of these approaches suffer from unacceptable levels of false positives. We developed two novel methods based on graph mining networks of drugs and targets. The first method (DASPfind) finds all

  5. Mapping Soil Erosion Factors and Potential Erosion Risk for the National Park "Central Balkan"

    Science.gov (United States)

    Ilieva, Diliana; Malinov, Ilia

    2014-05-01

    Soil erosion is widely recognised environmental problem. The report aims at presenting the main results from assessment and mapping of the factors of sheet water erosion and the potential erosion risk on the territory of National Park "Central Balkan". For this purpose, the Universal Soil Loss Equation (USLE) was used for predicting soil loss from erosion. The influence of topography (LS-factor) and soil erodibility (K-factor) was assessed using small-scale topographic and soil maps. Rainfall erosivity (R-factor) was calculated from data of rainfalls with amounts exceeding 9.5 mm from 14 hydro-meteorological stations. The values of the erosion factors (R, K and LS) were presented for the areas of forest, sub-alpine and alpine zones. Using the methods of GIS, maps were plotted presenting the area distribution among the classes of the soil erosion factors and the potential risk in the respective zones. The results can be used for making accurate decisions for soil conservation and sustainable land management in the park.

  6. HuMiTar: A sequence-based method for prediction of human microRNA targets

    Directory of Open Access Journals (Sweden)

    Chen Ke

    2008-12-01

    Full Text Available Abstract Background MicroRNAs (miRs are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to induce mRNA degradation or mRNA cleavage. The ability to perform accurate, high-throughput identification of physiologically active miR targets would enable functional characterization of individual miRs. Current target prediction methods include traditional approaches that are based on specific base-pairing rules in the miR's seed region and implementation of cross-species conservation of the target site, and machine learning (ML methods that explore patterns that contrast true and false miR-mRNA duplexes. However, in the case of the traditional methods research shows that some seed region matches that are conserved are false positives and that some of the experimentally validated target sites are not conserved. Results We present HuMiTar, a computational method for identifying common targets of miRs, which is based on a scoring function that considers base-pairing for both seed and non-seed positions for human miR-mRNA duplexes. Our design shows that certain non-seed miR nucleotides, such as 14, 18, 13, 11, and 17, are characterized by a strong bias towards formation of Watson-Crick pairing. We contrasted HuMiTar with several representative competing methods on two sets of human miR targets and a set of ten glioblastoma oncogenes. Comparison with the two best performing traditional methods, PicTar and TargetScanS, and a representative ML method that considers the non-seed positions, NBmiRTar, shows that HuMiTar predictions include majority of the predictions of the other three methods. At the same time, the proposed method is also capable of finding more true positive targets as a trade-off for an increased number of predictions. Genome-wide predictions show that the proposed method is characterized by 1.99 signal

  7. Development of an Integrated Water and Wind Erosion Model

    Science.gov (United States)

    Flanagan, D. C.; Ascough, J. C.; Wagner, L. E.; Geter, W. F.

    2006-12-01

    Prediction technologies for soil erosion by the forces of wind or water have largely been developed independently from one another, especially within the United States. Much of this has been due to the initial creation of equations and models which were empirical in nature (i.e., Universal Soil Loss Equation, Wind Erosion Equation) and based upon separate water erosion or wind erosion plot and field measurements. Additionally, institutional organizations in place typically divided research efforts and funding to unique wind or water erosion research and modeling projects. However, during the past 20 years computer technologies and erosion modeling have progressed to the point where it is now possible to merge physical process-based computer simulation models into an integrated water and wind erosion prediction system. In a physically- based model, many of the processes which must be simulated for wind and water erosion computations are the same, e.g., climate, water balance, runoff, plant growth, etc. Model components which specifically deal with the wind or water detachment, transport and deposition processes are those that must differ, as well as any necessary parameterization of input variables (e.g., adjusted soil erodibilities, critical shear stresses, etc.) for those components. This presentation describes current efforts towards development of a combined wind and water erosion model, based in part upon technologies present in the Water Erosion Prediction Project (WEPP) and the Wind Erosion Prediction System (WEPS) models. Initial efforts during the past two years have resulted in modular modeling components that allow for prediction of infiltration, surface runoff, and water erosion at a hillslope scale within an Object Modeling System. Additional components currently in development include wind detachment at a single field point, continuous water balance, and unified plant growth. Challenges in this project are many, and include adequate field

  8. Erosion-Oxidation Response of Boiler Grade Steels: A Mathematical Investigation

    Directory of Open Access Journals (Sweden)

    S. K. Das

    2008-01-01

    Full Text Available A ductile erosion model embodying the mechanisms of erosion involving cutting wear and repeated plastic deformation has been developed to predict erosion rates of boiler grade steels. The issue of erosion-oxidation interaction has also been addressed to further predict the mass loss resulted from this composite mechanism. A deterministic formalism for the kinetics of oxide-scale growth and a probabilistic approach to characterize the material loss are employed to describe simultaneous actions of high-temperature oxidation and mechanical erosion. The model predictions are in good agreement with the published data.

  9. Targeted intervention: Computational approaches to elucidate and predict relapse in alcoholism.

    Science.gov (United States)

    Heinz, Andreas; Deserno, Lorenz; Zimmermann, Ulrich S; Smolka, Michael N; Beck, Anne; Schlagenhauf, Florian

    2017-05-01

    Alcohol use disorder (AUD) and addiction in general is characterized by failures of choice resulting in repeated drug intake despite severe negative consequences. Behavioral change is hard to accomplish and relapse after detoxification is common and can be promoted by consumption of small amounts of alcohol as well as exposure to alcohol-associated cues or stress. While those environmental factors contributing to relapse have long been identified, the underlying psychological and neurobiological mechanism on which those factors act are to date incompletely understood. Based on the reinforcing effects of drugs of abuse, animal experiments showed that drug, cue and stress exposure affect Pavlovian and instrumental learning processes, which can increase salience of drug cues and promote habitual drug intake. In humans, computational approaches can help to quantify changes in key learning mechanisms during the development and maintenance of alcohol dependence, e.g. by using sequential decision making in combination with computational modeling to elucidate individual differences in model-free versus more complex, model-based learning strategies and their neurobiological correlates such as prediction error signaling in fronto-striatal circuits. Computational models can also help to explain how alcohol-associated cues trigger relapse: mechanisms such as Pavlovian-to-Instrumental Transfer can quantify to which degree Pavlovian conditioned stimuli can facilitate approach behavior including alcohol seeking and intake. By using generative models of behavioral and neural data, computational approaches can help to quantify individual differences in psychophysiological mechanisms that underlie the development and maintenance of AUD and thus promote targeted intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Coastal Erosion Control Methods

    Science.gov (United States)

    Greene, V.

    2016-12-01

    Coastal erosion is bad because the ecosystem there will be washed away and the animals could drown or be displaced and have to adapt to a new ecosystem that they are not prepared for. I'm interested in this problem because if there aren't beaches when I grow up I won't be able to do the things I would really like to do. I would like to be a marine biologist. Secondly, I don't want to see beach houses washed away. I would like to see people live in harmony with their environment. So, to study ways in which to preserve beaches I will make and use models that test different erosion controls. Two different ideas for erosion control I tested are using seaweed or a rock berm. I think the rock berm will work better than the model of seaweed because the seaweed is under water and the waves can carry the sand over the seaweed, and the rock berm will work better because the rocks will help break the waves up before they reach the shore and the waves can not carry the sand over the rocks that are above the water. To investigate this I got a container to use to model the Gulf of Mexico coastline. I performed several test runs using sand and water in the container to mimic the beach and waves from the Gulf of Mexico hitting the shoreline. I did three trials for the control (no erosion control), seaweed and a rock berm. Rock berms are a border of a raised area of rock. The model for seaweed that I used was plastic shopping bags cut into strips and glued to the bottom of my container to mimic seaweed. My results were that the control had the most erosion which ranged from 2.75 - 3 inches over 3 trials. The seaweed was a little better than the control but was very variable and ranged from 1.5 - 3 inches over 3 trials. The rock berm worked the best out of all at controlling erosion with erosion ranging from 1.5 - 2 inches. My hypothesis was correct because the rock berm did best to control erosion compared to the control which had no erosion control and the model with seaweed.

  11. Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

    Science.gov (United States)

    Basant, Nikita; Gupta, Shikha

    2018-03-01

    The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

  12. Erosivity, surface runoff, and soil erosion estimation using GIS-coupled runoff-erosion model in the Mamuaba catchment, Brazil.

    Science.gov (United States)

    Marques da Silva, Richarde; Guimarães Santos, Celso Augusto; Carneiro de Lima Silva, Valeriano; Pereira e Silva, Leonardo

    2013-11-01

    This study evaluates erosivity, surface runoff generation, and soil erosion rates for Mamuaba catchment, sub-catchment of Gramame River basin (Brazil) by using the ArcView Soil and Water Assessment Tool (AvSWAT) model. Calibration and validation of the model was performed on monthly basis, and it could simulate surface runoff and soil erosion to a good level of accuracy. Daily rainfall data between 1969 and 1989 from six rain gauges were used, and the monthly rainfall erosivity of each station was computed for all the studied years. In order to evaluate the calibration and validation of the model, monthly runoff data between January 1978 and April 1982 from one runoff gauge were used as well. The estimated soil loss rates were also realistic when compared to what can be observed in the field and to results from previous studies around of catchment. The long-term average soil loss was estimated at 9.4 t ha(-1) year(-1); most of the area of the catchment (60%) was predicted to suffer from a low- to moderate-erosion risk (soil erosion was estimated to exceed > 12 t ha(-1) year(-1). Expectedly, estimated soil loss was significantly correlated with measured rainfall and simulated surface runoff. Based on the estimated soil loss rates, the catchment was divided into four priority categories (low, moderate, high and very high) for conservation intervention. The study demonstrates that the AvSWAT model provides a useful tool for soil erosion assessment from catchments and facilitates the planning for a sustainable land management in northeastern Brazil.

  13. Effect of mechanical properties on erosion resistance of ductile materials

    Science.gov (United States)

    Levin, Boris Feliksovih

    Solid particle erosion (SPE) resistance of ductile Fe, Ni, and Co-based alloys as well as commercially pure Ni and Cu was studied. A model for SPE behavior of ductile materials is presented. The model incorporates the mechanical properties of the materials at the deformation conditions associated with SPE process, as well as the evolution of these properties during the erosion induced deformation. An erosion parameter was formulated based on consideration of the energy loss during erosion, and incorporates the material's hardness and toughness at high strain rates. The erosion model predicts that materials combining high hardness and toughness can exhibit good erosion resistance. To measure mechanical properties of materials, high strain rate compression tests using Hopkinson bar technique were conducted at strain rates similar to those during erosion. From these tests, failure strength and strain during erosion were estimated and used to calculate toughness of the materials. The proposed erosion parameter shows good correlation with experimentally measured erosion rates for all tested materials. To analyze subsurface deformation during erosion, microhardness and nanoindentation tests were performed on the cross-sections of the eroded materials and the size of the plastically deformed zone and the increase in materials hardness due to erosion were determined. A nanoindentation method was developed to estimate the restitution coefficient within plastically deformed regions of the eroded samples which provides a measure of the rebounding ability of a material during particle impact. An increase in hardness near the eroded surface led to an increase in restitution coefficient. Also, the stress rates imposed below the eroded surface were comparable to those measured during high strain-rate compression tests (10sp3-10sp4 ssp{-1}). A new parameter, "area under the microhardness curve" was developed that represents the ability of a material to absorb impact energy. By

  14. Rainfall erosivity factor estimation in Republic of Moldova

    Science.gov (United States)

    Castraveš, Tudor; Kuhn, Nikolaus

    2017-04-01

    Rainfall erosivity represents a measure of the erosive force of rainfall. Typically, it is expressed as variable such as the R factor in the Universal Soil Loss Equation (USLE) (Wischmeier and Smith, 1965, 1978) or its derivates. The rainfall erosivity index for a rainfall event (EI30) is calculated from the total kinetic energy and maximum 30 minutes intensity of individual events. However, these data are often unavailable for wide regions and countries. Usually, there are three issues regarding precipitation data: low temporal resolution, low spatial density and limited access to the data. This is especially true for some of postsoviet countries from Eastern Europe, such as Republic of Moldova, where soil erosion is a real and persistent problem (Summer, 2003) and where soils represents the main natural resource of the country. Consequently, researching and managing soil erosion is particularly important. The purpose of this study is to develop a model based on commonly available rainfall data, such as event, daily or monthly amounts, to calculate rainfall erosivity for the territory of Republic of Moldova. Rainfall data collected during 1994-2015 period at 15 meteorological stations in the Republic of Moldova, with 10 minutes temporal resolution, were used to develop and calibrate a model to generate an erosivity map of Moldova. References 1. Summer, W., (2003). Soil erosion in the Republic of Moldova — the importance of institutional arrangements. Erosion Prediction in Ungauged Basins: Integrating Methods and Techniques (Proceedings of symposium HS01 held during IUGG2003 at Sapporo. July 2003). IAHS Publ. no. 279. 2. Wischmeier, W.H., and Smith, D.D. (1965). Predicting rainfall-erosion losses from cropland east of the Rocky Mountains. Agr. Handbook No. 282, U.S. Dept. Agr., Washington, DC 3. Wischmeier, W.H., and Smith, D.D. (1978). Predicting rainfall erosion losses. Agr. handbook No. 537, U.S. Dept. of Agr., Science and Education Administration.

  15. Predicting the Noise of High Power Fluid Targets Using Computational Fluid Dynamics

    Science.gov (United States)

    Moore, Michael; Covrig Dusa, Silviu

    The 2.5 kW liquid hydrogen (LH2) target used in the Qweak parity violation experiment is the highest power LH2 target in the world and the first to be designed with Computational Fluid Dynamics (CFD) at Jefferson Lab. The Qweak experiment determined the weak charge of the proton by measuring the parity-violating elastic scattering asymmetry of longitudinally polarized electrons from unpolarized liquid hydrogen at small momentum transfer (Q2 = 0 . 025 GeV2). This target satisfied the design goals of bench-marked with the Qweak target data. This work is an essential component in future designs of very high power low noise targets like MOLLER (5 kW, target noise asymmetry contribution < 25 ppm) and MESA (4.5 kW).

  16. CFD simulation and experimental analysis of erosion in a slurry tank test rig

    Directory of Open Access Journals (Sweden)

    Bart Hans-Jörg

    2013-04-01

    Full Text Available Erosion occurring in equipment dealing with liquid-solid mixtures such as pipeline parts, slurry pumps, liquid-solid stirred reactors and slurry mixers in various industrial applications results in operational failure and economic costs. A slurry erosion tank test rig is designed and was built to investigate the erosion rates of materials and the influencing parameters such as flow velocity and turbulence, flow angle, solid particle concentration, particles size distribution, hardness and target material properties on the material loss and erosion profiles. In the present study, a computational fluid dynamics (CFD tool is used to simulate the erosion rate of sample plates in the liquid-solid slurry mixture in a cylindrical tank. The predictions were made in a steady state and also transient manner, applying the flow at the room temperature and using water and sand as liquid and solid phases, respectively. The multiple reference frame method (MRF is applied to simulate the flow behavior and liquid-solid interactions in the slurry tank test rig. The MRF method is used since it is less demanding than sliding mesh method (SM and gives satisfactory results. The computational domain is divided into three regions: a rotational or MRF zone containing the mixer, a rotational zone (MRF containing the erosion plates and a static zone (outer liquid zone. It is observed that changing the MRF zone diameter and height causes a very low impact on the results. The simulated results were obtained for two kinds of hard metals namely stainless steel and ST-50 under some various operating conditions and are found in good agreement with the experimental results.

  17. Erosive Lichen Planus.

    Science.gov (United States)

    Mauskar, Melissa

    2017-09-01

    Lichen planus is an inflammatory mucocutaneous condition with a myriad of clinical manifestations. There are 3 forms of lichen planus that effect the vulva: papulosquamous, hypertrophic, and erosive. Erosive lichen planus can progress to vulvar scaring, vaginal stenosis, and squamous cell carcinoma; these long-term sequelae cause sexual distress, depression, and decreased quality of life for patients. Diagnosis is often delayed because of patient embarrassment or clinician misdiagnosis. Early recognition and treatment is essential to decreasing the morbidity of this condition. Multimodal treatment, along with a multidisciplinary approach, will improve outcomes and further clinical advances in studying this condition. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Human amygdala engagement moderated by early life stress exposure is a biobehavioral target for predicting recovery on antidepressants.

    Science.gov (United States)

    Goldstein-Piekarski, Andrea N; Korgaonkar, Mayuresh S; Green, Erin; Suppes, Trisha; Schatzberg, Alan F; Hastie, Trevor; Nemeroff, Charles B; Williams, Leanne M

    2016-10-18

    Amygdala circuitry and early life stress (ELS) are both strongly and independently implicated in the neurobiology of depression. Importantly, animal models have revealed that the contribution of ELS to the development and maintenance of depression is likely a consequence of structural and physiological changes in amygdala circuitry in response to stress hormones. Despite these mechanistic foundations, amygdala engagement and ELS have not been investigated as biobehavioral targets for predicting functional remission in translational human studies of depression. Addressing this question, we integrated human neuroimaging and measurement of ELS within a controlled trial of antidepressant outcomes. Here we demonstrate that the interaction between amygdala activation engaged by emotional stimuli and ELS predicts functional remission on antidepressants with a greater than 80% cross-validated accuracy. Our model suggests that in depressed people with high ELS, the likelihood of remission is highest with greater amygdala reactivity to socially rewarding stimuli, whereas for those with low-ELS exposure, remission is associated with lower amygdala reactivity to both rewarding and threat-related stimuli. This full model predicted functional remission over and above the contribution of demographics, symptom severity, ELS, and amygdala reactivity alone. These findings identify a human target for elucidating the mechanisms of antidepressant functional remission and offer a target for developing novel therapeutics. The results also offer a proof-of-concept for using neuroimaging as a target for guiding neuroscience-informed intervention decisions at the level of the individual person.

  19. Perspective and predictive information in the cockpit as a target acquisition aid

    NARCIS (Netherlands)

    Breda, L. van

    1998-01-01

    In two flight simulation experiments, the potential benefits of 3D perspective) radar displays for situational awareness support were investigated. In the experimental set-up, a target acquisition task was employed in which subjects, flying a fighter aircraft, were required to locate a target that

  20. Predicting success of oligomerized pool engineering (OPEN for zinc finger target site sequences

    Directory of Open Access Journals (Sweden)

    Goodwin Mathew J

    2010-11-01

    Full Text Available Abstract Background Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. Results Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88% and specificity+ (92%, but with reduced ROC AUC (0.77. Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. Conclusion ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function

  1. Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

    Directory of Open Access Journals (Sweden)

    Page Grier P

    2009-03-01

    Full Text Available Abstract Background Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE. The aim of this study was to investigate whether a change in miRNA expression following hypoxia could account for changes in the cellular transcriptome based on currently available miRNA target prediction tools. Methods To identify changes induced by hypoxia, we conducted mRNA- and miRNA-array-based experiments in HT29 cells, and performed comparative analysis of the resulting data sets based on multiple target prediction algorithms. To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output. Results Comparison of miRNAs with predicted mRNA targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA. Conclusion Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways. Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species. The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA predictive algorithms.

  2. Mesh erosion after abdominal sacrocolpopexy.

    Science.gov (United States)

    Kohli, N; Walsh, P M; Roat, T W; Karram, M M

    1998-12-01

    To report our experience with erosion of permanent suture or mesh material after abdominal sacrocolpopexy. A retrospective chart review was performed to identify patients who underwent sacrocolpopexy by the same surgeon over 8 years. Demographic data, operative notes, hospital records, and office charts were reviewed after sacrocolpopexy. Patients with erosion of either suture or mesh were treated initially with conservative therapy followed by surgical intervention as required. Fifty-seven patients underwent sacrocolpopexy using synthetic mesh during the study period. The mean (range) postoperative follow-up was 19.9 (1.3-50) months. Seven patients (12%) had erosions after abdominal sacrocolpopexy with two suture erosions and five mesh erosions. Patients with suture erosion were asymptomatic compared with patients with mesh erosion, who presented with vaginal bleeding or discharge. The mean (+/-standard deviation) time to erosion was 14.0+/-7.7 (range 4-24) months. Both patients with suture erosion were treated conservatively with estrogen cream. All five patients with mesh erosion required transvaginal removal of the mesh. Mesh erosion can follow abdominal sacrocolpopexy over a long time, and usually presents as vaginal bleeding or discharge. Although patients with suture erosion can be managed successfully with conservative treatment, patients with mesh erosion require surgical intervention. Transvaginal removal of the mesh with vaginal advancement appears to be an effective treatment in patients failing conservative management.

  3. T2K Replica Target Hadron Production Measurements in NA61/SHINE and T2K Neutrino Flux Predictions

    CERN Document Server

    AUTHOR|(SzGeCERN)710687

    Accelerator based neutrino experiments generate their neutrino beams by impinging high energy protons on thick targets. The neutrino beam predictions are thus based on modeling the interactions of the beam protons inside the targets. Different hadronic models can be used with different accuracies depending on the energy range of the incident protons and on the target material. Nevertheless, none of the models can be seen as perfectly describing all different interactions. In order to reach high precision neutrino flux predictions, it is thus mandatory to be able to test and constrain the models with hadron production measurements. The T2K experiment in Japan uses the ancillary NA61/SHINE facility at CERN to constrain the production of hadrons resulting from the interactions of proton beam particles impinging on a 90cm long graphite target. Data taken by NA61/SHINE with a 30 GeV proton beam on a thin (4% interaction length) graphite target have been recorded in 2007 and 2009. They have been analysed and extens...

  4. Estimated erosion rate at the SRP burial ground

    International Nuclear Information System (INIS)

    Horton, J.H.; Wilhite, E.L.

    1978-04-01

    The rate of soil erosion at the Savannah River Plant (SRP) burial ground can be calculated by means of the universal soil loss equation. Erosion rates estimated by the equation are more suitable for long-term prediction than those which could be measured with a reasonable effort in field studies. The predicted erosion rate at the SRP burial ground ranges from 0.0007 cm/year under stable forest cover to 0.38 cm/year if farmed with cultivated crops. These values correspond to 170,000 and 320 years, respectively, to expose waste buried 4 ft deep

  5. Erosion of dust aggregates

    NARCIS (Netherlands)

    Seizinger, A.; Krijt, S.; Kley, W.

    2013-01-01

    Aims: The aim of this work is to gain a deeper insight into how much different aggregate types are affected by erosion. Especially, it is important to study the influence of the velocity of the impacting projectiles. We also want to provide models for dust growth in protoplanetary disks with simple

  6. 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...

  7. Bentonite erosion. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Birgersson, Martin; Boergesson, Lennart; Hedstroem, Magnus; Karnland, Ola; Nilsson, Ulf (Clay Technology AB, Lund (Sweden))

    2009-12-15

    Low saline water may reach KBS-3 repository depth, e.g. during periods of glaciation. Under such aqueous conditions, the montmorillonite part of the bentonite buffer might transform into a sol and thereby be transported away with flowing water in fractures. The primary aim with this report is to improve the understanding of the basic principles for this possible montmorillonite particle release. The report includes experimental and theoretical work performed at Clay Technology. Natural bentonite and ion-exchanged purified montmorillonite from three different geographical origins, Wyoming (U.S.), Milos (Greece) and Kutch (India) have been studied. Experimental and/or theoretical investigations have been performed with respect to: - Free swelling ability; - Rheological properties; - Rate of bentonite loss into fractures; - Filtering; - Ion exchange; - Sol formation ability; - Ion diffusion; - Mass loss due to erosion. The performed erosion experiments show that erosion does not occur in a mixed calcium/sodium montmorillonite with at least 20% calcium in exchange positions, when the external solution contains above 4 mM charge equivalents. This result is in agreement with the presented conceptual view of sol formation and measured equilibrium properties in mixed calcium/sodium montmorillonite. The findings imply that the buffer will be stable for non-glacial conditions. However, erosion due to sol formation cannot be ruled out for glacial conditions.

  8. Erosion scenarios for Wellenberg

    International Nuclear Information System (INIS)

    Klemenz, W.

    1993-09-01

    The proposed Wellenberg site for a radioactive waste repository is located between Altzellen in the Engelberger valley and the Oberrickenbach valley, in a thick Valanginian marl series. The marl is generally overlaid with unconsolidated rocks but reaches to the surface in some places. In contrast to the situation in the Oberbauenstock region this marl complex is not protected by an overlying erosion resistant series and exhibits a marked relief. The question therefore arises with respect to the Wellenberg site, to what extent will the marl (i.e. the repository host rock formation) be removed by erosion processes during the 100,000 years interval under consideration and what overburden will remain at the end of this period. This report presents the results of an investigation of the longterm behaviour of the proposed site in respect of those processes of erosion and deposition which can lead to changes in the terrain surface and its location relative to the repository. A wide range of possible scenarios encompassing different developments of climatic conditions during the 100,000 year period of interest, was investigated. In addition to the continuation of the present climate and the occurrence of a new ice age on the scale of the Wuerm glaciation the consequences of altered climatic conditions on erosion removal of the repository overburden were considered. Within the 100,000 year period of interest none of the scenarios considered leads to the exposure of the repository. (author) figs., tabs, refs

  9. Dune erosion above revetments

    NARCIS (Netherlands)

    Van Thiel de Vries, J.S.M.

    2012-01-01

    In a situation with a narrow dune, the dune base can be protected with a revetment to reduce dune erosion during extreme events. To quantify the effects of a revetment on storm impact, the functionality of the numerical storm impact model XBeach (Roelvink et al., 2009) is extended to account for the

  10. Bentonite erosion. Final report

    International Nuclear Information System (INIS)

    Birgersson, Martin; Boergesson, Lennart; Hedstroem, Magnus; Karnland, Ola; Nilsson, Ulf

    2009-12-01

    Low saline water may reach KBS-3 repository depth, e.g. during periods of glaciation. Under such aqueous conditions, the montmorillonite part of the bentonite buffer might transform into a sol and thereby be transported away with flowing water in fractures. The primary aim with this report is to improve the understanding of the basic principles for this possible montmorillonite particle release. The report includes experimental and theoretical work performed at Clay Technology. Natural bentonite and ion-exchanged purified montmorillonite from three different geographical origins, Wyoming (U.S.), Milos (Greece) and Kutch (India) have been studied. Experimental and/or theoretical investigations have been performed with respect to: - Free swelling ability; - Rheological properties; - Rate of bentonite loss into fractures; - Filtering; - Ion exchange; - Sol formation ability; - Ion diffusion; - Mass loss due to erosion. The performed erosion experiments show that erosion does not occur in a mixed calcium/sodium montmorillonite with at least 20% calcium in exchange positions, when the external solution contains above 4 mM charge equivalents. This result is in agreement with the presented conceptual view of sol formation and measured equilibrium properties in mixed calcium/sodium montmorillonite. The findings imply that the buffer will be stable for non-glacial conditions. However, erosion due to sol formation cannot be ruled out for glacial conditions.

  11. Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants

    Science.gov (United States)

    Iqbal, Muhammad S.; Hafeez, Muhammad N.; Wattoo, Javed I.; Ali, Arfan; Sharif, Muhammad N.; Rashid, Bushra; Tabassum, Bushra; Nasir, Idrees A.

    2016-01-01

    Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future. PMID:27683585

  12. Prediction of host-derived miRNAs with the potential to target PVY in potato plants

    Directory of Open Access Journals (Sweden)

    Muhammad Shahzad Iqbal

    2016-09-01

    Full Text Available Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe PVY reduces the yield and quality of potato cultivars. During last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in PVY genome. PVY genome is about 9 thousand nucleotides approximately which transcribes 6 genes CI, NIa, NIb-Pro, HC-Pro, CP and VPg. A total of 343 mature miRNAs were retrieved from miRbase database and searched for their target sequences in PVY genes using minimum free energy (mfe, minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. Identified Potato miRNAs against viral mRNA targets have antiviral activities leading to either translational inhibition by mRNA cleavage/mRNA blockage or both. We have found 86 miRNAs targeting PVY genome at 151 different sites on PVY genome. Moreover, only 36 miRNA potentially targeted the PVY genome at 101 loci. CI gene of PVY genome was targeted by 32 miRNAs followed by complementarity by 26, 19, 18, 16 and 13 miRNAs respectively. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h and miR5303d could target CI, NIa, NIb-Pro, HC-Pro, CP and VPg genes of PVY. The predicted miRNAs can be used for development of PVY resistant potato crops in future.

  13. Categorization of erosion control matting.

    Science.gov (United States)

    2012-05-29

    Erosion control is a critical aspect of any Georgia Department of Transportation (GDOT) : construction project, with the extreme negative impacts of high sediment loads in natural : waterways having been well documented. A variety of erosion control ...

  14. Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion

    Science.gov (United States)

    Fox, G. A.; Sheshukov, A.; Cruse, R.; Kolar, R. L.; Guertault, L.; Gesch, K. R.; Dutnell, R. C.

    2016-05-01

    The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

  15. Phosphoproteomic analysis for the identification of predictive molecular factors and new molecular targets in breast, colorectal, ovary, and lung cancer

    International Nuclear Information System (INIS)

    Belluco, C.; De Paoli, P.

    2009-01-01

    Neoadjuvant chemotherapy is a standard therapeutic approach for several types of locally advanced and metastatic tumors. Molecular factors predictive of response to therapy are highly needed for exploiting the potential benefit of properative chemotherapy. Moreover, neoadjuvant chemotherapy represents an ideal clinical model for studying predictive factors since it allows to obtain pre-treatment tissue biopsies which can be analyzed and the results compared to clinical and pathological response. Protein kinases represent some of the most important drug targets in medicine today and their aberrant activation are involved in many disease processes including cancer development and progression

  16. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

    Science.gov (United States)

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

  17. Supplementary Material for: DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail; Soufan, Othman; Essack, Magbubah; Kalnis, Panos; Bajic, Vladimir B.

    2016-01-01

    Abstract Background Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient computational

  18. In vitro Perturbations of Targets in Cancer Hallmark Processes Predict Rodent Chemical Carcinogenesis

    Science.gov (United States)

    Thousands of untested chemicals in the environment require efficient characterization of carcinogenic potential in humans. A proposed solution is rapid testing of chemicals using in vitro high-throughput screening (HTS) assays for targets in pathways linked to disease processes ...

  19. Impacts of Climate Change on Soil Erosion in the Great Lakes Region

    Directory of Open Access Journals (Sweden)

    Lili Wang

    2018-06-01

    Full Text Available Quantifying changes in potential soil erosion under projections of changing climate is important for the sustainable management of land resources, as soil loss estimates will be helpful in identifying areas susceptible to erosion, targeting future erosion control efforts, and/or conservation funding. Therefore, the macro-scale Variable Infiltration Capacity—Water Erosion Prediction Project (VIC-WEPP soil erosion model was utilized to quantify soil losses under three climate change scenarios (A2, A1B, B1 using projections from three general circulation models (GFDL, PCM, HadCM3 for the Great Lakes region from 2000 to 2100. Soil loss was predicted to decrease throughout three future periods (2030s, 2060s, and 2090s by 0.4–0.7 ton ha−1 year−1 (4.99–23.2% relative to the historical period (2000s with predicted air temperature increases of 0.68–4.34 °C and precipitation increases of 1.74–63.7 mm year−1 (0.23–8.6%. In the forested northern study domain erosion kept increasing by 0.01–0.18 ton ha−1 year−1 over three future periods due to increased precipitation of 9.7–68.3 mm year−1. The southern study domain covered by cropland and grassland had predicted soil loss decreases of 0.01–1.43 ton ha−1 year−1 due to air temperature increases of 1.75–4.79 °C and reduced precipitation in the summer. Fall and winter had greater risks of increased soil loss based on predictions for these two seasons under the A2 scenario, with the greatest cropland soil loss increase due to increased fall precipitation, and combined effects of increases in both precipitation and air temperature in the winter. Fall was identified with higher risks under the A1B scenario, while spring and summer were identified with the greatest risk of increased soil losses under the B1 scenario due to the increases in both precipitation and air temperature.

  20. Combining on-chip synthesis of a focused combinatorial library with computational target prediction reveals imidazopyridine GPCR ligands.

    Science.gov (United States)

    Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra; Schneider, Gisbert

    2014-01-07

    Using the example of the Ugi three-component reaction we report a fast and efficient microfluidic-assisted entry into the imidazopyridine scaffold, where building block prioritization was coupled to a new computational method for predicting ligand-target associations. We identified an innovative GPCR-modulating combinatorial chemotype featuring ligand-efficient adenosine A1/2B and adrenergic α1A/B receptor antagonists. Our results suggest the tight integration of microfluidics-assisted synthesis with computer-based target prediction as a viable approach to rapidly generate bioactivity-focused combinatorial compound libraries with high success rates. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Are predictions of cancer response to targeted drugs, based on effects in unrelated tissues, the 'Black Swan' events?

    Science.gov (United States)

    Kurbel, Beatrica; Golem, Ante Zvonimir; Kurbel, Sven

    2015-01-01

    Adverse effects of targeted drugs on normal tissues can predict the cancer response. Rash correlates with efficacy of erlotinib, cetuximab and gefitinib and onset of arterial hypertension with response to bevacizumab, sunitinib, axitinib and sorafenib, possible examples of 'Black Swan' events, unexpected scientific observations, as described by Karl Popper in 1935. The proposition is that our patients have individual intrinsic variants of cell growth control, important for tumor response and adverse effects on tumor-unrelated tissue. This means that the lack of predictive side effects in healthy tissue is linked with poor results of tumor therapy when tumor resistance is caused by mechanisms that protect all cells of that patient from the targeted drug effects.

  2. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.

    Directory of Open Access Journals (Sweden)

    Manuel Stemmer

    Full Text Available Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

  3. Analysis of C-MOD molybdenum divertor erosion and code/data comparison

    Energy Technology Data Exchange (ETDEWEB)

    Brooks, J.N., E-mail: brooksjn@purdue.edu [Purdue University, West Lafayette, IN (United States); Allain, J.P. [Purdue University, West Lafayette, IN (United States); Whyte, D.G.; Ochoukov, R.; Lipschultz, B. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    2011-08-01

    We analyze an important 15 year old Alcator C-MOD study of campaign-integrated molybdenum divertor erosion in which the measured net erosion was significantly higher ({approx}X3) than originally predicted by a simple model . We perform full process sputtering erosion/redeposition computational analysis including the effect of a possible RF induced sheath. The simulations show that most sputtered Mo atoms are ionized close to the surface and strongly redeposited, via Lorentz force motion and collisional friction with the high density incoming plasma. The predicted gross erosion profile is a reasonable match to MoI influx data, however, the critically important net erosion comparison with post-exposure Mo tile analysis is poor, with {approx}X10 higher peak erosion measured than computed. An RF sheath increases predicted erosion by {approx}45%, thus being significant but not fundamental. We plan future analysis.

  4. Quantitative PET Imaging with Novel HER3 Targeted Peptides Selected by Phage Display to Predict Androgen Independent Prostate Cancer Progression

    Science.gov (United States)

    2017-08-01

    Independent Prostate Cancer Progression PRINCIPAL INVESTIGATOR: Benjamin Larimer, PhD CONTRACTING ORGANIZATION: Massachusetts General Hospital Boston...3. DATES COVERED 1 Aug 2016 – 31 July 2017 4. TITLE AND SUBTITLE Cancer Progression 5a. CONTRACT NUMBER Quantitative PET Imaging with Novel HER3...Targeted Peptides Selected by Phage Display to Predict Androgen-Independent Prostate Cancer Progression 5b. GRANT NUMBER W81XWH-16-1-0447 5c

  5. Using remote sensing data to predict road fill areas and areas affected by fill erosion with planned forest road construction: a case study in Kastamonu Regional Forest Directorate (Turkey).

    Science.gov (United States)

    Aricak, Burak

    2015-07-01

    Forest roads are essential for transport in managed forests, yet road construction causes environmental disturbance, both in the surface area the road covers and in erosion and downslope deposition of road fill material. The factors affecting the deposition distance of eroded road fill are the slope gradient and the density of plant cover. Thus, it is important to take these factors into consideration during road planning to minimize their disturbance. The aim of this study was to use remote sensing and field surveying to predict the locations that would be affected by downslope deposition of eroding road fill and to compile the data into a geographic information system (GIS) database. The construction of 99,500 m of forest roads is proposed for the Kastamonu Regional Forest Directorate in Turkey. Using GeoEye satellite images and a digital elevation model (DEM) for the region, the location and extent of downslope deposition of road fill were determined for the roads as planned. It was found that if the proposed roads were constructed by excavators, the fill material would cover 910,621 m(2) and the affected surface area would be 1,302,740 m(2). Application of the method used here can minimize the adverse effects of forest roads.

  6. The Search for Biosignatures on Mars: Using Predictive Geology to Optimize Exploration Targets

    Science.gov (United States)

    Oehler, Dorothy Z.; Allen, Carlton C.

    2011-01-01

    Predicting geologic context from satellite data is a method used on Earth for exploration in areas with limited ground truth. The method can be used to predict facies likely to contain organic-rich shales. Such shales concentrate and preserve organics and are major repositories of organic biosignatures on Earth [1]. Since current surface conditions on Mars are unfavorable for development of abundant life or for preservation of organic remains of past life, the chances are low of encountering organics in surface samples. Thus, focusing martian exploration on sites predicted to contain organic-rich shales would optimize the chances of discovering evidence of life, if it ever existed on that planet.

  7. Erosion Modeling of the High Contraction Chromium Plated Crusader Gun System

    National Research Council Canada - National Science Library

    Sopok, S

    2003-01-01

    Thermal-chemical- mechanical erosion modeling predictions are given for the high contraction chromium plated Crusader gun system based on extensive cannon firing, inspection, characterization, and experimental data...

  8. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

    Science.gov (United States)

    Mitra, A K; Mukherjee, U K; Harding, T; Jang, J S; Stessman, H; Li, Y; Abyzov, A; Jen, J; Kumar, S; Rajkumar, V; Van Ness, B

    2016-05-01

    Multiple myeloma (MM) is characterized by significant genetic diversity at subclonal levels that have a defining role in the heterogeneity of tumor progression, clinical aggressiveness and drug sensitivity. Although genome profiling studies have demonstrated heterogeneity in subclonal architecture that may ultimately lead to relapse, a gene expression-based prediction program that can identify, distinguish and quantify drug response in sub-populations within a bulk population of myeloma cells is lacking. In this study, we performed targeted transcriptome analysis on 528 pre-treatment single cells from 11 myeloma cell lines and 418 single cells from 8 drug-naïve MM patients, followed by intensive bioinformatics and statistical analysis for prediction of proteasome inhibitor sensitivity in individual cells. Using our previously reported drug response gene expression profile signature at the single-cell level, we developed an R Statistical analysis package available at https://github.com/bvnlabSCATTome, SCATTome (single-cell analysis of targeted transcriptome), that restructures the data obtained from Fluidigm single-cell quantitative real-time-PCR analysis run, filters missing data, performs scaling of filtered data, builds classification models and predicts drug response of individual cells based on targeted transcriptome using an assortment of machine learning methods. Application of SCATT should contribute to clinically relevant analysis of intratumor heterogeneity, and better inform drug choices based on subclonal cellular responses.

  9. Prediction of Bispectral Index during Target-controlled Infusion of Propofol and Remifentanil: A Deep Learning Approach.

    Science.gov (United States)

    Lee, Hyung-Chul; Ryu, Ho-Geol; Chung, Eun-Jin; Jung, Chul-Woo

    2018-03-01

    The discrepancy between predicted effect-site concentration and measured bispectral index is problematic during intravenous anesthesia with target-controlled infusion of propofol and remifentanil. We hypothesized that bispectral index during total intravenous anesthesia would be more accurately predicted by a deep learning approach. Long short-term memory and the feed-forward neural network were sequenced to simulate the pharmacokinetic and pharmacodynamic parts of an empirical model, respectively, to predict intraoperative bispectral index during combined use of propofol and remifentanil. Inputs of long short-term memory were infusion histories of propofol and remifentanil, which were retrieved from target-controlled infusion pumps for 1,800 s at 10-s intervals. Inputs of the feed-forward network were the outputs of long short-term memory and demographic data such as age, sex, weight, and height. The final output of the feed-forward network was the bispectral index. The performance of bispectral index prediction was compared between the deep learning model and previously reported response surface model. The model hyperparameters comprised 8 memory cells in the long short-term memory layer and 16 nodes in the hidden layer of the feed-forward network. The model training and testing were performed with separate data sets of 131 and 100 cases. The concordance correlation coefficient (95% CI) were 0.561 (0.560 to 0.562) in the deep learning model, which was significantly larger than that in the response surface model (0.265 [0.263 to 0.266], P deep learning model-predicted bispectral index during target-controlled infusion of propofol and remifentanil more accurately compared to the traditional model. The deep learning approach in anesthetic pharmacology seems promising because of its excellent performance and extensibility.

  10. Soil erosion in Iran: Issues and solutions

    Science.gov (United States)

    Hamidreza Sadeghi, Seyed; Cerdà, Artemi

    2015-04-01

    Iran currently faces many soil erosion-related problems (see citations below). These issues are resulted from some inherent characteristic and anthropogenic triggering forces. Nowadays, the latter plays more important rule to accelerate the erosion with further emphasis on soil erosion-prone arid and semi arid regions of the country. This contribution attempts to identify and describe the existing main reasons behind accelerated soil erosion in Iran. Appropriate solutions viz. structural and non-structural approaches will be then advised to combat or minimise the problems. Iran can be used as a pilot research site to understand the soil erosion processes in semiarid, arid and mountainous terrain and our research will review the scientific literature and will give an insight of the soil erosion rates in the main factors of the soil erosion in Iran. Key words: Anthropogenic Erosion, Land Degradation; Sediment Management; Sediment Problems Acknowledgements The research projects GL2008-02879/BTE, LEDDRA 243857 and PREVENTING AND REMEDIATING DEGRADATION OF SOILS IN EUROPE THROUGH LAND CARE (RECARE)FP7-ENV-2013- supported this research. References Aghili Nategh, N., Hemmat, A., & Sadeghi, M. (2014). Assessing confined and semi-confined compression curves of highly calcareous remolded soil amended with farmyard manure. Journal of Terramechanics, 53, 75-82. Arekhi, S., Bolourani, A. D., Shabani, A., Fathizad, H., Ahamdy-Asbchin, S. 2012. Mapping Soil Erosion and Sediment Yield Susceptibility using RUSLE, Remote Sensing and GIS (Case study: Cham Gardalan Watershed, Iran). Advances in Environmental Biology, 6(1), 109-124. Arekhi, S., Shabani, A., Rostamizad, G. 2012. Application of the modified universal soil loss equation (MUSLE) in prediction of sediment yield (Case study: Kengir Watershed, Iran). Arabian Journal of Geosciences, 5(6), 1259-1267.Sadeghi, S. H., Moosavi, V., Karami, A., Behnia, N. 2012. Soil erosion assessment and prioritization of affecting factors at plot

  11. Molecular Imaging to Predict Response to Targeted Therapies in Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Ingrid Leguerney

    2017-01-01

    Full Text Available Molecular magnetic resonance imaging targeted to an endothelial integrin involved in neoangiogenesis was compared to DCE-US and immunochemistry to assess the early response of three different therapeutic agents in renal cell carcinoma. Human A498 renal cells carcinoma was subcutaneously inoculated into 24 nude mice. Mice received either phosphate-buffered saline solution, sunitinib, everolimus, or bevacizumab during 4 days. DCE-US and molecular MRI targeting αvβ3 were performed at baseline and 4 days after treatment initiation. PI, AUC, relaxation rate variations ΔR2⁎, and percentage of vessels area quantified on CD31-stained microvessels were compared. Significant decreases were observed for PI and AUC parameters measured by DCE-US for bevacizumab group as early as 4 days, whereas molecular αvβ3-targeted MRI was able to detect significant changes in both bevacizumab and everolimus groups. Percentage of CD31-stained microvessels was significantly correlated with DCE-US parameters, PI (R=0.87, p=0.0003 and AUC (R=0.81, p=0.0013. The percentage of vessel tissue area was significantly reduced (p<0.01 in both sunitinib and bevacizumab groups. We report an early detection of neoangiogenesis modification after induction of targeted therapies, using DCE-US or αvβ3-targeted MRI. We consider these outcomes should encourage clinical trial developments to further evaluate the potential of this molecular MRI technique.

  12. Calculation of attainable superheats and predicted embryonic flux rates in commercial water isotope targets

    International Nuclear Information System (INIS)

    Alvord, Charles W.; Ruggles, Arthur E.; West, Colin D.

    2008-01-01

    Phase change in a fluid subject to a large spectrum of radiations is examined. The statistical variation in the fluid energy is considered in concert with the radiation field attributes to establish conditions for spinodal decomposition and bulk nucleation. This approach is developed in general and carried forward for the specific case of 18 O-enriched water used in commercial targets for the production of 18 F. Sensitivities of the outcome to specific attributes of the fluid state model are examined. The possibility for very high bulk nucleation site densities is exposed and may explain the observed thermal-fluid behavior in commercial water targets. These targets operate at elevated pressure and temperatures at and in excess of the saturation temperature. They are also subjected to a large spectrum of radiations, with differing levels of energy deposition. The conditions for spinodal decomposition and bulk nucleation (with and without radiation) in these targets are evaluated. It is likely that some bulk nucleation is occurring, and causing the density reduction locally in the target. Suitable experiments to evaluate this potential are more fully possible

  13. Soil erodibility for water erosion: A perspective and Chinese experiences

    Science.gov (United States)

    Wang, Bin; Zheng, Fenli; Römkens, Mathias J. M.; Darboux, Frédéric

    2013-04-01

    Knowledge of soil erodibility is an essential requirement for erosion prediction, conservation planning, and the assessment of sediment related environmental effects of watershed agricultural practices. This paper reviews the status of soil erodibility evaluations and determinations based on 80 years of upland area erosion research mainly in China and the USA. The review synthesizes the general research progress made by discussing the basic concepts of erodibility and its evaluation, determination, and prediction as well as knowledge of its spatio-temporal variations. The authors found that soil erodibility is often inappropriately or inaccurately applied in describing soil loss caused by different soil erosion component processes and mechanisms. Soil erodibility indicators were related to intrinsic soil properties and exogenic erosional forces, measurements, and calculations. The present review describes major needs including: (1) improved definition of erodibility, (2) modified erodibility determinations in erosion models, especially for specific geographical locations and in the context of different erosion sub-processes, (3) advanced methodologies for quantifying erodibilities of different soil erosion sub-processes, and (4) a better understanding of the mechanism that causes temporal variations in soil erodibility. The review also provides a more rational basis for future research on soil erodibility and supports predictive modeling of soil erosion processes and the development of improved conservation practices.

  14. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity.

    Science.gov (United States)

    Penrod, Nadia M; Greene, Casey S; Moore, Jason H

    2014-01-01

    Molecularly targeted drugs promise a safer and more effective treatment modality than conventional chemotherapy for cancer patients. However, tumors are dynamic systems that readily adapt to these agents activating alternative survival pathways as they evolve resistant phenotypes. Combination therapies can overcome resistance but finding the optimal combinations efficiently presents a formidable challenge. Here we introduce a new paradigm for the design of combination therapy treatment strategies that exploits the tumor adaptive process to identify context-dependent essential genes as druggable targets. We have developed a framework to mine high-throughput transcriptomic data, based on differential coexpression and Pareto optimization, to investigate drug-induced tumor adaptation. We use this approach to identify tumor-essential genes as druggable candidates. We apply our method to a set of ER(+) breast tumor samples, collected before (n = 58) and after (n = 60) neoadjuvant treatment with the aromatase inhibitor letrozole, to prioritize genes as targets for combination therapy with letrozole treatment. We validate letrozole-induced tumor adaptation through coexpression and pathway analyses in an independent data set (n = 18). We find pervasive differential coexpression between the untreated and letrozole-treated tumor samples as evidence of letrozole-induced tumor adaptation. Based on patterns of coexpression, we identify ten genes as potential candidates for combination therapy with letrozole including EPCAM, a letrozole-induced essential gene and a target to which drugs have already been developed as cancer therapeutics. Through replication, we validate six letrozole-induced coexpression relationships and confirm the epithelial-to-mesenchymal transition as a process that is upregulated in the residual tumor samples following letrozole treatment. To derive the greatest benefit from molecularly targeted drugs it is critical to design combination

  15. Macroscopic erosion of divertor and first wall armour in future tokamaks

    Science.gov (United States)

    Würz, H.; Bazylev, B.; Landman, I.; Pestchanyi, S.; Safronov, V.

    2002-12-01

    Sputtering, evaporation and macroscopic erosion determine the lifetime of the 'in vessel' armour materials CFC, tungsten and beryllium presently under discussion for future tokamaks. For CFC armour macroscopic erosion means brittle destruction and dust formation whereas for metallic armour melt layer erosion by melt motion and droplet splashing. Available results on macroscopic erosion from hot plasma and e-beam simulation experiments and from tokamaks are critically evaluated and a comprehensive discussion of experimental and numerical macroscopic erosion and its extrapolation to future tokamaks is given. Shielding of divertor armour materials by their own vapor exists during plasma disruptions. The evolving plasma shield protects the armour from high heat loads, absorbs the incoming energy and reradiates it volumetrically thus reducing drastically the deposited energy. As a result, vertical target erosion by vaporization turns out to be of the order of a few microns per disruption event and macroscopic erosion becomes the dominant erosion source.

  16. Macroscopic erosion of divertor and first wall armour in future tokamaks

    International Nuclear Information System (INIS)

    Wuerz, H.; Bazylev, B.; Landman, I.; Pestchanyi, S.; Safronov, V.

    2002-01-01

    Sputtering, evaporation and macroscopic erosion determine the lifetime of the 'in vessel' armour materials CFC, tungsten and beryllium presently under discussion for future tokamaks. For CFC armour macroscopic erosion means brittle destruction and dust formation whereas for metallic armour melt layer erosion by melt motion and droplet splashing. Available results on macroscopic erosion from hot plasma and e-beam simulation experiments and from tokamaks are critically evaluated and a comprehensive discussion of experimental and numerical macroscopic erosion and its extrapolation to future tokamaks is given. Shielding of divertor armour materials by their own vapor exists during plasma disruptions. The evolving plasma shield protects the armour from high heat loads, absorbs the incoming energy and reradiates it volumetrically thus reducing drastically the deposited energy. As a result, vertical target erosion by vaporization turns out to be of the order of a few microns per disruption event and macroscopic erosion becomes the dominant erosion source

  17. Critical Source Area Delineation: The representation of hydrology in effective erosion modeling.

    Science.gov (United States)

    Fowler, A.; Boll, J.; Brooks, E. S.; Boylan, R. D.

    2017-12-01

    Despite decades of conservation and millions of conservation dollars, nonpoint source sediment loading associated with agricultural disturbance continues to be a significant problem in many parts of the world. Local and national conservation organizations are interested in targeting critical source areas for control strategy implementation. Currently, conservation practices are selected and located based on the Revised Universal Soil Loss Equation (RUSLE) hillslope erosion modeling, and the National Resource Conservation Service will soon be transiting to the Watershed Erosion Predict Project (WEPP) model for the same purpose. We present an assessment of critical source areas targeted with RUSLE, WEPP and a regionally validated hydrology model, the Soil Moisture Routing (SMR) model, to compare the location of critical areas for sediment loading and the effectiveness of control strategies. The three models are compared for the Palouse dryland cropping region of the inland northwest, with un-calibrated analyses of the Kamiache watershed using publicly available soils, land-use and long-term simulated climate data. Critical source areas were mapped and the side-by-side comparison exposes the differences in the location and timing of runoff and erosion predictions. RUSLE results appear most sensitive to slope driving processes associated with infiltration excess. SMR captured saturation excess driven runoff events located at the toe slope position, while WEPP was able to capture both infiltration excess and saturation excess processes depending on soil type and management. A methodology is presented for down-scaling basin level screening to the hillslope management scale for local control strategies. Information on the location of runoff and erosion, driven by the runoff mechanism, is critical for effective treatment and conservation.

  18. Bayesian Nonparametric Estimation of Targeted Agent Effects on Biomarker Change to Predict Clinical Outcome

    Science.gov (United States)

    Graziani, Rebecca; Guindani, Michele; Thall, Peter F.

    2015-01-01

    Summary The effect of a targeted agent on a cancer patient's clinical outcome putatively is mediated through the agent's effect on one or more early biological events. This is motivated by pre-clinical experiments with cells or animals that identify such events, represented by binary or quantitative biomarkers. When evaluating targeted agents in humans, central questions are whether the distribution of a targeted biomarker changes following treatment, the nature and magnitude of this change, and whether it is associated with clinical outcome. Major difficulties in estimating these effects are that a biomarker's distribution may be complex, vary substantially between patients, and have complicated relationships with clinical outcomes. We present a probabilistically coherent framework for modeling and estimation in this setting, including a hierarchical Bayesian nonparametric mixture model for biomarkers that we use to define a functional profile of pre-versus-post treatment biomarker distribution change. The functional is similar to the receiver operating characteristic used in diagnostic testing. The hierarchical model yields clusters of individual patient biomarker profile functionals, and we use the profile as a covariate in a regression model for clinical outcome. The methodology is illustrated by analysis of a dataset from a clinical trial in prostate cancer using imatinib to target platelet-derived growth factor, with the clinical aim to improve progression-free survival time. PMID:25319212

  19. Perceptual load vs. dilution: the roles of attentional focus, stimulus category, and target predictability

    Directory of Open Access Journals (Sweden)

    Zhe eChen

    2013-06-01

    Full Text Available Many studies have shown that increasing the number of neutral stimuli in a display decreases distractor interference. This result has been interpreted within two different frameworks; a perceptual load account, based on a reduction in spare resources, and a dilution account, based on a degradation in distractor representation and/or an increase in crosstalk between the distractor and the neutral stimuli that contain visually similar features. In four experiments, we systematically manipulated the extent of attentional focus, stimulus category, and preknowledge of the target to examine how these factors would interact with the display set size to influence the degree of distractor processing. Display set size did not affect the degree of distractor processing in all situations. Increasing the number of neutral items decreased distractor processing only when a task induced a broad attentional focus that included the neutral stimuli, when the neutral stimuli were in the same category as the target and distractor, and when the preknowledge of the target was insufficient to guide attention to the target efficiently. These results suggest that the effect of neutral stimuli on the degree of distractor processing is more complex than previously assumed. They provide new insight into the competitive interactions between bottom-up and top-down processes that govern the efficiency of visual selective attention.

  20. Perceptual load vs. dilution: the roles of attentional focus, stimulus category, and target predictability.

    Science.gov (United States)

    Chen, Zhe; Cave, Kyle R

    2013-01-01

    Many studies have shown that increasing the number of neutral stimuli in a display decreases distractor interference. This result has been interpreted within two different frameworks; a perceptual load account, based on a reduction in spare resources, and a dilution account, based on a degradation in distractor representation and/or an increase in crosstalk between the distractor and the neutral stimuli that contain visually similar features. In four experiments, we systematically manipulated the extent of attentional focus, stimulus category, and preknowledge of the target to examine how these factors would interact with the display set size to influence the degree of distractor processing. Display set size did not affect the degree of distractor processing in all situations. Increasing the number of neutral items decreased distractor processing only when a task induced a broad attentional focus that included the neutral stimuli, when the neutral stimuli were in the same category as the target and distractor, and when the preknowledge of the target was insufficient to guide attention to the target efficiently. These results suggest that the effect of neutral stimuli on the degree of distractor processing is more complex than previously assumed. They provide new insight into the competitive interactions between bottom-up and top-down processes that govern the efficiency of visual selective attention.

  1. TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM.

    Science.gov (United States)

    Hu, Jun; Han, Ke; Li, Yang; Yang, Jing-Yu; Shen, Hong-Bin; Yu, Dong-Jun

    2016-11-01

    The accurate prediction of whether a protein will crystallize plays a crucial role in improving the success rate of protein crystallization projects. A common critical problem in the development of machine-learning-based protein crystallization predictors is how to effectively utilize protein features extracted from different views. In this study, we aimed to improve the efficiency of fusing multi-view protein features by proposing a new two-layered SVM (2L-SVM) which switches the feature-level fusion problem to a decision-level fusion problem: the SVMs in the 1st layer of the 2L-SVM are trained on each of the multi-view feature sets; then, the outputs of the 1st layer SVMs, which are the "intermediate" decisions made based on the respective feature sets, are further ensembled by a 2nd layer SVM. Based on the proposed 2L-SVM, we implemented a sequence-based protein crystallization predictor called TargetCrys. Experimental results on several benchmark datasets demonstrated the efficacy of the proposed 2L-SVM for fusing multi-view features. We also compared TargetCrys with existing sequence-based protein crystallization predictors and demonstrated that the proposed TargetCrys outperformed most of the existing predictors and is competitive with the state-of-the-art predictors. The TargetCrys webserver and datasets used in this study are freely available for academic use at: http://csbio.njust.edu.cn/bioinf/TargetCrys .

  2. Rainfall erosivity map for Ghana

    International Nuclear Information System (INIS)

    Oduro Afriyie, K.

    1995-10-01

    Monthly rainfall data, spanning over a period of more than thirty years, were used to compute rainfall erosivity indices for various stations in Ghana, using the Fournier index, c, defined as p 2 /P, where p is the rainfall amount in the wettest month and P is the annual rainfall amount. Values of the rainfall erosivity indices ranged from 24.5 mm at Sunyani in the mid-portion of Ghana to 180.9 mm at Axim in the south western coastal portion. The indices were used to construct a rainfall erosivity map for the country. The map revealed that Ghana may be broadly divided into five major erosion risk zones. The middle sector of Ghana is generally in the low erosion risk zone; the northern sector is in the moderate to severe erosion risk zone, while the coastal sector is in the severe to extreme severe erosion risk zone. (author). 11 refs, 1 fig., 1 tab

  3. Fundamental study on cavitation erosion in liquid metal. Effect of liquid parameter on cavitation erosion in liquid metals (Joint research)

    International Nuclear Information System (INIS)

    Hattori, Shuji; Kurachi, Hiroaki; Inoue, Fumitaka; Watashi, Katsumi; Tsukimori, Kazuyuki; Yada, Hiroki; Hashimoto, Takashi

    2009-02-01

    Cavitation erosion, which possibly occurs on the surfaces of fluid machineries and components contacting flowing liquid and causes sponge-like damage on the material surface, is important problem, since it may become the cause of performance deduction, life shortening, noise, vibration of mechanical components and moreover failure of machine. Research on cavitation erosion in liquid metal is very important to confirm the safety of fast breeder reactor using sodium coolant and to avoid serious damage of the target vessel of spallation neutron source containing liquid-mercury. But the research on cavitation erosion in liquid metal has been hardly performed because of its specially in comparison with that in water. In this study, a cavitation erosion test apparatus was developed to carry out the erosion tests in low-temperature liquid metals. Cavitation erosion tests were carried out in liquid lead-bismuth alloy and in deionized water. We discuss the effect of liquid parameters and temperature effects on the erosion rate. We reach to the following conclusions. The erosion rate was evaluated in terms of a relative temperature which was defind as the percentage between freezing and boiling points. At 14degC relative temperature, the erosion rate is 10 times in lead-bismuth alloy, and 2 to 5 times in sodium, compared with that in deionized water. At 14degC relative temperature, the erosion rate can be evaluated in terms of the following parameter. 1 / (1/ρ L /C L +1/ρ S C S )√ρ L . Where ρ is the material density and c is the velocity of sound, L and S denote liquid and solid. In the relative temperature between 14 and 30degC, the temperature dependence on the erosion rate is due to the increase in vapor pressure. (author)

  4. A program to Evaluate the Erosion on the CFC tiles of the ITER Divertor

    International Nuclear Information System (INIS)

    DAgata, E.; Tivey, R.; Ogorodnikova, O.; Lowry, Ch.; Schlosser, J.

    2006-01-01

    The plasma-facing surfaces of the ITER divertor are armoured with tungsten in the upper part of the inner and outer vertical targets and carbon-fibre composite (CFC) in the lower part, the region where the scrape-off layer intercepts the divertor. The CFC in the form of a monoblock in the vertical target is the most loaded part of the plasma-facing surfaces, and hence it is subjected to high erosion and has a significant risk of failure. A program has been developed with the aim of understanding the impact on the erosion lifetime and on the probability of a critical heat flux event in the heat sink of a combination of two main effects: the material property variations (particularly pronounced in CFC) and the presence of joining defects. The software allows the evolution of the surface profile of the armour to be predicted and the margin on critical heat flux at the heat-sink-to-coolant interface to be estimated for a range of postulated defects, for start-of-life through to end-of-life of the component. In assessing erosion, the code takes account of geometry and sublimation, and physical and chemical erosion of the CFC armour. The code allows the computation of the effect of normal and off-normal (ELMs, etc.) operation. The incident angle (a glancing angle of a few degrees) of the particle and heat flux onto the target is taken into account. The program has been validated by comparison with analytical approximations and experimental data. The code has been developed in APDL language to operate inside a commercial and certificate finite element program such as ANSYS. (author)

  5. A Mechanistic Model of Waterfall Plunge Pool Erosion into Bedrock

    Science.gov (United States)

    Scheingross, Joel S.; Lamb, Michael P.

    2017-11-01

    Landscapes often respond to changes in climate and tectonics through the formation and upstream propagation of knickzones composed of waterfalls. Little work has been done on the mechanics of waterfall erosion, and instead most landscape-scale models neglect waterfalls or use rules for river erosion, such as stream power, that may not be applicable to waterfalls. Here we develop a physically based model to predict waterfall plunge pool erosion into rock by abrasion from particle impacts and test the model against flume experiments. Both the model and experiments show that evolving plunge pools have initially high vertical erosion rates due to energetic particle impacts, and erosion slows and eventually ceases as pools deepen and deposition protects the pool floor from further erosion. Lateral erosion can continue after deposition on the pool floor, but it occurs at slow rates that become negligible as pools widen. Our work points to the importance of vertical drilling of successive plunge pools to drive upstream knickzone propagation in homogenous rock, rather than the classic mechanism of headwall undercutting. For a series of vertically drilling waterfalls, we find that upstream knickzone propagation is faster under higher combined water and sediment fluxes and for knickzones composed of many waterfalls that are closely spaced. Our model differs significantly from stream-power-based erosion rules in that steeper knickzones can retreat faster or more slowly depending on the number and spacing of waterfalls within a knickzone, which has implications for interpreting climatic and tectonic history through analysis of river longitudinal profiles.

  6. Prediction of pesticide acute toxicity using two-dimensional chemical descriptors and target species classification

    Science.gov (United States)

    Previous modelling of the median lethal dose (oral rat LD50) has indicated that local class-based models yield better correlations than global models. We evaluated the hypothesis that dividing the dataset by pesticidal mechanisms would improve prediction accuracy. A linear discri...

  7. Targeting chronic illness together. Health plans support providers through predictive analytics.

    Science.gov (United States)

    Raths, David

    2012-05-01

    Health insurers that used to focus on individual claims are now looking across their entire membership to better define the appropriate level of financial risk to assign and to drive the right kinds of interventions. Many are making a determined effort to share their predictive analytics findings with clinicians.

  8. Identification of Predictive Response Markers and Novel Treatment Targets for Gliomas

    NARCIS (Netherlands)

    L. Erdem-Eraslan (Lale)

    2016-01-01

    markdownabstractGliomas are the most frequent primary brain tumors in adults. Despite multimodality treatment strategies, the survival of patients with a diffuse glioma remains poor. There has been an increasing use of molecular markers to assist diagnosis and predict prognosis and response to

  9. Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this study, we developed a computational approach to predict viral sequence hotspots for binding to host proteins based on sequences of viral and host proteins and literature-curated virus-host protein interactome data. We use a motif discovery algorithm repeatedly on collections of sequences of viral proteins and immediate binding partners of their host targets and choose only those motifs that are conserved on viral sequences and highly statistically enriched among binding partners of virus protein targeted host proteins. Our results match experimental data on binding sites of Nef to host proteins such as MAPK1, VAV1, LCK, HCK, HLA-A, CD4, FYN, and GNB2L1 with high statistical significance but is a poor predictor of Nef binding sites on highly flexible, hoop-like regions. Predicted hotspots recapture CD8 cell epitopes of HIV Nef highlighting their importance in modulating virus-host interactions. Host proteins potentially targeted or outcompeted by Nef appear crowding the T cell receptor, natural killer cell mediated cytotoxicity, and neurotrophin signaling pathways. Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk.

  10. GLRS-R 2-colour retroreflector target design and predicted performance

    Science.gov (United States)

    Lund, Glenn

    1993-01-01

    This paper reports on the retroreflector ground-target design for the GLRS-R spaceborne dual-wavelength laser ranging system. The described passive design flows down from the requirements of high station autonomy, high global FOV (up to 60 degrees zenith angle), little or no multiple pulse returns, and adequate optical cross section for most ranging geometries. The proposed solution makes use of 5 hollow cube-corner retroreflectors of which one points to the zenith and the remaining four are inclined from the vertical at uniform azimuthal spacings. The need for fairly large (is approximately 10 cm) retroreflectors is expected (within turbulence limitations) to generate quite narrow diffraction lobes, thus placing non-trivial requirements on the vectorial accuracy of velocity aberration corrections. A good compromise solution is found by appropriately spoiling just one of the retroreflector dihedral angles from 90 degrees, thus generating two symmetrically oriented diffraction lobes in the return beam. The required spoil angles are found to have little dependence on ground target latitude. Various link budget analyses are presented, showing the influence of such factors as point-ahead optimization, turbulence, ranging angle, atmospheric visibility and ground target thermal deformations.

  11. Erosion-corrosion synergistics in the low erosion regime

    International Nuclear Information System (INIS)

    Corey, R.G.; Sethi, V.K.

    1986-01-01

    Many engineering alloys display good high temperature corrosion resistance. However, when they are used in corrosive environments where they are subjected to erosion also, the corrosion resistance has been adversely affected. The phenomenon known as erosion-corrosion is complex and requires detailed investigation of how the erosion and corrosion kinetics interact and compete. At the Kentucky Center for Energy Research Laboratory, an erosion-corrosion tester was used to perform erosion-oxidation tests on 2 1/4 Cr-1 Mo steel at 500-600 0 C using alumina abrasive at low velocities. The erosion-oxidation rate data and morphology of exposed surfaces are consistent with oxide chipping and fracturing being the mode of material loss

  12. First-trimester multimarker prediction of gestational diabetes mellitus using targeted mass spectrometry

    DEFF Research Database (Denmark)

    Ravnsborg, Tina; Andersen, Lise Lotte T; Trabjerg, Natacha D.

    2016-01-01

    –control study was performed on first-trimester serum samples from 199 GDM cases and 208 controls, each divided into an obese group (BMI ≥27 kg/m2) and a non-obese group (BMI 2). Based on their biological relevance to GDM or type 2 diabetes mellitus or on their previously reported potential as biomarkers......Aims/hypothesis: Gestational diabetes mellitus (GDM) is associated with an increased risk of pre-eclampsia, macrosomia and the future development of type 2 diabetes mellitus in both mother and child. Although an early and accurate prediction of GDM is needed to allow intervention and improve...... perinatal outcome, no single protein biomarker has yet proven useful for this purpose. In the present study, we hypothesised that multimarker panels of serum proteins can improve first-trimester prediction of GDM among obese and non-obese women compared with single markers. Methods: A nested case...

  13. Narrowing the scope of failure prediction using targeted fault load injection

    Science.gov (United States)

    Jordan, Paul L.; Peterson, Gilbert L.; Lin, Alan C.; Mendenhall, Michael J.; Sellers, Andrew J.

    2018-05-01

    As society becomes more dependent upon computer systems to perform increasingly critical tasks, ensuring that those systems do not fail becomes increasingly important. Many organizations depend heavily on desktop computers for day-to-day operations. Unfortunately, the software that runs on these computers is written by humans and, as such, is still subject to human error and consequent failure. A natural solution is to use statistical machine learning to predict failure. However, since failure is still a relatively rare event, obtaining labelled training data to train these models is not a trivial task. This work presents new simulated fault-inducing loads that extend the focus of traditional fault injection techniques to predict failure in the Microsoft enterprise authentication service and Apache web server. These new fault loads were successful in creating failure conditions that were identifiable using statistical learning methods, with fewer irrelevant faults being created.

  14. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

    OpenAIRE

    Huthmacher, Carola; Hoppe, Andreas; Bulik, Sascha; Holzh?tter, Hermann-Georg

    2010-01-01

    Abstract Background Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed. Results Here, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicte...

  15. EVALUATION OF SOIL EROSION IN REGHIN HILLS USING THE USLE METHOD

    Directory of Open Access Journals (Sweden)

    J. SZILAGYI

    2016-03-01

    Full Text Available Soil erosion is one of the main causes of degradation of large areas of agricultural land, causing great economic loss by removing fertile soil. The Universal Soil Loss Equation (USLE predicts the long term average annual rate of erosion on a field slope based on rainfall pattern, soil type, topography, crop system and management practices but does not however predict the soil loss resulting from gully erosion.

  16. A terminological matter: paragenesis, antigravitative erosion or antigravitational erosion ?

    Directory of Open Access Journals (Sweden)

    Pasini G.

    2009-07-01

    Full Text Available In the speleological literature three terms are utilized to designate the “ascending erosion”: paragenesis (= paragénésis, coined in1968, antigravitative erosion (= erosione antigravitativa, coined in 1966 and antigravitational erosion (wrong English translation ofthe Italian term erosione antigravitativa, utilized later on. The term paragenesis should be abandoned because of the priority of theterm erosione antigravitativa - on the ground of the “law of priority” – and because of its ambiguous etimology. On the other hand,the term antigravitational erosion should be forsaken in favour of the term antigravitative erosion, given the meaning that the termsgravitation and gravity have in Physics. Therefore, to designate the phenomenon of the “ascending erosion” there would be nothingleft but the term antigravitative erosion.The antigravitative erosion process and its recognizability are illustrated.Examples of caves with evident antigravitative erosion phenomena, developed in different karstifiable rocks and in several partsof the world, are given.It is recalled that the antigravitative erosion is a phenomenon well-known since 1942 and widely proven and supported, and that it isrelatively easy – in many cases - to recognize the antigravitative origin of karstic passages.It is stressed that the antigravitative erosion is an important phenomenon, exclusive of the karstic caves and unique in nature.

  17. Erosive potential of soft drinks on human enamel: An in vitro study

    Directory of Open Access Journals (Sweden)

    Yin-Lin Wang

    2014-11-01

    Conclusion: All tested soft drinks were found to be erosive. Soft drinks with high calcium contents have significantly lower erosive potential. Low pH value and high citrate content may cause more surface enamel loss. As the erosive time increased, the titratable acidity to pH 7 may be a predictor of the erosive potential for acidic soft drinks. The erosive potential of the soft drinks may be predicted based on the types of acid content, pH value, titratable acidity, and ion concentration.

  18. Fine and Predictable Tuning of TALEN Gene Editing Targeting for Improved T Cell Adoptive Immunotherapy.

    Science.gov (United States)

    Gautron, Anne-Sophie; Juillerat, Alexandre; Guyot, Valérie; Filhol, Jean-Marie; Dessez, Emilie; Duclert, Aymeric; Duchateau, Philippe; Poirot, Laurent

    2017-12-15

    Using a TALEN-mediated gene-editing approach, we have previously described a process for the large-scale manufacturing of "off-the-shelf" CAR T cells from third-party donor T cells by disrupting the gene encoding TCRα constant chain (TRAC). Taking advantage of a previously described strategy to control TALEN targeting based on the exclusion capacities of non-conventional RVDs, we have developed highly efficient and specific nucleases targeting a key T cell immune checkpoint, PD-1, to improve engineered CAR T cells' functionalities. Here, we demonstrate that this approach allows combined TRAC and PDCD1 TALEN processing at the desired locus while eliminating low-frequency off-site processing. Thus, by replacing few RVDs, we provide here an easy and rapid redesign of optimal TALEN combinations. We anticipate that this method can greatly benefit multiplex editing, which is of key importance especially for therapeutic applications where high editing efficiencies need to be associated with maximal specificity and safety. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Fine and Predictable Tuning of TALEN Gene Editing Targeting for Improved T Cell Adoptive Immunotherapy

    Directory of Open Access Journals (Sweden)

    Anne-Sophie Gautron

    2017-12-01

    Full Text Available Using a TALEN-mediated gene-editing approach, we have previously described a process for the large-scale manufacturing of “off-the-shelf” CAR T cells from third-party donor T cells by disrupting the gene encoding TCRα constant chain (TRAC. Taking advantage of a previously described strategy to control TALEN targeting based on the exclusion capacities of non-conventional RVDs, we have developed highly efficient and specific nucleases targeting a key T cell immune checkpoint, PD-1, to improve engineered CAR T cells’ functionalities. Here, we demonstrate that this approach allows combined TRAC and PDCD1 TALEN processing at the desired locus while eliminating low-frequency off-site processing. Thus, by replacing few RVDs, we provide here an easy and rapid redesign of optimal TALEN combinations. We anticipate that this method can greatly benefit multiplex editing, which is of key importance especially for therapeutic applications where high editing efficiencies need to be associated with maximal specificity and safety.

  20. SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes

    Directory of Open Access Journals (Sweden)

    Atul Kumar

    2017-06-01

    Full Text Available Type II diabetes is a chronic condition that affects the way our body metabolizes sugar. The body's important source of fuel is now becoming a chronic disease all over the world. It is now very necessary to identify the new potential targets for the drugs which not only control the disease but also can treat it. Support vector machines are the classifier which has a potential to make a classification of the discriminatory genes and non-discriminatory genes. SVMRFE a modification of SVM ranks the genes based on their discriminatory power and eliminate the genes which are not involved in causing the disease. A gene regulatory network has been formed with the top ranked coding genes to identify their role in causing diabetes. To further validate the results pathway study was performed to identify the involvement of the coding genes in type II diabetes. The genes obtained from this study showed a significant involvement in causing the disease, which may be used as a potential drug target.

  1. Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets

    DEFF Research Database (Denmark)

    Ali, Amjad; Soares, Siomar C.; Santos, Anderson R.

    2012-01-01

    . The potential candidate factors identified for attenuation and/or subunit vaccine development against C. fetus subspecies contain: nucleoside diphosphate kinase (Ndk), type IV secretion systems (T4SS), outer membrane proteins (OMP), substrate binding proteins CjaA and CjaC, surface array proteins, sap gene......, and cytolethal distending toxin (CDT). Significantly, many of those genes were found in genomic regions with signals of horizontal gene transfer and, therefore, predicted as putative pathogenicity islands. We found CRISPR loci and dam genes in an island specific for C. fetus subsp. fetus, and T4SS and sap genes...

  2. The prognostic and predictive value of sstr_2-immunohistochemistry and sstr_2-targeted imaging in neuroendocrine tumors

    International Nuclear Information System (INIS)

    Brunner, Philippe; Joerg, Ann-Catherine; Mueller-Brand, Jan; Glatz, Katharina; Bubendorf, Lukas; Radojewski, Piotr; Umlauft, Maria; Spanjol, Petar-Marko; Krause, Thomas; Dumont, Rebecca A.; Walter, Martin A.; Marincek, Nicolas; Maecke, Helmut R.; Briel, Matthias; Schmitt, Anja; Perren, Aurel

    2017-01-01

    Our aim was to assess the prognostic and predictive value of somatostatin receptor 2 (sstr_2) in neuroendocrine tumors (NETs). We established a tissue microarray and imaging database from NET patients that received sstr_2-targeted radiopeptide therapy with yttrium-90-DOTATOC, lutetium-177-DOTATOC or alternative treatment. We used univariate and multivariate analyses to identify prognostic and predictive markers for overall survival, including sstr_2-imaging and sstr_2-immunohistochemistry. We included a total of 279 patients. In these patients, sstr_2-immunohistochemistry was an independent prognostic marker for overall survival (HR: 0.82, 95 % CI: 0.67 - 0.99, n = 279, p = 0.037). In DOTATOC patients, sstr_2-expression on immunohistochemistry correlated with tumor uptake on sstr_2-imaging (n = 170, p < 0.001); however, sstr_2-imaging showed a higher prognostic accuracy (positive predictive value: +27 %, 95 % CI: 3 - 56 %, p = 0.025). Sstr_2-expression did not predict a benefit of DOTATOC over alternative treatment (p = 0.93). Our results suggest sstr_2 as an independent prognostic marker in NETs. Sstr_2-immunohistochemistry correlates with sstr_2-imaging; however, sstr_2-imaging is more accurate for determining the individual prognosis. (orig.)

  3. The influence of material hardness on liquid droplet impingement erosion

    International Nuclear Information System (INIS)

    Fujisawa, Nobuyuki; Yamagata, Takayuki; Takano, Shotaro; Saito, Kengo; Morita, Ryo; Fujiwara, Kazutoshi; Inada, Fumio

    2015-01-01

    Highlights: • Liquid droplet impingement erosion is studied for various metal materials. • Average power dependency on droplet velocity is found as 7. • Power dependency on Vickers hardness is found as −4.5. • An empirical formula is constructed for erosion rates of metal materials. • Predicted erosion rate is well correlated with experiment within a factor of 1.5. - Abstract: This paper describes the experimental study on the liquid droplet impingement erosion of metal materials to understand the influence of material hardness on the erosion rate. The experiment is carried out using a water spray jet apparatus with a condition of relatively thin liquid film thickness. The metal materials tested are pure aluminum, aluminum alloy, brass, mild steel, carbon steel and stainless steel. The liquid droplets considered are 30 ± 5 μm in volume average diameter of water, which is the same order of droplet diameter in the actual pipeline in nuclear/fossil power plants. In order to understand the influence of material hardness on the liquid droplet impingement erosion, the scanning electron microscope (SEM) observation on the eroded surface and the measurement of erosion rate are carried out in the terminal stage of erosion. The experimental results indicate that the erosion rates are expressed by the droplet velocity, volume flux, Vickers hardness and the liquid film thickness, which are fundamentals of the liquid droplet impingement erosion. The empirical formula shows that the power index for droplet velocity dependency is found to be 7 with a scattering from 5 to 9 depending on the materials, while the power index for Vickers hardness dependency is found as −4.5

  4. Headcut erosive regimes influenced by groundwater on disturbed agricultural soils.

    Science.gov (United States)

    Rockwell, D L

    2011-02-01

    A series of simulated rainfall experiments, testing several soils and slope gradients in a 10 m x 0.8m laboratory flume, displayed close correlations between initial development of a water table at a 10 cm depth and highly erosive headcut formation. On some soils and gradients, highly erosive headcuts formed consistently and predictably within minutes or seconds of initial water table rise. However, headcuts alone were not good indicators of increased erosion. In most experiments some headcuts formed early, often when surface hydraulic parameter values reached established rill initiation thresholds, but resulted in little or no erosion increase. Later, at initial water table rise, other headcuts formed coincident with major erosion increase, often with surface hydraulic values then less than rill initiation thresholds. On the four soils tested, highly erosive headcuts never formed without groundwater development, except on steep 9 ° slopes. Common visual indicators such as headcut morphology and headcut advance rates were not effective means of determining either erosion or the existence of groundwater. Only local monitoring of subsurface moisture conditions with micro-standpipes and TDR aided in determining headcut processes and erosive regimes. Groundwater-influenced headcut formation was likely caused by increased soil pore-water pressures and decreased soil shear strengths in surface rainflow, not by sapping or seepage from the soil matrix. Highly erosive headcuts can thus form under common agricultural conditions where reductions in permeability, such as plow pans, exist near the surface--without the need for saturated soils. Headcut erosive regimes were also significantly influenced by soil type and slope gradient, with the greatest effects of groundwater on moderate slopes and fairly permeable soils. Copyright © 2010. Published by Elsevier Ltd.

  5. The influence of material hardness on liquid droplet impingement erosion

    Energy Technology Data Exchange (ETDEWEB)

    Fujisawa, Nobuyuki, E-mail: fujisawa@eng.niigata-u.ac.jp [Visualization Research Center, Niigata University, 8050, Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181 (Japan); Yamagata, Takayuki, E-mail: yamagata@eng.niigata-u.ac.jp [Visualization Research Center, Niigata University, 8050, Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181 (Japan); Takano, Shotaro; Saito, Kengo [Graduate School of Science and Technology, Niigata University, 8050, Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181 (Japan); Morita, Ryo; Fujiwara, Kazutoshi; Inada, Fumio [Central Research Institute of Electric Power Industry, 2-11-1, Iwatokita, Komae, Tokyo 201-8511 (Japan)

    2015-07-15

    Highlights: • Liquid droplet impingement erosion is studied for various metal materials. • Average power dependency on droplet velocity is found as 7. • Power dependency on Vickers hardness is found as −4.5. • An empirical formula is constructed for erosion rates of metal materials. • Predicted erosion rate is well correlated with experiment within a factor of 1.5. - Abstract: This paper describes the experimental study on the liquid droplet impingement erosion of metal materials to understand the influence of material hardness on the erosion rate. The experiment is carried out using a water spray jet apparatus with a condition of relatively thin liquid film thickness. The metal materials tested are pure aluminum, aluminum alloy, brass, mild steel, carbon steel and stainless steel. The liquid droplets considered are 30 ± 5 μm in volume average diameter of water, which is the same order of droplet diameter in the actual pipeline in nuclear/fossil power plants. In order to understand the influence of material hardness on the liquid droplet impingement erosion, the scanning electron microscope (SEM) observation on the eroded surface and the measurement of erosion rate are carried out in the terminal stage of erosion. The experimental results indicate that the erosion rates are expressed by the droplet velocity, volume flux, Vickers hardness and the liquid film thickness, which are fundamentals of the liquid droplet impingement erosion. The empirical formula shows that the power index for droplet velocity dependency is found to be 7 with a scattering from 5 to 9 depending on the materials, while the power index for Vickers hardness dependency is found as −4.5.

  6. Blood pressure variability predicts cardiovascular events independently of traditional cardiovascular risk factors and target organ damage

    DEFF Research Database (Denmark)

    Vishram, Julie K K; Dahlöf, Björn; Devereux, Richard B

    2015-01-01

    ). METHODS: In 8505 patients randomized to losartan vs. atenolol-based treatment in the LIFE study, we tested whether BP variability assessed as SD and range for BP6-24months measured at 6, 12, 18 and 24 months of treatment was associated with target organ damage (TOD) defined by LVH on ECG and urine albumin......BACKGROUND: Assessment of antihypertensive treatment is normally based on the mean value of a number of blood pressure (BP) measurements. However, it is uncertain whether high in-treatment visit-to-visit BP variability may be harmful in hypertensive patients with left ventricular hypertrophy (LVH.......05), but MI was not. CONCLUSION: In LIFE patients, higher in-treatment BP6-24months variability was independently of mean BP6-24months associated with later CEP and stroke, but not with MI or TOD after 24 months....

  7. 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.

  8. Identification and target prediction of miRNAs specifically expressed in rat neural tissue

    Directory of Open Access Journals (Sweden)

    Tu Kang

    2009-05-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs. Results In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values Conclusion Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.

  9. Erosion in extruder flow

    Science.gov (United States)

    Kaufman, Miron; Fodor, Petru S.

    A detailed analysis of the fluid flow in Tadmor's unwound channel model of the single screw extruder is performed by combining numerical and analytical methods. Using the analytical solution for the longitudinal velocity field (in the limit of zero Reynolds number) allows us to devote all the computational resources solely for a detailed numerical solution of the transversal velocity field. This high resolution 3D model of the fluid flow in a single-screw extruder allows us to identify the position and extent of Moffatt eddies that impede mixing. We further consider the erosion of particles (e.g. carbon-black agglomerates) advected by the polymeric flow. We assume a particle to be made of primary fragments bound together. In the erosion process a primary fragment breaks out of a given particle. Particles are advected by the laminar flow and they disperse because of the shear stresses imparted by the fluid. The time evolution of the numbers of particles of different sizes is described by the Bateman coupled differential equations used to model radioactivity. Using the particle size distribution we compute an entropic fragmentation index which varies from 0 for a monodisperse system to 1 for an extreme poly-disperse system.

  10. Identification and targeting of a TACE-dependent autocrine loopwhich predicts poor prognosis in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kenny, Paraic A.; Bissell, Mina J.

    2005-06-15

    The ability to proliferate independently of signals from other cell types is a fundamental characteristic of tumor cells. Using a 3D culture model of human breast cancer progression, we have delineated a protease-dependent autocrine loop which provides an oncogenic stimulus in the absence of proto-oncogene mutation. Inhibition of this protease, TACE/ADAM17, reverts the malignant phenotype by preventing mobilization of two crucial growth factors, Amphiregulin and TGF{alpha}. We show further that the efficacy of EGFR inhibitors is overcome by physiological levels of growth factors and that successful EGFR inhibition is dependent on reducing ligand bioavailability. Using existing patient outcome data, we demonstrate a strong correlation between TACE and TGF{alpha} expression in human breast cancers that is predictive of poor prognosis.

  11. Synergistic erosion/corrosion of superalloys in PFB coal combustor effluent

    Science.gov (United States)

    Benford, S. M.; Zellars, G. R.; Lowell, C. E.

    1981-01-01

    Two Ni-based superalloys were exposed to the high velocity effluent of a pressurized fluidized bed coal combustor. Targets were 15 cm diameter rotors operating at 40,000 rpm and small flat plate specimens. Above an erosion rate threshold, the targets were eroded to bare metal. The presence of accelerated oxidation at lower erosion rates suggests erosion/corrosion synergism. Various mechanisms which may contribute to the observed oxide growth enhancement include erosive removal of protective oxide layers, oxide and subsurface cracking, and chemical interaction with sulfur in the gas and deposits through damaged surface layers.

  12. Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations.

    Directory of Open Access Journals (Sweden)

    Frances Hutchings

    2015-12-01

    Full Text Available Temporal lobe epilepsy (TLE is a prevalent neurological disorder resulting in disruptive seizures. In the case of drug resistant epilepsy resective surgery is often considered. This is a procedure hampered by unpredictable success rates, with many patients continuing to have seizures even after surgery. In this study we apply a computational model of epilepsy to patient specific structural connectivity derived from diffusion tensor imaging (DTI of 22 individuals with left TLE and 39 healthy controls. We validate the model by examining patient-control differences in simulated seizure onset time and network location. We then investigate the potential of the model for surgery prediction by performing in silico surgical resections, removing nodes from patient networks and comparing seizure likelihood post-surgery to pre-surgery simulations. We find that, first, patients tend to transit from non-epileptic to epileptic states more often than controls in the model. Second, regions in the left hemisphere (particularly within temporal and subcortical regions that are known to be involved in TLE are the most frequent starting points for seizures in patients in the model. In addition, our analysis also implicates regions in the contralateral and frontal locations which may play a role in seizure spreading or surgery resistance. Finally, the model predicts that patient-specific surgery (resection areas chosen on an individual, model-prompted, basis and not following a predefined procedure may lead to better outcomes than the currently used routine clinical procedure. Taken together this work provides a first step towards patient specific computational modelling of epilepsy surgery in order to inform treatment strategies in individuals.

  13. Specific decontamination methods: water nozzle, cavitation erosion

    International Nuclear Information System (INIS)

    Boulitrop, D.; Gauchon, J.P.; Lecoffre, Y.

    1984-05-01

    The erosion and decontamination tests carried out in the framework of this study, allowed to specify the fields favourable to the use of the high pressure jet taking into account the determinant parameters that are the pressure and the target-nozzle distance. The previous spraying of gels with chemical reagents (sulfuric acid anf hydrazine) allows to get better decontamination factors. Then, the feasibility study of a decontamination method by cavitation erosion is presented. Gelled compounds for decontamination have been developed; their decontamination quality has been evaluated by comparative contamination tests in laboratory and decontamination tests of samples of materials used in nuclear industry; this last method is adapted to remote handling devices and produces a low quantity of secondary effluents, so it allows to clean high contaminated installation on the site without additional exposure of the personnel [fr

  14. Instrumentation and methods evaluations for shallow land burial of waste materials: water erosion

    International Nuclear Information System (INIS)

    Hostetler, D.D.; Murphy, E.M.; Childs, S.W.

    1981-08-01

    The erosion of geologic materials by water at shallow-land hazardous waste disposal sites can compromise waste containment. Erosion of protective soil from these sites may enhance waste transport to the biosphere through water, air, and biologic pathways. The purpose of this study was to review current methods of evaluating soil erosion and to recommend methods for use at shallow-land, hazardous waste burial sites. The basic principles of erosion control are: minimize raindrop impact on the soil surface; minimize runoff quantity; minimize runoff velocity; and maximize the soil's resistance to erosion. Generally soil erosion can be controlled when these principles are successfully applied at waste disposal sites. However, these erosion control practices may jeopardize waste containment. Typical erosion control practices may enhance waste transport by increasing subsurface moisture movement and biologic uptake of hazardous wastes. A two part monitoring program is recommended for US Department of Energy (DOE) hazardous waste disposal sites. The monitoring programs and associated measurement methods are designed to provide baseline data permitting analysis and prediction of long term erosion hazards at disposal sites. These two monitoring programs are: (1) site reconnaissance and tracking; and (2) site instrumentation. Some potential waste transport problems arising from erosion control practices are identified. This report summarizes current literature regarding water erosion prediction and control

  15. Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions

    Science.gov (United States)

    Melnikova, Nataliya V.; Dmitriev, Alexey A.; Belenikin, Maxim S.; Koroban, Nadezhda V.; Speranskaya, Anna S.; Krinitsina, Anastasia A.; Krasnov, George S.; Lakunina, Valentina A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Klimina, Kseniya M.; Amosova, Alexandra V.; Zelenin, Alexander V.; Muravenko, Olga V.; Bolsheva, Nadezhda L.; Kudryavtseva, Anna V.

    2016-01-01

    Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stably inherit the changes, are called genotrophs. MicroRNAs (miRNAs) are involved in a crucial regulatory mechanism of gene expression. They have previously been assumed to take part in nutrient stress response and can, therefore, participate in genotroph formation. In the present study, we performed high-throughput sequencing of small RNAs (sRNAs) extracted from flax plants grown under normal, phosphate deficient and nutrient excess conditions to identify miRNAs and evaluate their expression. Our analysis revealed expression of 96 conserved miRNAs from 21 families in flax. Moreover, 475 novel potential miRNAs were identified for the first time, and their targets were predicted. However, none of the identified miRNAs were transcribed from LIS-1. Expression of seven miRNAs (miR168, miR169, miR395, miR398, miR399, miR408, and lus-miR-N1) with up- or down-regulation under nutrient stress (on the basis of high-throughput sequencing data) was evaluated on extended sampling using qPCR. Reference gene search identified ETIF3H and ETIF3E genes as most suitable for this purpose. Down-regulation of novel potential lus-miR-N1 and up-regulation of conserved miR399 were revealed under the phosphate deficient conditions. In addition, the negative correlation of expression of lus-miR-N1 and its predicted target, ubiquitin-activating enzyme E1 gene, as well as, miR399 and its predicted target, ubiquitin-conjugating enzyme E2 gene, was observed. Thus, in our study, miRNAs expressed in flax plastic lines and genotrophs were identified and their expression and expression of their targets was evaluated using high-throughput sequencing and qPCR for the first time. These data provide new insights

  16. Subsoil erosion dominates the supply of fine sediment to rivers draining into Princess Charlotte Bay, Australia.

    Science.gov (United States)

    Olley, Jon; Brooks, Andrew; Spencer, John; Pietsch, Timothy; Borombovits, Daniel

    2013-10-01

    distributions for (137)Cs and (210)Pbex concentrations were determined for each of the end members, with these distributions then used to estimate the surface soil contribution to each of the collected river sediment samples. The mean estimate of contribution of surface derived sediment for all river samples (n = 70) is 16 ± 2%. This study reinforces the importance of testing model predictions before they are used to target investment in remedial action and adds to the body of evidence that the primary source of sediment delivered to tropical river systems is derived from subsoil erosion. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Subsoil erosion dominates the supply of fine sediment to rivers draining into Princess Charlotte Bay, Australia

    International Nuclear Information System (INIS)

    Olley, Jon; Brooks, Andrew; Spencer, John; Pietsch, Timothy; Borombovits, Daniel

    2013-01-01

    The Laura–Normanby River (catchment area: 24,350 km 2 ), which drains into Princess Charlotte Bay, has been identified in previous studies as the third largest contributor of sediment to the Great Barrier Reef World Heritage Area. These catchment scale modelling studies also identified surface soil erosion as supplying >80% of the sediment. Here we use activity concentrations of the fallout radionuclides 137 Cs and 210 Pb ex to test the hypothesis that surface soil erosion dominates the supply of fine ( 137 Cs and 210 Pb ex activity concentrations between samples collected using these two methods. Two methods were also used to collect samples to characterise 137 Cs and 210 Pb ex concentrations in sediment derived from surface soil erosion; sampling of surface-wash deposits and deployment of surface runoff traps that collected samples during rain events. While there was no difference in the 137 Cs activity concentrations for samples collected using these two methods, 210 Pb ex activity concentrations were significantly higher in the samples collected using the runoff traps. The higher 210 Pb ex concentrations are shown to be correlated with loss-on-ignition (r 2 = 0.79) and therefore are likely to be related to higher organic concentrations in the runoff trap samples. As a result of these differences we use a three end member mixing model (channel/gully, hillslope surface-wash and hillslope runoff traps) to determine the relative contribution from surface soil erosion. Probability distributions for 137 Cs and 210 Pb ex concentrations were determined for each of the end members, with these distributions then used to estimate the surface soil contribution to each of the collected river sediment samples. The mean estimate of contribution of surface derived sediment for all river samples (n = 70) is 16 ± 2%. This study reinforces the importance of testing model predictions before they are used to target investment in remedial action and adds to the body of evidence

  18. Soil erosion assessment on hillslope of GCE using RUSLE model

    Science.gov (United States)

    Islam, Md. Rabiul; Jaafar, Wan Zurina Wan; Hin, Lai Sai; Osman, Normaniza; Din, Moktar Aziz Mohd; Zuki, Fathiah Mohamed; Srivastava, Prashant; Islam, Tanvir; Adham, Md. Ibrahim

    2018-06-01

    A new method for obtaining the C factor (i.e., vegetation cover and management factor) of the RUSLE model is proposed. The method focuses on the derivation of the C factor based on the vegetation density to obtain a more reliable erosion prediction. Soil erosion that occurs on the hillslope along the highway is one of the major problems in Malaysia, which is exposed to a relatively high amount of annual rainfall due to the two different monsoon seasons. As vegetation cover is one of the important factors in the RUSLE model, a new method that accounts for a vegetation density is proposed in this study. A hillslope near the Guthrie Corridor Expressway (GCE), Malaysia, is chosen as an experimental site whereby eight square plots with the size of 8× 8 and 5× 5 m are set up. A vegetation density available on these plots is measured by analyzing the taken image followed by linking the C factor with the measured vegetation density using several established formulas. Finally, erosion prediction is computed based on the RUSLE model in the Geographical Information System (GIS) platform. The C factor obtained by the proposed method is compared with that of the soil erosion guideline Malaysia, thereby predicted erosion is determined by both the C values. Result shows that the C value from the proposed method varies from 0.0162 to 0.125, which is lower compared to the C value from the soil erosion guideline, i.e., 0.8. Meanwhile predicted erosion computed from the proposed C value is between 0.410 and 3.925 t ha^{-1 } yr^{-1} compared to 9.367 to 34.496 t ha^{-1} yr^{-1 } range based on the C value of 0.8. It can be concluded that the proposed method of obtaining a reasonable C value is acceptable as the computed predicted erosion is found to be classified as a very low zone, i.e. less than 10 t ha^{-1 } yr^{-1} whereas the predicted erosion based on the guideline has classified the study area as a low zone of erosion, i.e., between 10 and 50 t ha^{-1 } yr^{-1}.

  19. Predicting bat colony survival under controls targeting multiple transmission routes of white-nose syndrome.

    Science.gov (United States)

    Meyer, A D; Stevens, D F; Blackwood, J C

    2016-11-21

    White-nose syndrome (WNS) is a lethal infection of bats caused by the psychrophilic fungus Pseudogymnoascus destructans (Pd). Since the first cases of WNS were documented in 2006, it is estimated that as many as 5.5million bats have succumbed in the United States-one of the fastest mammalian die-offs due to disease ever observed, and the first known sustained epizootic of bats. WNS is contagious between bats, and mounting evidence suggests that a persistent environmental reservoir of Pd plays a significant role in transmission as well. It is unclear, however, the relative contributions of bat-to-bat and environment-to-bat transmission to disease propagation within a colony. We analyze a mathematical model to investigate the consequences of both avenues of transmission on colony survival in addition to the efficacy of disease control strategies. Our model shows that selection of the most effective control strategies is highly dependent on the primary route of WNS transmission. Under all scenarios, however, generalized culling is ineffective and while targeted culling of infected bats may be effective under idealized conditions, it primarily has negative consequences. Thus, understanding the significance of environment-to-bat transmission is paramount to designing effective management plans. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. In silico models for predicting vector control chemicals targeting Aedes aegypti

    Science.gov (United States)

    Devillers, J.; Lagneau, C.; Lattes, A.; Garrigues, J.C.; Clémenté, M.M.; Yébakima, A.

    2014-01-01

    Human arboviral diseases have emerged or re-emerged in numerous countries worldwide due to a number of factors including the lack of progress in vaccine development, lack of drugs, insecticide resistance in mosquitoes, climate changes, societal behaviours, and economical constraints. Thus, Aedes aegypti is the main vector of the yellow fever and dengue fever flaviviruses and is also responsible for several recent outbreaks of the chikungunya alphavirus. As for the other mosquito species, the A. aegypti control relies heavily on the use of insecticides. However, because of increasing resistance to the different families of insecticides, reduction of Aedes populations is becoming increasingly difficult. Despite the unquestionable utility of insecticides in fighting mosquito populations, there are very few new insecticides developed and commercialized for vector control. This is because the high cost of the discovery of an insecticide is not counterbalanced by the ‘low profitability’ of the vector control market. Fortunately, the use of quantitative structure–activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes. In this context, the goal of the present study was to review all the existing QSAR models on A. aegypti. The homology and pharmacophore models were also reviewed. Specific attention was paid to show the variety of targets investigated in Aedes in relation to the physiology and ecology of the mosquito as well as the diversity of the chemical structures which have been proposed, encompassing man-made and natural substances. PMID:25275884

  1. Investigation of erosion mechanisms and erosion products in divertor armour materials under conditions relevant to elms and mitigated disruptions in ITER

    International Nuclear Information System (INIS)

    Safronov, V.M.; Arkhipov, N.I.; Klimov, N.S.; Kovalenko, D.V.; Moskaleva, A.A.; Podkovyrov, V.L.; Toporkov, D.A.; Zhitlukhin, A.M.; Landman, I.S.; Poznyak, I.M.

    2008-01-01

    Carbon fibre composite (CFC) and tungsten were irradiated by intense plasma streams at plasma gun facilities MK-200UG and QSPA-T. The targets were tested by plasma loads relevant to Edge Localised Modes (ELM) and mitigated disruptions in ITER. Onset condition of material erosion and properties of erosion products have been studied

  2. Erosion evaluation capability of the IVVS for ITER applications

    Energy Technology Data Exchange (ETDEWEB)

    Pollastrone, Fabio, E-mail: fabio.pollastrone@enea.it [Associazione EURATOM-ENEA sulla Fusione, Via Enrico Fermi 45, 00044 Frascati, Rome (Italy); Ferri de Collibus, Mario; Florean, Marco; Francucci, Massimo; Mugnaini, Giampiero; Neri, Carlo; Rossi, Paolo [Associazione EURATOM-ENEA sulla Fusione, Via Enrico Fermi 45, 00044 Frascati, Rome (Italy); Dubus, Gregory; Damiani, Carlo [Fusion For Energy c/Josep Pla, 2 Torres Diagonal Litoral, 08019 Barcelona (Spain)

    2014-10-15

    Highlights: •High resolution laser radar range images for hostile environment (IVVS). •Evaluation of the erosion on the surface scanned by IVVS laser radar. •Erosion evaluation procedure and software. •Test and results of the erosion evaluation procedure. -- Abstract: In ITER it is foreseen the use of the In Vessel Viewing System (IVVS), whose scanning head is a 3D laser imaging system able to obtain high-resolution intensity and range images in hostile environments. The IVVS will be permanently installed into a port extension, therefore it has to be compliant with ITER primary vacuum requirements. In the frame of a Fusion for Energy Grant, an investigation of the expected IVVS metrology performances was required to evaluate the device capability to detect erosions on ITER first wall and divertor and to estimate the amount of eroded material. In ENEA Frascati laboratories, an IVVS probe prototype was developed along with a method and a computational procedure applied to a reference erosion plate target simulating ITER vessel components and their possible erosions. Experimental tests were carried out by this system performing several scans of the reference target with different incidence angles, estimating the eroded volume and comparing this volume with its true value. A dedicated study has been also done by changing the power of the laser source; a discussion about the quality of the 3D laser images is reported. The main results obtained during laboratory tests and data processing are presented and discussed.

  3. Microinvasion of liver metastases from colorectal cancer: predictive factors and application for determining clinical target volume

    International Nuclear Information System (INIS)

    Qian, Yang; Zeng, Zhao-Chong; Ji, Yuan; Xiao, Yin-Ping

    2015-01-01

    This study evaluates the microscopic characteristics of liver metastases from colorectal cancer (LMCRC) invasion and provides a reference for expansion from gross tumor volume (GTV) to clinical targeting volume (CTV). Data from 129 LMCRC patients treated by surgical resection at our hospital between January 2008 and September 2009 were collected for study. Tissue sections used for pathology and clinical data were reviewed. Patient information used for the study included gender, age, original tumor site, number of tumors, tumor size, levels of carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA199), synchronous or metachronous liver metastases, and whether patients received chemotherapy. The distance of liver microinvasion from the tumor boundary was measured microscopically by two senior pathologists. Of 129 patients evaluated, 81 (62.8 %) presented microinvasion distances from the tumor boundary ranging between 1.0 − 7.0 mm. A GTV-to-CTV expansion of 5, 6.7, or 7.0 mm was required to provide a 95, 99, or 100 % probability, respectively, of obtaining clear resection margins by microscopic observation. The extent of invasion was not related to gender, age, synchronous or metachronous liver metastases, tumor size, CA199 level, or chemotherapy. The extent of invasion was related to original tumor site, CEA level, and number of tumors. A scoring system was established based on the latter three positive predictors. Using this system, an invasion distance less than 3 mm was measured in 93.4 % of patients with a score of ≤1 point, but in only 85.7 % of patients with a score of ≤2 points. The extent of tumor invasion in our LMCRC patient cohort correlated with original tumor site, CEA level, and number of tumors. These positive predictors may potentially be used as a scoring system for determining GTV-to-CTV expansion

  4. Predicting ground contact events for a continuum of gait types: An application of targeted machine learning using principal component analysis.

    Science.gov (United States)

    Osis, Sean T; Hettinga, Blayne A; Ferber, Reed

    2016-05-01

    An ongoing challenge in the application of gait analysis to clinical settings is the standardized detection of temporal events, with unobtrusive and cost-effective equipment, for a wide range of gait types. The purpose of the current study was to investigate a targeted machine learning approach for the prediction of timing for foot strike (or initial contact) and toe-off, using only kinematics for walking, forefoot running, and heel-toe running. Data were categorized by gait type and split into a training set (∼30%) and a validation set (∼70%). A principal component analysis was performed, and separate linear models were trained and validated for foot strike and toe-off, using ground reaction force data as a gold-standard for event timing. Results indicate the model predicted both foot strike and toe-off timing to within 20ms of the gold-standard for more than 95% of cases in walking and running gaits. The machine learning approach continues to provide robust timing predictions for clinical use, and may offer a flexible methodology to handle new events and gait types. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Laser processing of cast iron for enhanced erosion resistance

    International Nuclear Information System (INIS)

    Chen, C.H.; Altstetter, C.J.; Rigsbee, J.M.

    1984-01-01

    The surfaces of nodular and gray cast iron have been modified by CO 2 laser processing for enhanced hardness and erosion resistance. Control of the near-surface microstructure was achieved primarily by controlling resolidification of the laser melted layer through variations in laser beam/target interaction time and beam power density. Typical interaction times and power densities used were 5 msec and 500 kW/cm 2 . Two basic kinds of microstructure can be produced-a feathery microstructure with high hardness (up to 1245 HV) and a dendritic microstructure with a metastable, fully austenitic matrix and lower hardness (600 to 800 HV). Erosion testing was done using slurries of SiO 2 or SiC in water. Weight loss and crater profile measurements were used to evaluate the erosion characteristics of the various microstructures. Both ductile and gray cast iron showed marked improvement in erosion resistance after laser processing

  6. Predicting the establishment success of introduced target species in grassland restoration by functional traits.

    Science.gov (United States)

    Engst, Karina; Baasch, Annett; Bruelheide, Helge

    2017-09-01

    potential of functional trait analysis to predict success in restoration projects.

  7. The erosive potential of lollipops

    NARCIS (Netherlands)

    Brand, H.S.; Gambon, D.L.; Paap, A.; Bulthuis, M.S.; Veerman, E.C.I.; Nieuw Amerongen, A.V.

    2009-01-01

    Aim: To determine the erosive potential of several commercially available lollipops and the protective effect of saliva. Methods: The erosive potential of lollipops was determined in vitro by measuring the pH and neutralisable acidity. Subsequently, 10 healthy volunteers tested different types of

  8. Wind erosion processes and control

    Science.gov (United States)

    Wind erosion continues to threaten the sustainability of our nations' soil, air, and water resources. To effectively apply conservation systems to prevent wind driven soil loss, an understanding of the fundamental processes of wind erosion is necessary so that land managers can better recognize the ...

  9. Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer

    Science.gov (United States)

    Makondi, Precious Takondwa; Lee, Chia-Hwa; Huang, Chien-Yu; Chu, Chi-Ming; Chang, Yu-Jia

    2018-01-01

    can be potential targets and predictors of therapeutic resistance and prognosis in bevacizumab-treated patients with mCRC. PMID:29342159

  10. Postprandial regulation of hepatic microRNAs predicted to target the insulin pathway in rainbow trout.

    Directory of Open Access Journals (Sweden)

    Jan A Mennigen

    Full Text Available Rainbow trout are carnivorous fish and poor metabolizers of carbohydrates, which established this species as a model organism to study the comparative physiology of insulin. Following the recent characterisation of key roles of several miRNAs in the insulin action on hepatic intermediary metabolism in mammalian models, we investigated the hypothesis that hepatic miRNA expression is postprandially regulated in the rainbow trout and temporally coordinated in the context of insulin-mediated regulation of metabolic gene expression in the liver. To address this hypothesis, we used a time-course experiment in which rainbow trout were fed a commercial diet after short-term fasting. We investigated hepatic miRNA expression, activation of the insulin pathway, and insulin regulated metabolic target genes at several time points. Several miRNAs which negatively regulate hepatic insulin signaling in mammalian model organisms were transiently increased 4 h after the meal, consistent with a potential role in acute postprandial negative feed-back regulation of the insulin pathway and attenuation of gluconeogenic gene expression. We equally observed a transient increase in omy- miRNA-33 and omy-miRNA-122b 4 h after feeding, whose homologues have potent lipogenic roles in the liver of mammalian model systems. A concurrent increase in the activity of the hepatic insulin signaling pathway and the expression of lipogenic genes (srebp1c, fas, acly was equally observed, while lipolytic gene expression (cpt1a and cpt1b decreased significantly 4 h after the meal. This suggests lipogenic roles of omy-miRNA-33 and omy-miRNA-122b may be conserved between rainbow trout and mammals and that these miRNAs may furthermore contribute to acute postprandial regulation of de novo hepatic lipid synthesis in rainbow trout. These findings provide a framework for future research of miRNA regulation of hepatic metabolism in trout and will help to further elucidate the metabolic

  11. Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Precious Takondwa Makondi

    can be potential targets and predictors of therapeutic resistance and prognosis in bevacizumab-treated patients with mCRC.

  12. Erosion--corrosion

    International Nuclear Information System (INIS)

    Vyas, B.

    1978-01-01

    The deterioration of materials by corrosion or erosion by itself presents a formidable problem and for this reason investigators have studied these two phenomena independently. In fact, there are very few systematic studies on E-C and the majority of references mention it only in passing. In most real systems, however, the two destructive processes take place simultaneously, hence the purpose of this review is to present the various interactions between the chemical and mechanical agents leading to accelerated degradation of the material. The papers cited in the review are those that lead to a better understanding of the process involved in the accelerated rate of material loss under E-C conditions

  13. Soil erosion assessment in the core area of the Loss Plateau

    Science.gov (United States)

    Yang, Bo; Wang, Quanjiu

    2017-11-01

    In order to explore the spatiotemporal evolution of erosion and sediment yield before and after Grain for Green Project in the Loss Plateau. The soil loss of Yulin is estimated by Chinese Water Erosion on Hill Slope Prediction Model. The result shows that the spatiotemporal variations of soil erosion are largely related to rainfall erosion distribution, slope, and land use type. The overall soil erosion categories in the south region are higher than that of the northwest. Mid slopes and valleys are the major topographical contributors to soil erosion. With the growth of slope gradient, soil erosion significantly increased. The soil loss has a decreasing tendency after Grain for Green Project. The results indicate that the vegetation restoration as part of the Grain for Green Project on the Loess Plateau is effective.

  14. Predicting target vessel location on robot-assisted coronary artery bypass graft using CT to ultrasound registration

    International Nuclear Information System (INIS)

    Cho, Daniel S.; Linte, Cristian; Chen, Elvis C. S.; Bainbridge, Daniel; Wedlake, Chris; Moore, John; Barron, John; Patel, Rajni; Peters, Terry

    2012-01-01

    Purpose: Although robot-assisted coronary artery bypass grafting (RA-CABG) has gained more acceptance worldwide, its success still depends on the surgeon's experience and expertise, and the conversion rate to full sternotomy is in the order of 15%-25%. One of the reasons for conversion is poor pre-operative planning, which is based solely on pre-operative computed tomography (CT) images. In this paper, the authors propose a technique to estimate the global peri-operative displacement of the heart and to predict the intra-operative target vessel location, validated via both an in vitro and a clinical study. Methods: As the peri-operative heart migration during RA-CABG has never been reported in the literatures, a simple in vitro validation study was conducted using a heart phantom. To mimic the clinical workflow, a pre-operative CT as well as peri-operative ultrasound images at three different stages in the procedure (Stage 0 --following intubation; Stage 1 --following lung deflation; and Stage 2 --following thoracic insufflation) were acquired during the experiment. Following image acquisition, a rigid-body registration using iterative closest point algorithm with the robust estimator was employed to map the pre-operative stage to each of the peri-operative ones, to estimate the heart migration and predict the peri-operative target vessel location. Moreover, a clinical validation of this technique was conducted using offline patient data, where a Monte Carlo simulation was used to overcome the limitations arising due to the invisibility of the target vessel in the peri-operative ultrasound images. Results: For the in vitro study, the computed target registration error (TRE) at Stage 0 , Stage 1 , and Stage 2 was 2.1, 3.3, and 2.6 mm, respectively. According to the offline clinical validation study, the maximum TRE at the left anterior descending (LAD) coronary artery was 4.1 mm at Stage 0 , 5.1 mm at Stage 1 , and 3.4 mm at Stage 2 . Conclusions: The authors

  15. Erosion of ITER divertor armour and contamination of sol after transient events erosion products

    International Nuclear Information System (INIS)

    Bazylev, B.N.; Landman, I.S.; Pestchanyi, S.E.

    2005-01-01

    Plasma impact to the divertor expected in the tokamak ITER during ELMs or disruptions can result in a significant surface damage to CFC- and tungsten armours (brittle destruction and melting respectively) as well as in contamination of SOL by evaporated impurities. Numerical investigations for tungsten and CFC targets provide important details of the material erosion process. The simulations carried out in FZK on the material damage, carbon plasma expansion and the radiation fluxes from the carbon impurity are surveyed

  16. Mapping soil erosion hotspots and assessing the potential impacts of land management practices in the highlands of Ethiopia

    Science.gov (United States)

    Tamene, Lulseged; Adimassu, Zenebe; Ellison, James; Yaekob, Tesfaye; Woldearegay, Kifle; Mekonnen, Kindu; Thorne, Peter; Le, Quang Bao

    2017-09-01

    An enormous effort is underway in Ethiopia to address soil erosion and restore overall land productivity. Modelling and participatory approaches can be used to delineate erosion hotspots, plan site- and context-specific interventions and assess their impacts. In this study, we employed a modelling interface developed based on the Revised Universal Soil Loss Equation adjusted by the sediment delivery ratio to map the spatial distribution of net soil loss and identify priority areas of intervention. Using the modelling interface, we also simulated the potential impacts of different soil and water conservation measures in reducing net soil loss. Model predictions showed that net soil loss in the study area ranges between 0.4 and 88 t ha- 1 yr- 1 with an average of 12 t ha- 1 yr- 1. The dominant soil erosion hotspots were associated with steep slopes, gullies, communal grazing and cultivated areas. The average soil loss observed in this study is higher than the tolerable soil loss rate estimated for the highland of Ethiopia. The scenario analysis results showed that targeting hotspot areas where soil loss exceeds 10 t ha- 1 yr- 1 could reduce net soil loss to the tolerable limit (interventions. Future work should include cost-benefit and tradeoff analyses of the various management options for achieving a given level of erosion reduction.

  17. Methods for assessing mine site rehabilitation design for erosion impact

    International Nuclear Information System (INIS)

    Evans, K. G.

    2000-01-01

    Erosion of rehabilitated mines may result in landform instability, which in turn may result in exposure of encapsulated contaminants, elevated sediment delivery at catchment outlets, and subsequent degradation of downstream water quality. Rehabilitation design can be assessed using erosion and hydrology models calibrated to mine site conditions. Incision rates in containment structures can be quantified using 3-dimensional landform evolution simulation techniques. Sediment delivery at catchment outlets for various landform amelioration techniques can be predicted using process-based and empirical erosion-prediction models and sediment delivery ratios. The predicted sediment delivery can be used to estimate an average annual stream sediment load that can, in turn, be used to assess water quality impacts. Application of these techniques is demonstrated through a case study applied to a proposed rehabilitation design option for the Energy Resources of Australia Ltd (ERA) Ranger Mine in the Northern Territory of Australia. Copyright (2000) CSIRO Australia

  18. Using REE tracers to measure sheet erosion changing to rill erosion

    International Nuclear Information System (INIS)

    Liu Puling; Xue Yazhou; Song Wei; Wang Mingyi; Ju Tongjun

    2004-01-01

    Rare Earth Elements (REE) tracer method was used to study sheet erosion changing to rill erosion on slope land. By placing different rare earth elements of different soil depth across a slope in an indoor plot, two simulated rainfalls were applied to study the change of erosion type and the rill erosion process. The results indicate that the main erosion type is sheet erosion at the beginning of the rainfalls, and serious erosion happens after rill erosion appears. Accumulated sheet and rill erosion amounts increase with the rainfalls time. The percentage of sheet erosion amount decreases and rill erosion percentage increases with time. At the end of the rainfalls, the total rill erosion amounts are 4-5 times more than sheet erosion. In this paper, a new REE tracer method was used to quantitatively distinguish sheet and rill erosion amounts. The new REE tracer method should be useful to future studying of erosion processes on slope lands. (authors)

  19. Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species.

    Directory of Open Access Journals (Sweden)

    My Thanh Le

    Full Text Available Assembly of flagella requires strict hierarchical and temporal control via flagellar sigma and anti-sigma factors, regulatory proteins and the assembly complex itself, but to date non-coding RNAs (ncRNAs have not been described to regulate genes directly involved in flagellar assembly. In this study we have investigated the possible role of two ncRNA paralogs (CjNC1, CjNC4 in flagellar assembly and gene regulation of the diarrhoeal pathogen Campylobacter jejuni. CjNC1 and CjNC4 are 37/44 nt identical and predicted to target the 5' untranslated region (5' UTR of genes transcribed from the flagellar sigma factor σ54. Orthologs of the σ54-dependent 5' UTRs and ncRNAs are present in the genomes of other thermophilic Campylobacter species, and transcription of CjNC1 and CNC4 is dependent on the flagellar sigma factor σ28. Surprisingly, inactivation and overexpression of CjNC1 and CjNC4 did not affect growth, motility or flagella-associated phenotypes such as autoagglutination. However, CjNC1 and CjNC4 were able to mediate sequence-dependent, but Hfq-independent, partial repression of fluorescence of predicted target 5' UTRs in an Escherichia coli-based GFP reporter gene system. This hints towards a subtle role for the CjNC1 and CjNC4 ncRNAs in post-transcriptional gene regulation in thermophilic Campylobacter species, and suggests that the currently used phenotypic methodologies are insufficiently sensitive to detect such subtle phenotypes. The lack of a role of Hfq in the E. coli GFP-based system indicates that the CjNC1 and CjNC4 ncRNAs may mediate post-transcriptional gene regulation in ways that do not conform to the paradigms obtained from the Enterobacteriaceae.

  20. Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species

    Science.gov (United States)

    Le, My Thanh; van Veldhuizen, Mart; Porcelli, Ida; Bongaerts, Roy J.; Gaskin, Duncan J. H.; Pearson, Bruce M.; van Vliet, Arnoud H. M.

    2015-01-01

    Assembly of flagella requires strict hierarchical and temporal control via flagellar sigma and anti-sigma factors, regulatory proteins and the assembly complex itself, but to date non-coding RNAs (ncRNAs) have not been described to regulate genes directly involved in flagellar assembly. In this study we have investigated the possible role of two ncRNA paralogs (CjNC1, CjNC4) in flagellar assembly and gene regulation of the diarrhoeal pathogen Campylobacter jejuni. CjNC1 and CjNC4 are 37/44 nt identical and predicted to target the 5' untranslated region (5' UTR) of genes transcribed from the flagellar sigma factor σ54. Orthologs of the σ54-dependent 5' UTRs and ncRNAs are present in the genomes of other thermophilic Campylobacter species, and transcription of CjNC1 and CNC4 is dependent on the flagellar sigma factor σ28. Surprisingly, inactivation and overexpression of CjNC1 and CjNC4 did not affect growth, motility or flagella-associated phenotypes such as autoagglutination. However, CjNC1 and CjNC4 were able to mediate sequence-dependent, but Hfq-independent, partial repression of fluorescence of predicted target 5' UTRs in an Escherichia coli-based GFP reporter gene system. This hints towards a subtle role for the CjNC1 and CjNC4 ncRNAs in post-transcriptional gene regulation in thermophilic Campylobacter species, and suggests that the currently used phenotypic methodologies are insufficiently sensitive to detect such subtle phenotypes. The lack of a role of Hfq in the E. coli GFP-based system indicates that the CjNC1 and CjNC4 ncRNAs may mediate post-transcriptional gene regulation in ways that do not conform to the paradigms obtained from the Enterobacteriaceae. PMID:26512728

  1. A Systems-Pharmacology Analysis of Herbal Medicines Used in Health Improvement Treatment: Predicting Potential New Drugs and Targets

    Directory of Open Access Journals (Sweden)

    Jianling Liu

    2013-01-01

    Full Text Available For thousands of years, tonic herbs have been successfully used all around the world to improve health, energy, and vitality. However, their underlying mechanisms of action in molecular/systems levels are still a mystery. In this work, two sets of tonic herbs, so called Qi-enriching herbs (QEH and Blood-tonifying herbs (BTH in TCM, were selected to elucidate why they can restore proper balance and harmony inside body, organ and energy system. Firstly, a pattern recognition model based on artificial neural network and discriminant analysis for assessing the molecular difference between QEH and BTH was developed. It is indicated that QEH compounds have high lipophilicity while BTH compounds possess high chemical reactivity. Secondly, a systematic investigation integrating ADME (absorption, distribution, metabolism, and excretion prediction, target fishing and network analysis was performed and validated on these herbs to obtain the compound-target associations for reconstructing the biologically-meaningful networks. The results suggest QEH enhance physical strength, immune system and normal well-being, acting as adjuvant therapy for chronic disorders while BTH stimulate hematopoiesis function in body. As an emerging approach, the systems pharmacology model might facilitate to understand the mechanisms of action of the tonic herbs, which brings about new development for complementary and alternative medicine.

  2. Simulation of erosion in drilling tools for oil and gas industry

    Energy Technology Data Exchange (ETDEWEB)

    Arefi, B.; Settari, A. [Calgary Univ., AB (Canada); Angman, P. [Tesco Corp., Calgary, AB (Canada)

    2004-07-01

    Erosion in oil well drilling tools is a form of wear which occurs when fluid containing solid particles impacts a solid surface. The intensity of erosion is generally measured as the rate of material removal from the surface, and is expressed as E{sub r}, the weight of material removed by unit weight of impacting particles. Erosion can also be reduced by tool improvement and modification, thereby extending the life of drilling tools. To date, no attempt has been made to model the erosion phenomenon in drilling tools. This paper presents a newly developed erosion simulator which is the first design tool for the drilling industry. This work demonstrates that erosion can be simulated. A model was developed to calibrate the erosion coefficients for drilling tool conditions. The mechanism of erosion can be controlled by the impact velocity and angle. Algorithms were developed for transient simulation of the erosion of any surface in 2-dimensional geometry. The Erosion Simulator has been validated and calibrated against data provided by TESCO Corporation's casing drilling tools. The model has been shown to successfully predict and minimize erosion by modifying the tool geometry and metallurgy. 21 refs., 1 tab., 15 figs.

  3. Towards estimates of future rainfall erosivity in Europe based on REDES and WorldClim datasets

    Science.gov (United States)

    Panagos, Panos; Ballabio, Cristiano; Meusburger, Katrin; Spinoni, Jonathan; Alewell, Christine; Borrelli, Pasquale

    2017-05-01

    The policy requests to develop trends in soil erosion changes can be responded developing modelling scenarios of the two most dynamic factors in soil erosion, i.e. rainfall erosivity and land cover change. The recently developed Rainfall Erosivity Database at European Scale (REDES) and a statistical approach used to spatially interpolate rainfall erosivity data have the potential to become useful knowledge to predict future rainfall erosivity based on climate scenarios. The use of a thorough statistical modelling approach (Gaussian Process Regression), with the selection of the most appropriate covariates (monthly precipitation, temperature datasets and bioclimatic layers), allowed to predict the rainfall erosivity based on climate change scenarios. The mean rainfall erosivity for the European Union and Switzerland is projected to be 857 MJ mm ha-1 h-1 yr-1 till 2050 showing a relative increase of 18% compared to baseline data (2010). The changes are heterogeneous in the European continent depending on the future projections of most erosive months (hot period: April-September). The output results report a pan-European projection of future rainfall erosivity taking into account the uncertainties of the climatic models.

  4. Towards estimates of future rainfall erosivity in Europe based on REDES and WorldClim datasets.

    Science.gov (United States)

    Panagos, Panos; Ballabio, Cristiano; Meusburger, Katrin; Spinoni, Jonathan; Alewell, Christine; Borrelli, Pasquale

    2017-05-01

    The policy requests to develop trends in soil erosion changes can be responded developing modelling scenarios of the two most dynamic factors in soil erosion, i.e. rainfall erosivity and land cover change. The recently developed Rainfall Erosivity Database at European Scale (REDES) and a statistical approach used to spatially interpolate rainfall erosivity data have the potential to become useful knowledge to predict future rainfall erosivity based on climate scenarios. The use of a thorough statistical modelling approach (Gaussian Process Regression), with the selection of the most appropriate covariates (monthly precipitation, temperature datasets and bioclimatic layers), allowed to predict the rainfall erosivity based on climate change scenarios. The mean rainfall erosivity for the European Union and Switzerland is projected to be 857 MJ mm ha -1  h -1  yr -1 till 2050 showing a relative increase of 18% compared to baseline data (2010). The changes are heterogeneous in the European continent depending on the future projections of most erosive months (hot period: April-September). The output results report a pan-European projection of future rainfall erosivity taking into account the uncertainties of the climatic models.

  5. Gastric Mucosal Erosions - Radiologic evaluation -

    International Nuclear Information System (INIS)

    Kim, Seung Hyup

    1985-01-01

    70 cases of gastric mucosal erosions were diagnosed by double contrast upper gastrointestinal examinations and endoscopic findings. Analyzing the radiologic findings of these 70 cases of gastric mucosal erosions, the following results were obtained. 1. Among the total 70 cases, 65 cases were typical varioliform erosions showing central depressions and surrounding mucosal elevations. Remaining 5 cases were erosions of acute phase having multiple irregular depressions without surrounding elevations. 2. The gastric antrum was involved alone or in part in all cases. Duodenal bulb was involved with gastric antrum in 4 cases. 3. The majority of the cases had multiple erosions. There were only 2 cases of single erosion. 4. In 65 cases of varioliform erosions; 1) The diameter of the surrounding elevations varied from 3 to 20 mm with the majority (47 cases) between 6 and 10 mm. 2) In general, the surrounding elevations with sharp margin on double contrast films were also clearly demonstrated on compression films but those with faint margin were not. 3) The size of the central barium collections varied from pinpoint to 10 mm with the majority under 5 mm. The shape of the central barium collections in majority of the cases were round with a few cases of linear, triangular or star-shape. 5. In 5 cases of acute phase erosions; 1) All the 5 cases were females. 2) On double contrast radiography, all the cases showed multiple irregular depressed lesions without surrounding elevations. 3) 1 case had the history of hematemesis. 4) In 1 case, there was marked radiological improvement on follow-up study of 2 months interval. 6. In 23 cases, there were coexistent diseases with gastric mucosal erosions. These were 13 cases of duodenal bulb ulcers,7 cases of benign gastric ulcers and 3 others

  6. Dune Erosion Models and Swash Zone Kinematics from Remote Video Observations

    Science.gov (United States)

    2010-12-09

    system. Thus, successful prediction of dune erosion requires knowledge of the expected trajectory of the eroding dune toe . If we describe the... dune toe trajectory as following a slope, βT, two end member retreat trajectories exist. The first would be direct landward erosion so that zb never...changes     0 0   T bb ztz  (2.24) The second end member trajectory is that erosion moves the dune toe directly up the foreshore slope

  7. Soil erosion, sedimentation and the carbon cycle

    Science.gov (United States)

    Cammeraat, L. H.; Kirkels, F.; Kuhn, N. J.

    2012-04-01

    Historically soil erosion focused on the effects of on-site soil quality loss and consequently reduced crop yields, and off-site effects related to deposition of material and water quality issues such as increased sediment loads of rivers. In agricultural landscapes geomorphological processes reallocate considerable amounts of soil and soil organic carbon (SOC). The destiny of SOC is of importance because it constitutes the largest C pool of the fast carbon cycle, and which cannot only be understood by looking at the vertical transfer of C from soil to atmosphere. Therefore studies have been carried out to quantify this possible influence of soil erosion and soil deposition and which was summarized by Quinton et al. (2010) by "We need to consider soils as mobile systems to make accurate predictions about the consequences of global change for terrestrial biogeochemical cycles and climate feedbacks". Currently a debate exists on the actual fate of SOC in relation to the global carbon cycle, represented in a controversy between researchers claiming that erosion is a sink, and those who claim the opposite. This controversy is still continuing as it is not easy to quantify and model the dominating sink and source processes at the landscape scale. Getting insight into the balance of the carbon budget requires a comprehensive research of all relevant processes at broad spatio-temporal scales, from catchment to regional scales and covering the present to the late Holocene. Emphasising the economic and societal benefits, the merits for scientific knowledge of the carbon cycle and the potential to sequester carbon and consequently offset increasing atmospheric CO2 concentrations, make the fate of SOC in agricultural landscapes a high-priority research area. Quinton, J.N., Govers, G., Van Oost, K., Bardgett, R.D., 2010. The impact of agricultural soil erosion on biogeochemical cycling. Nature Geosci, 3, 311-314.

  8. How well does the Post-fire Erosion Risk Management Tool (ERMiT) really work?

    Science.gov (United States)

    Robichaud, Peter; Elliot, William; Lewis, Sarah; Miller, Mary Ellen

    2016-04-01

    The decision of where, when, and how to apply the most effective postfire erosion mitigation treatments requires land managers to assess the risk of damaging runoff and erosion events occurring after a fire. The Erosion Risk Management Tool (ERMiT) was developed to assist post fire assessment teams identify high erosion risk areas and effectiveness of various mitigation treatments to reduce that risk. ERMiT is a web-based application that uses the Water Erosion Prediction Project (WEPP) technology to estimate erosion, in probabilistic terms, on burned and recovering forest, range, and chaparral lands with and without the application of mitigation treatments. User inputs are processed by ERMiT to combine rain event variability with spatial and temporal variabilities of hillslope burn severity and soil properties which are then used as WEPP inputs. Since 2007, the model has been used in making hundreds of land management decisions in the US and elsewhere. We use eight published field study sites in the Western US to compare ERMiT predictions to observed hillslope erosion rates. Most sites experience only a few rainfall events that produced runoff and sediment except for a California site with a Mediterranean climate. When hillslope erosion occurred, significant correlations occurred between the observed hillslope erosion and those predicted by ERMiT. Significant correlation occurred for most mitigation treatments as well as the five recovery years. These model validation results suggest reasonable estimates of probabilistic post-fire hillslope sediment delivery when compared to observation.

  9. Quantification of Net Erosion and Uplift Experienced by the Barmer Basin, Rajasthan Using Sonic Log

    Science.gov (United States)

    Mitra, K.; Schulz, S.; Sarkar, A.

    2015-12-01

    Barmer Basin of Rajasthan, Western India is a hydrocarbon rich sedimentary basin currently being explored by Cairn India Limited. The hydrocarbon bearing Fatehgarh Formation is being found at different depths in different oil fields (e.g. From south to north: Guda, Vijaya & Vandana, Air field High) of the basin. The net uplift and erosion in the Barmer Basin has been quantified using compaction methodology. The sonic log, which is strongly controlled by porosity, is an appropriate indicator of compaction, and hence used for quantification of net uplift and erosion from compaction. The compaction methodology has been applied to the shale rich Dharvi Dungar Formation of Barmer Basin of Late Paleocene age. The net uplift and erosion is also being checked with the help of AFTA-VR and seismic sections. The results show relatively no uplift in the southernmost part of the basin and a Guda field well is thus taken to be the reference well with respect to which the uplifts in different parts of the basin have been calculated. The northern part of the basin i.e. Air Field High wells experienced maximum uplift (~2150m). Interestingly, a few wells further south of the reference well show evidence for uplift. The study was able to point out errors in the report produced with the help of AFTA-VR which found out less uplift in Vijaya & Vandana oil fields as opposed to sonic log data. The process of finding out uplift using sonic log has a standard deviation of 200m as compared to about 500m error in AFTA-VR method. This study has major implications for hydrocarbon exploration. Maturation of source rock will be higher for any given geothermal history if net uplift and erosion is incorporated in maturation modeling. They can also be used for porosity predictions of reservoir units in undrilled targets.

  10. Acquired pellicle as a modulator for dental erosion.

    Science.gov (United States)

    Vukosavljevic, Dusa; Custodio, William; Buzalaf, Marilia A R; Hara, Anderson T; Siqueira, Walter L

    2014-06-01

    Dental erosion is a multifactorial condition that can result in the loss of tooth structure and function, potentially increasing tooth sensitivity. The exposure of enamel to acids from non-bacterial sources is responsible for the progression of erosion. These erosive challenges are counteracted by the anti-erosive properties of the acquired pellicle (AP), an integument formed in vivo as a result of selective adsorption of salivary proteins on the tooth surface, containing also lipids and glycoproteins. This review provides an in-depth discussion regarding how the physical structure of the AP, along with its composition, contributes to AP anti-erosive properties. The physical properties that contribute to AP protective nature include pellicle thickness, maturation time, and site of development. The pellicle contains salivary proteins embedded within its structure that demonstrate anti-erosive properties; however, rather than individual proteins, protein-protein interactions play a fundamental role in the protective nature of the AP. In addition, dietary and synthetic proteins can modify the pellicle, enhancing its protective efficiency against dental erosion. The salivary composition of the AP and its corresponding protein-profile may be employed as a diagnostic tool, since it likely contains salivary biomarkers for oral diseases that initiate at the enamel surface, including dental erosion. Finally, by modifying the composition and structure of the AP, this protein integument has the potential to be used as a target-specific treatment option for oral diseases related to tooth demineralization. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Erosive tooth wear in children

    NARCIS (Netherlands)

    Carvalho, T.S.; Lussi, A.; Jaeggi, T.; Gambon, D.L.; Lussi, A.; Ganss, C.

    2014-01-01

    Erosive tooth wear in children is a common condition. Besides the anatomical differences between deciduous and permanent teeth, additional histological differences may influence their susceptibility to dissolution. Considering laboratory studies alone, it is not clear whether deciduous teeth are

  12. Erosion-resistant composite material

    Science.gov (United States)

    Finch, C.B.; Tennery, V.J.; Curlee, R.M.

    A highly erosion-resistant composite material is formed of chemical vapor-deposited titanium diboride on a sintered titanium diboride-nickel substrate. This material may be suitable for use in cutting tools, coal liquefaction systems, etc.

  13. Soil Erosion and Agricultural Sustainability

    Science.gov (United States)

    Montgomery, D. R.

    2009-04-01

    Data drawn from a global compilation of studies support the long articulated contention that erosion rates from conventionally plowed agricultural fields greatly exceed rates of soil production, erosion under native vegetation, and long-term geological erosion. Whereas data compiled from around the world show that soil erosion under conventional agriculture exceeds both rates of soil production and geological erosion rates by up to several orders of magnitude, similar global distributions of soil production and geological erosion rates suggest an approximate balance. Net soil erosion rates in conventionally plowed fields on the order of 1 mm/yr can erode typical hillslope soil profiles over centuries to millennia, time-scales comparable to the longevity of major civilizations. Well-documented episodes of soil loss associated with agricultural activities date back to the introduction of erosive agricultural methods in regions around the world, and stratigraphic records of accelerated anthropogenic soil erosion have been recovered from lake, fluvial, and colluvial stratigraphy, as well as truncation of soil stratigraphy (such as truncated A horizons). A broad convergence in the results from studies based on various approaches employed to study ancient soil loss and rates of downstream sedimentation implies that widespread soil loss has accompanied human agricultural intensification in examples drawn from around the world. While a broad range of factors, including climate variability and society-specific social and economic contexts — such as wars or colonial relationships — all naturally influence the longevity of human societies, the ongoing loss of topsoil inferred from studies of soil erosion rates in conventional agricultural systems has obvious long-term implications for agricultural sustainability. Consequently, modern agriculture — and therefore global society — faces a fundamental question over the upcoming centuries. Can an agricultural system

  14. OEDGE modeling of outer wall erosion in NSTX and the effect of changes in neutral pressure

    Energy Technology Data Exchange (ETDEWEB)

    Nichols, J.H., E-mail: jnichols@pppl.gov; Jaworski, M.A.; Kaita, R.; Abrams, T.; Skinner, C.H.; Stotler, D.P.

    2015-08-15

    Gross erosion from the outer wall is expected to be a major source of impurities for high power fusion devices due to the low redeposition fraction. Scaling studies of sputtering from the all-carbon outer wall of NSTX are reported. It is found that wall erosion decreases with divertor plasma pressure in low/mid temperature regimes, due to increasing divertor neutral opacity. Wall erosion is found to consistently decrease with reduced recycling coefficient, with outer target recycling providing the largest contribution. Upper and lower bounds are calculated for the increase in wall erosion due to a low-field-side gas puff.

  15. Erosion behavior of W-Ta coatings in plasmas of stationary mirror penning discharges

    International Nuclear Information System (INIS)

    Belous, V.A.; Bondarenko, M.N.; Glazunov, G.P.; Ilchenko, A.V.; Kuprin, A.S.; Konotopskiy, A.L.; Lunyov, V.M.; Ovcharenko, V.D.

    2016-01-01

    Investigations had been carried out of the influence of Ta alloying (2...16 wt.%) in W-coatings on their erosion behavior in steady state plasmas of Penning discharges in different gases: argon, nitrogen, and hydrogen. The coatings were deposited on stainless steel substrates by argon ion sputtering of targets made from appropriate metals. For comparison the erosion behavior had been examined of pure W and Ta coatings obtained by the same method. It was shown the essential decrease of an erosion rate after Ta addition in W coatings. The possible physical mechanism is suggested to explain such erosion behavior

  16. A comparison of methods in estimating soil water erosion

    Directory of Open Access Journals (Sweden)

    Marisela Pando Moreno

    2012-02-01

    Full Text Available A comparison between direct field measurements and predictions of soil water erosion using two variant; (FAO and R/2 index of the Revised Universal Soil Loss Equation (RUSLE was carried out in a microcatchment o 22.32 km2 in Northeastern Mexico. Direct field measurements were based on a geomorphologic classification of the area; while environmental units were defined for applying the equation. Environmental units were later grouped withir geomorphologic units to compare results. For the basin as a whole, erosion rates from FAO index were statistical!; equal to those measured on the field, while values obtained from the R/2 index were statistically different from the res and overestimated erosion. However, when comparing among geomorphologic units, erosion appeared overestimate! in steep units and underestimated in more flat areas. The most remarkable differences on erosion rates, between th( direct and FAO methods, were for those units where gullies have developed, fn these cases, erosion was underestimated by FAO index. Hence, it is suggested that a weighted factor for presence of gullies should be developed and included in RUSLE equation.

  17. Modelling Soil Erosion in the Densu River Basin Using RUSLE and GIS Tools.

    Science.gov (United States)

    Ashiagbori, G; Forkuo, E K; Laari, P; Aabeyir, R

    2014-07-01

    Soil erosion involves detachment and transport of soil particles from top soil layers, degrading soil quality and reducing the productivity of affected lands. Soil eroded from the upland catchment causes depletion of fertile agricultural land and the resulting sediment deposited at the river networks creates river morphological change and reservoir sedimentation problems. However, land managers and policy makers are more interested in the spatial distribution of soil erosion risk than in absolute values of soil erosion loss. The aim of this paper is to model the spatial distribution of soil erosion in Densu River Basin of Ghana using RUSLE and GIS tools and to use the model to explore the relationship between erosion susceptibility, slope and land use/land cover (LULC) in the Basin. The rainfall map, digital elevation model, soil type map, and land cover map, were input data in the soil erosion model developed. This model was then categorized into four different erosion risk classes. The developed soil erosion map was then overlaid with the slope and LULC maps of the study area to explore their effects on erosion susceptibility of the soil in the Densu River Basin. The Model, predicted 88% of the basin as low erosion risk and 6% as moderate erosion risk, 3% as high erosion risk and 3% as severe risk. The high and severe erosion areas were distributed mainly within the areas of high slope gradient and also sections of the moderate forest LULC class. Also, the areas within the moderate forest LULC class found to have high erosion risk, had an intersecting high erodibility soil group.

  18. Erosion properties of unipolar arcs

    International Nuclear Information System (INIS)

    Chekalin, Eh.K.

    1982-01-01

    Processes modelling the formation of unipolar arcs on the elements of the first wall in limiters of the vacuum chamber and on active elements of tokamak divertor, are experimentally investigated. Erosion, processes that take place at two types of non-stationary cathode spots are considered. Experimental data prove the possibility of reducing erosion intensity by coating the surface of electrodes by oxide films, reduction of the temperature of electrode and discharge current

  19. Wind erosion of soils burned by wildfire

    Science.gov (United States)

    N. S. Wagenbrenner; M. J. Germino; B. K. Lamb; R. B. Foltz; P. R. Robichaud

    2011-01-01

    Wind erosion and aeolian transport processes are largely unstudied in the post-wildfire environment, but recent studies have shown that wind erosion can play a major role in burned landscapes. A wind erosion monitoring system was installed immediately following a wildfire in southeastern Idaho, USA to measure wind erosion from the burned area (Figure 1). This paper...

  20. Three Gorges Reservoir Area: soil erosion under natural condition vs. soil erosion under current land use

    Science.gov (United States)

    Schönbrodt, Sarah; Behrens, Thorsten; Scholten, Thomas

    2010-05-01

    Apparently, the current most prominent human-induced example for large scale environmental impact is the Three Gorges Dam in China. The flooding alongside the Yangtze River, and its tributaries results in a vast loss of settlement and farmland area with productive, fertile valley soils. Due to the associated high land use dynamic on uphill-sites, the soil resources are underlying high land use pressure. Within our study, the soil erosion under natural conditions is compared to the soil erosion under current land use after the impoundment. Both were modeled using the empirical Universal Soil Loss Equation (USLE) which is able to predict long-term annual soil loss with limited data. The database consists of digital terrain data (45 m resolution DEM, erosive slope length based on Monte-Carlo-Aggregation according to Behrens et al. (2008)), field investigations of recent erosion forms, and literature studies. The natural disposition to soil erosion was calculated considering the USLE factors R, S, and K. The soil erosion under current land use was calculated taking into account all USLE factors. The study area is the catchment of the Xiangxi River in the Three Gorges Reservoir area. Within the Xiangxi Catchment (3,200 km²) the highly dynamic backwater area (580 km²), and two micro-scale study sites (Xiangjiaba with 2.8 km², and Quyuan with 88 km²) are considered more detailed as they are directly affected by the river impoundment. Central features of the Xiangxi Catchment are the subtropical monsoon climate, an extremely steep sloping relief (mean slope angle 39°, SD 22.8°) artificially fractured by farmland terraces, and a high soil erodibility (mean K factor 0.37, SD 0.13). On the catchment scale the natural disposition to soil erosion makes up to mean 518.0 t ha-1 a-1. The maximum potential soil loss of 1,730.1 t ha-1 a-1 under natural conditions is reached in the Quyuan site (mean 635.8 t ha-1 a-1) within the backwater area (mean 582.9 t ha-1 a-1). In the

  1. Signaling Network Assessment of Mutations and Copy Number Variations Predict Breast Cancer Subtype-Specific Drug Targets

    Directory of Open Access Journals (Sweden)

    Naif Zaman

    2013-10-01

    Full Text Available Individual cancer cells carry a bewildering number of distinct genomic alterations (e.g., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here, we performed exome sequencing on several breast cancer cell lines that represent two subtypes, luminal and basal. We integrated these sequencing data and functional RNAi screening data (for the identification of genes that are essential for cell proliferation and survival onto a human signaling network. Two subtype-specific networks that potentially represent core-signaling mechanisms underlying tumorigenesis were identified. Within both networks, we found that genes were differentially affected in different cell lines; i.e., in some cell lines a gene was identified through RNAi screening, whereas in others it was genomically altered. Interestingly, we found that highly connected network genes could be used to correctly classify breast tumors into subtypes on the basis of genomic alterations. Further, the networks effectively predicted subtype-specific drug targets, which were experimentally validated.

  2. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

    Science.gov (United States)

    Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-01-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

  3. High energy density physics effects predicted in simulations of the CERN HiRadMat beam-target interaction experiments

    Science.gov (United States)

    Tahir, N. A.; Burkart, F.; Schmidt, R.; Shutov, A.; Wollmann, D.; Piriz, A. R.

    2016-12-01

    Experiments have been done at the CERN HiRadMat (High Radiation to Materials) facility in which large cylindrical copper targets were irradiated with 440 GeV proton beam generated by the Super Proton Synchrotron (SPS). The primary purpose of these experiments was to confirm the existence of hydrodynamic tunneling of ultra-relativistic protons and their hadronic shower in solid materials, that was predicted by previous numerical simulations. The experimental measurements have shown very good agreement with the simulation results. This provides confidence in our simulations of the interaction of the 7 TeV LHC (Large Hadron Collider) protons and the 50 TeV Future Circular Collider (FCC) protons with solid materials, respectively. This work is important from the machine protection point of view. The numerical simulations have also shown that in the HiRadMat experiments, a significant part of thetarget material is be converted into different phases of High Energy Density (HED) matter, including two-phase solid-liquid mixture, expanded as well as compressed hot liquid phases, two-phase liquid-gas mixture and gaseous state. The HiRadMat facility is therefore a unique ion beam facility worldwide that is currently available for studying the thermophysical properties of HED matter. In the present paper we discuss the numerical simulation results and present a comparison with the experimental measurements.

  4. Role of Erosion in Shaping Point Bars

    Science.gov (United States)

    Moody, J.; Meade, R.

    2012-04-01

    A powerful metaphor in fluvial geomorphology has been that depositional features such as point bars (and other floodplain features) constitute the river's historical memory in the form of uniformly thick sedimentary deposits waiting for the geomorphologist to dissect and interpret the past. For the past three decades, along the channel of Powder River (Montana USA) we have documented (with annual cross-sectional surveys and pit trenches) the evolution of the shape of three point bars that were created when an extreme flood in 1978 cut new channels across the necks of two former meander bends and radically shifted the location of a third bend. Subsequent erosion has substantially reshaped, at different time scales, the relic sediment deposits of varying age. At the weekly to monthly time scale (i.e., floods from snowmelt or floods from convective or cyclonic storms), the maximum scour depth was computed (by using a numerical model) at locations spaced 1 m apart across the entire point bar for a couple of the largest floods. The maximum predicted scour is about 0.22 m. At the annual time scale, repeated cross-section topographic surveys (25 during 32 years) indicate that net annual erosion at a single location can be as great as 0.5 m, and that the net erosion is greater than net deposition during 8, 16, and 32% of the years for the three point bars. On average, the median annual net erosion was 21, 36, and 51% of the net deposition. At the decadal time scale, an index of point bar preservation often referred to as completeness was defined for each cross section as the percentage of the initial deposit (older than 10 years) that was still remaining in 2011; computations indicate that 19, 41, and 36% of the initial deposits of sediment were eroded. Initial deposits were not uniform in thickness and often represented thicker pods of sediment connected by thin layers of sediment or even isolated pods at different elevations across the point bar in response to multiple

  5. Effect of stone coverage on soil erosion

    Science.gov (United States)

    Jomaa, S.; Barry, D. A.; Heng, B. P.; Brovelli, A.; Sander, G. C.; Parlange, J.

    2010-12-01

    Soil surface coverage has a significant impact on water infiltration, runoff and soil erosion yields. In particular, surface stones protect the soils from raindrop detachment, they retard the overland flow therefore decreasing its sediment transport capacity, and they prevent surface sealing. Several physical and environmental factors control to what extent stones on the soil surface modify the erosion rates and the related hydrological response. Among the most important factors are the moisture content of the topsoil, stone size, emplacement, coverage density and soil texture. Owing to the different inter-related processes, there is ambiguity concerning the quantitative effect of stones, and process-based understanding is limited. Experiments were performed (i) to quantify how stone features affect sediment yields, (ii) to understand the local effect of isolated surface stones, that is, the changes of the soil particle size distribution in the vicinity of a stone and (iii) to determine how stones attenuate the development of surface sealing and in turn how this affects the local infiltration rate. A series of experiments using the EPFL 6-m × 2-m erosion flume were conducted at different rainfall intensities (28 and 74 mm h-1) and stone coverage (20 and 40%). The total sediment concentration, the concentration of the individual size classes and the flow discharge were measured. In order to analyze the measurements, the Hairsine and Rose (HR) erosion model was adapted to account for the shielding effect of the stone cover. This was done by suitably adjusting the parameters based on the area not covered by stones. It was found that the modified HR model predictions agreed well with the measured sediment concentrations especially for the long time behavior. Changes in the bulk density of the topsoil due to raindrop-induced compaction with and without stone protection revealed that the stones protect the upper soil surface against the structural seals resulting in

  6. Seasonal variation and climate change impact in Rainfall Erosivity across Europe

    Science.gov (United States)

    Panagos, Panos; Borrelli, Pasquale; Meusburger, Katrin; Alewell, Christine; Ballabio, Cristiano

    2017-04-01

    residues, reduced tillage) in regions with high erosivity. Besides soil erosion mapping, the intra-annual analysis of rainfall erosivity is an important step towards flood prevention, hazard mitigation, ecosystem services, land use change and agricultural production. The application of REDES in combination with moderate climate change scenarios scenario (HadGEM RCP 4.5) resulted in predictions of erosivity in 2050. The overall increase of rainfall erosivity in Europe by 18% until 2050 are in line with projected increases of 17% for the U.S.A. The predicted mean rise of erosivity is also expected to increase the threat of soil erosion in Europe. The most noticeable increase of erosivity is projected for North-Central Europe, the English Channel, The Netherlands and Northern France. On the contrary, the Mediterranean basin show mixed trends. The success story with the compilation of REDES and first rainfall erosivity map of Europe was a driver to implement a Global Rainfall Erosivity Database (GloREDa). During the last 3 years, JRC was leading an effort to collect high temporal resolution rainfall data worldwide. In collaboration with 50 scientists worldwide and 100+ Meteorological and environmental Organisations, we have developed a Global Erosivity Database. In this database, we managed to include calculated erosivity values for 3,625 stations covering 63 countries worldwide.

  7. Soil erosion assessment on hillslope of GCE using RUSLE model

    Indian Academy of Sciences (India)

    61

    based on the RUSLE model in the Geographical Information System (GIS) platform. ... process of soil erosion happens in two stages; the first stage involves the ..... deep or surface cover of undecayed residue; c) appreciable brush of 2 m height ..... Kanungo D and Sharma S 2014 Rainfall thresholds for prediction of shallow ...

  8. Mechanics of interrill erosion with wind-driven rain

    Science.gov (United States)

    The vector physics of wind-driven rain (WDR) differs from that of wind-free rain, and the interrill soil detachment equations in the Water Erosion Prediction Project (WEPP) model were not originally developed to deal with this phenomenon. This article provides an evaluation of the performance of the...

  9. Mechanics of Interrill Erosion with Wind-Driven Rain (WDR)

    Science.gov (United States)

    This article provides an evaluation analysis for the performance of the interrill component of the Water Erosion Prediction Project (WEPP) model for Wind-Driven Rain (WDR) events. The interrill delivery rates (Di) were collected in the wind tunnel rainfall simulator facility of the International Cen...

  10. The Future Role of Information Technology in Erosion Modelling

    Science.gov (United States)

    Natural resources management and decision-making is a complex process requiring cooperation and communication among federal, state, and local stakeholders balancing biophysical and socio-economic concerns. Predicting soil erosion is common practice in natural resource management for assessing the e...

  11. Predicción de la erosión eólica potencial con el modelo EWEQ en dos suelos loesicos: efectos de las condiciones climáticas Wind erosion prediction with the EWEQ model in two loess soils: effects of climatic condition

    Directory of Open Access Journals (Sweden)

    Silvia Beatriz Aimar

    2011-12-01

    Full Text Available La erosión eólica potencial del suelo (EEP es un dato básico utilizado en varios modelos de predicción para calcular la erosión eólica de suelos agrícolas. El objetivo de este estudio fue cuantificar la EEP de un Haplustol y un Ustipsammente de la Región Semiárida Pampeana (RSP y compararla con las predicciones del modelo Ecuación de Erosión Eólica en Español (EWEQ, realizadas con diferentes factores climáticos (C. Se efectuaron mediciones de EEP a campo durante un año en ambos suelos, mantenidos sin cobertura y con mínima rugosidad. Los resultados indicaron que la EEP medida a campo fue mayor en el Ustipsammente (270 Mg ha-1 año-1 que en el Haplustol (40 Mg ha-1 año -1 , con una reducción en el espesor del horizonte de 21,3 y 3,1 mm, respectivamente. La erosión del Ustipsammente fue dos veces mayor en primavera-verano que en otoño-invierno. Este efecto no se observó en el Haplustol, debido a su menor desecamiento y mayores contenidos de humedad luego de las lluvias. La erosión del Haplustol, por desecarse más lentamente luego de una lluvia, fue más condicionada por las precipitaciones que la del Ustipsammente. Un 40% de la erosión de ambos suelos fue definida por la duración de las tormentas. Las tasas de erosión (EEP por unidad de tiempo, Qt se correlacionaron positivamente con la velocidad promedio del viento (V, ajustando a una función polinómica en ambos suelos. A la misma V, Qt fue siempre mayor en el Ustipsammente. La EEP calculada con la EWEQ, utilizando el factor C correspondiente al año de muestreo (30,3, fue la más semejante a la erosión medida a campo, aunque el modelo la subestimó en un 43% en el Haplustol y en un 18% en el Ustipsammente. La EWEQ deberá ofrecer al usuario distintos factores C para poder predecir EEP en escenarios climáticos variables.The potential wind erosion of a soil (EEP is a basic data for predicting wind erosion of agricultural soils in most wind erosion prediction models

  12. Effect of hard second-phase particles on the erosion resistance of model alloys

    International Nuclear Information System (INIS)

    Kosel, T.H.; Aptekar, S.S.

    1986-01-01

    The dependence of erosion rate on second phase volume fraction (SPVF) has been studied for Cu/Al/sub 2/O/sub 3/ and Cu/WC(W/sub 2/C) model alloys produced by pressing and sintering. The intention was to investigate the reasons for the poor contribution to erosion resistance made by large hard second phase particles (SPP) in other studies. The results show that for Cu/Al/sub 2/O/sub 3/ alloys, the erosion rate generally increased with SPVF, demonstrating a negative contribution to erosion resistance. This occurred despite the fact that the measured erosion rate of monolithic Al/sub 2/O/sub 3/ was lower by one to two orders of magnitude than that of the pure matrix. Changing from severe erosion with large erodent particles at high velocity to mild conditions with small erodent at low velocity caused a change from depression of the SPPs to protrusion from the surface, with some improvement of the relative erosion resistance compared to the pure matrix. For Cu/WC(W/sub 2/C) alloys, changing from severe to mild erosion conditions caused a change from an increase of erosion with SPVF to a decrease. The results are discussed in terms of the increased microfracture of the unsupported edges of the second phase particles compared to a flat single-phase surface. This edge is consistent with the results, and explains observations not predicted by existing theories for erosion of single-phase materials. A model is introduced which predicts a new averaging law for the erosion rate of a two-phase alloy in terms of erosion rates of its constituent phases

  13. Viewpoint: Sustainability of piñon-juniper ecosystems - A unifying perspective of soil erosion thresholds

    Science.gov (United States)

    Davenport, David W.; Breshears, D.D.; Wilcox, B.P.; Allen, Craig D.

    1998-01-01

    Many pinon-juniper ecosystem in the western U.S. are subject to accelerated erosion while others are undergoing little or no erosion. Controversy has developed over whether invading or encroaching pinon and juniper species are inherently harmful to rangeland ecosystems. We developed a conceptual model of soil erosion in pinon-jumper ecosystems that is consistent with both sides of the controversy and suggests that the diverse perspectives on this issue arise from threshold effects operating under very different site conditions. Soil erosion rate can be viewed as a function of (1) site erosion potential (SEP), determined by climate, geomorphology and soil erodibility; and (2) ground cover. Site erosion potential and cove act synergistically to determine soil erosion rates, as evident even from simple USLE predictions of erosion. In pinon-juniper ecosystem with high SEP, the erosion rate is highly sensitive to ground cover and can cross a threshold so that erosion increases dramatically in response to a small decrease in cover. The sensitivity of erosion rate to SEP and cover can be visualized as a cusp catastrophe surface on which changes may occur rapidly and irreversibly. The mechanisms associated with a rapid shift from low to high erosion rate can be illustrated using percolation theory to incorporate spatial, temporal, and scale-dependent patterns of water storage capacity on a hillslope. Percolation theory demonstrates how hillslope runoff can undergo a threshold response to a minor change in storage capacity. Our conceptual model suggests that pinion and juniper contribute to accelerated erosion only under a limited range of site conditions which, however, may exist over large areas.

  14. Auto consolidated cohesive sediments erosion

    International Nuclear Information System (INIS)

    Ternat, F.

    2007-02-01

    Pollutants and suspended matters of a river can accumulate into the sedimentary column. Once deposited, they are submitted to self-weight consolidation processes, ageing and burying, leading to an increase of their erosion resistance. Pollutant fluxes can be related to sedimentary fluxes, determined by threshold laws. In this work, an erosion threshold model is suggested by introducing a cohesion force into the usual force balance. A model of cohesion is developed on the basis of interactions between argillaceous cohesive particles (clays), particularly the Van der Waals force, whose parameterization is ensured by means of granulometry and porosity. Artificial erosion experiments were performed in a recirculating erosion flume with natural cored sediments where critical shear stress measurements were performed. Other analyses provided granulometry and porosity. The results obtained constitute a good database for the literature. The model is then applied to the experimental conditions and gives good agreement with measurements. An example of the accounting for self-weight consolidation processes is finally suggested, before finishing on a Mohr like diagram dedicated to soft cohesive sediment erosion. (author)

  15. Advancements in Hydrology and Erosion Process Understanding and Post-Fire Hydrologic and Erosion Model Development for Semi-Arid Landscapes

    Science.gov (United States)

    Williams, C. Jason; Pierson, Frederick B.; Al-Hamdan, Osama Z.; Robichaud, Peter R.; Nearing, Mark A.; Hernandez, Mariano; Weltz, Mark A.; Spaeth, Kenneth E.; Goodrich, David C.

    2017-04-01

    Fire activity continues to increase in semi-arid regions around the globe. Private and governmental land management entities are challenged with predicting and mitigating post-fire hydrologic and erosion responses on these landscapes. For more than a decade, a team of scientists with the US Department of Agriculture has collaborated on extensive post-fire hydrologic field research and the application of field research to development of post-fire hydrology and erosion predictive technologies. Experiments funded through this research investigated the impacts of fire on vegetation and soils and the effects of these fire-induced changes on infiltration, runoff generation, erodibility, and soil erosion processes. The distribution of study sites spans diverse topography across grassland, shrubland, and woodland landscapes throughout the western United States. Knowledge gleaned from the extensive field experiments was applied to develop and enhance physically-based models for hillslope- to watershed-scale runoff and erosion prediction. Our field research and subsequent data syntheses have identified key knowledge gaps and challenges regarding post-fire hydrology and erosion modeling. Our presentation details some consistent trends across a diverse domain and varying landscape conditions based on our extensive field campaigns. We demonstrate how field data have advanced our understanding of post-fire hydrology and erosion for semi-arid landscapes and highlight remaining key knowledge gaps. Lastly, we briefly show how our well-replicated experimental methodologies have contributed to advancements in hydrologic and erosion model development for the post-fire environment.

  16. Analyses of Potential Predictive Markers and Response to Targeted Therapy in Patients with Advanced Clear-cell Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Yan Song

    2015-01-01

    Full Text Available Background: Vascular endothelial growth factor-targeted agents are standard treatments in advanced clear-cell renal cell carcinoma (ccRCC, but biomarkers of activity are lacking. The aim of this study was to investigate the association of Von Hippel-Lindau (VHL gene status, vascular endothelial growth factor receptor (VEGFR or stem cell factor receptor (KIT expression, and their relationships with characteristics and clinical outcome of advanced ccRCC. Methods: A total of 59 patients who received targeted treatment with sunitinib or pazopanib were evaluated for determination at Cancer Hospital and Institute, Chinese Academy of Medical Sciences between January 2010 and November 2012. Paraffin-embedded tumor samples were collected and status of the VHL gene and expression of VEGFR and KIT were determined by VHL sequence analysis and immunohistochemistry. Clinical-pathological features were collected and efficacy such as response rate and Median progression-free survival (PFS and overall survival (OS were calculated and then compared based on expression status. The Chi-square test, the Kaplan-Meier method, and the Lon-rank test were used for statistical analyses. Results: Of 59 patients, objective responses were observed in 28 patients (47.5%. The median PFS was 13.8 months and median OS was 39.9 months. There was an improved PFS in patients with the following clinical features: Male gender, number of metastatic sites 2 or less, VEGFR-2 positive or KIT positive. Eleven patients (18.6% had evidence of VHL mutation, with an objective response rate of 45.5%, which showed no difference with patients with no VHL mutation (47.9%. VHL mutation status did not correlate with either overall response rate (P = 0.938 or PFS (P = 0.277. The PFS was 17.6 months and 22.2 months in VEGFR-2 positive patients and KIT positive patients, respectively, which was significantly longer than that of VEGFR-2 or KIT negative patients (P = 0.026 and P = 0.043. Conclusion

  17. Bentonite erosion. Laboratory studies

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, Mats (Div. of Nuclear Chemistry, Royal Inst. of Technology, Stockholm (Sweden), School of Chemical Science and Engineering)

    2009-11-15

    This report covers the laboratory studies that have been performed at Nuclear Chemistry, KTH in the project 'Bentonite Erosion'. Many of the experiments in this report were performed to support the work of the modelling group and were often relatively simple. One of the experiment series was performed to see the impact of gravity and concentration of mono- and di-valent cations. A clay suspension was prepared in a test tube. A net was placed in contact with the suspension, the test tube was filled with solutions of different concentrations and the system was left overnight to settle. The tube was then turned upside down and the behaviour was visually observed. Either the clay suspension fell through the net or stayed on top. By using this method surprisingly sharp determinations of the Critical Coagulation (Flocculation) Concentration (CCC/CFC) could be made. The CCC/CFC of Ca2+ was for sodium montmorillonite determined to be between 1 and 2 mM. An artificial fracture was manufactured in order to simulate the real case scenario. The set-up was two Plexiglas slabs separated by 1 mm thick spacers with a bentonite container at one side of the fracture. Water was pumped with a very low flow rate perpendicular to bentonite container and the water exiting the fracture was sampled and analyzed for colloid content. The bentonite used was treated in different ways. In the first experiment a relatively montmorillonite rich clay was used while in the second bentonite where only the readily soluble minerals had been removed was used. Since Plexiglas was used it was possible to visually observe the bentonite dispersing into the fracture. After the compacted bentonite (1,000 kg/m3) had been water saturated the clay had expanded some 12 mm out into the fracture. As the experiment progressed the clay expanded more out into the fracture and seemed to fractionate in two different phases with less material in the outmost phase. A dark rim which was later analyzed to contain

  18. Bentonite erosion - Laboratory studies

    International Nuclear Information System (INIS)

    Jansson, Mats

    2010-01-01

    Document available in extended abstract form only. Bentonite clay is proposed as buffer material in the KBS-3 concept of storing spent nuclear fuel. Since the clay is plastic it will protect the canisters containing the spent fuel from movements in the rock. Furthermore, the clay will expand when taking up water, become very compact and hence limit the transport of solutes to and from the canister to only diffusion. The chemical stability of the bentonite barrier is of vital importance. If much material would be lost the barrier will lose its functions. As a side effect, lots of colloids will be released which may facilitate radionuclide transport in case of a breach in the canister. There are scenarios where during an ice age fresh melt water may penetrate down to repository depths with relatively high flow rates and not mix with older waters of high salinity. Under such conditions bentonite colloids will be more stable and there is a possibility that the bentonite buffer would start to disperse and bentonite colloids be carried away by the passing water. This work is a part of a larger project called Bentonite Erosion, initiated and supported by SKB. In this work several minor experiments have been performed in order to investigate the influence of for instance di-valent cations, gravity, etc. on the dispersion behaviour of bentonite and/or montmorillonite. A bigger experiment where the real situation was simulated using an artificial fracture was conducted. Two Plexiglas slabs were placed on top of each other, separated by plastic spacers. Bentonite was placed in a container in contact with a fracture. The bentonite was water saturated before deionized water was pumped through the fracture. The evolution of the bentonite profile in the fracture was followed visually. The eluate was collected in five different slots at the outlet side and analyzed for colloid concentration employing Photon Correlation Spectroscopy (PCS) and a Single Particle Counter (SPC). Some

  19. Plume Mitigation: Soil Erosion and Lunar Prospecting Sensor Project

    Science.gov (United States)

    Metzger, Philip T.

    2014-01-01

    Demonstrate feasibility of the simplest, lowest-mass method of measuring density of a cloud of lunar soil ejected by rocket exhaust, using new math techniques with a small baseline laser/camera system. Focus is on exploring the erosion process that occurs when the exhaust plume of a lunar rocket impacts the regolith. Also, predicting the behavior of the lunar soil that would be blasted from a lunar landing/launch site shall assist in better design and protection of any future lunar settlement from scouring of structures and equipment. NASA is gathering experimental data to improve soil erosion models and understand how lunar particles enter the plume flow.

  20. Determining long-term regional erosion rates using impact craters

    Science.gov (United States)

    Hergarten, Stefan; Kenkmann, Thomas

    2015-04-01

    More than 300,000 impact craters have been found on Mars, while the surface of Moon's highlands is even saturated with craters. In contrast, only 184 impact craters have been confirmed on Earth so far with only 125 of them exposed at the surface. The spatial distribution of these impact craters is highly inhomogeneous. Beside the large variation in the age of the crust, consumption of craters by erosion and burial by sediments are the main actors being responsible for the quite small and inhomogeneous crater record. In this study we present a novel approach to infer long-term average erosion rates at regional scales from the terrestrial crater inventory. The basic idea behind this approach is a dynamic equilibrium between the production of new craters and their consumption by erosion. It is assumed that each crater remains detectable until the total erosion after the impact exceeds a characteristic depth depending on the crater's diameter. Combining this model with the terrestrial crater production rate, i.e., the number of craters per unit area and time as a function of their diameter, allows for a prediction of the expected number of craters in a given region as a function of the erosion rate. Using the real crater inventory, this relationship can be inverted to determine the regional long-term erosion rate and its statistical uncertainty. A limitation by the finite age of the crust can also be taken into account. Applying the method to the Colorado Plateau and the Deccan Traps, both being regions with a distinct geological history, yields erosion rates in excellent agreement with those obtained by other, more laborious methods. However, these rates are formally exposed to large statistical uncertainties due to the small number of impact craters. As higher crater densities are related to lower erosion rates, smaller statistical errors can be expected when large regions in old parts of the crust are considered. Very low long-term erosion rates of less than 4

  1. Soil erosion in Slovene Istria

    Directory of Open Access Journals (Sweden)

    Matjaž Mikoš

    2009-12-01

    Full Text Available From the end of nineties of the 20th century, intense hydrologic and geomorphologic research is taking place in the Slovene Istria. As a part of this research also studies on soil erosion were undertaken in the period from 2005 to 2008. The field measurements were under taken onclosed 1m2 large erosion plots under three different land uses (on bare soils in an olive grove, on an overgrown meadow, in a forest, placed south of the Marezige village in the Rokava River basin.We show weekly measurements of surface erosion (interrill erosion for the period of 13 months (the end of March 2005 – the end of April 2006, as well as monthly and seasonal averages together with selected linear statistical correlations between soil erosion and weather parameters.From May 2005 to April 2006 the interrill erosion on bare soils in an olive grove with an inclination of 5.5° amounted to 9013 g/m2 (90 t/ha that corresponds to surface lowering rate of 8.5 mm/yr; on an overgrown meadow with an inclination of 9.4° it amounted to 168 g/m2 (1,68 t/ha that corresponds to surface lowering rate of 0.16 mm//yr; and in a forest with an inclination of 7.8° it amounted to 391 g/m2 (3,91 t/ha and in a forest with an inclination of 21.4° it amounted to 415 g/m2 (4,15 t/ha, respectively, that corresponds to surface lowering rate of 0.4 mm/yr.

  2. Estimativa da produção de sedimentos mediante uso de um modelo hidrossedimentológico acoplado a um SIG Sediment yield prediction through the use of a runoff-erosion model coupled to a GIS

    Directory of Open Access Journals (Sweden)

    Richarde M. da Silva

    2008-10-01

    Full Text Available O Kineros é um modelo hidrossedimentológico usado para se estimar a vazão e a produção de sedimentos em bacias urbanas e rurais. No presente trabalho, o modelo foi aplicado à bacia do rio Pirapama, localizada na zona litorânea do Estado de Pernambuco, cujos resultados foram acoplados a um SIG com o objetivo de identificar, temporal e espacialmente, os principais locais em que o processo de erosão foi mais atuante na bacia do rio Pirapama. O modelo foi calibrado com dados diários de 1990 a 2001 de dois postos pluviométricos. Através do acoplamento dos resultados da modelagem no SIG, foi possível a identificação das principais áreas susceptíveis ao processo erosivo. Os resultados da produção de sedimentos na bacia mostraram que os planos com maior produção produziram mais de 200 t ha-1 ano-1, perfazendo o total de 653.079 t, correspondentes a uma área de 67,87 km² (11,3% da área total da bacia revelando, assim, que grande parte da bacia é realmente susceptível ao processo de erosão. Este trabalho mostra que o modelo Kineros é viável para bacias maiores que 100 km² e o seu acoplamento ao SIG é de grande valia para a identificação e análise das principais áreas de produção de sedimentos na bacia deste rio podendo ser, assim, considerado ferramenta promissora para simulação da produção de sedimentos em bacias hidrográficas do nordeste brasileiro.Kineros is a runoff-erosion model used to compute runoff and sediment yield in urban and rural basins. In this paper, the model was applied to the Pirapama river basin, located in the coastal zone of the State of Pernambuco. The obtained results were linked to a GIS in order to temporally and spatially identify the areas susceptible to the erosion process within the Pirapama river basin. The model was calibrated with daily rainfall data from two raingauges for the period from 1990 to 2001. From the coupling of the modeling results into a GIS, it was possible to

  3. The dominant erosion processes supplying fine sediment to three major rivers in tropical Australia, the Daly (NT), Mitchell (Qld) and Flinders (Qld) Rivers

    Science.gov (United States)

    Caitcheon, Gary G.; Olley, Jon M.; Pantus, Francis; Hancock, Gary; Leslie, Christopher

    2012-05-01

    The tropics of northern Australia have received relatively little attention with regard to the impact of soil erosion on the many large river systems that are an important part of Australia's water resource, especially given the high potential for erosion when long dry seasons are followed by intense wet season rain. Here we use 137Cs concentrations to determine the erosion processes supplying sediment to two major northern Australian Rivers; the Daly River (Northern Territory), and the Mitchell River (Queensland). We also present data from five sediment samples collected from a 100 km reach of the Cloncurry River, a major tributary of the Flinders River (Queensland). Concentrations of 137Cs in the surface soil and subsurface (channel banks and gully) samples were used to derive 'best fit' probability density functions describing their distributions. These modelled distributions are then used to estimate the relative contribution of these two components to the river sediments. Our results are consistent with channel and gully erosion being the dominant source of sediment, with more than 90% of sediment transported along the main stem of these rivers originating from subsoil. We summarize the findings of similar studies on tropical Australian rivers and conclude that the primary source of sediment delivered to these systems is gully and channel bank erosion. Previously, as a result of catchment scale modelling, sheet-wash and rill erosion was considered to be the major sediment source in these rivers. Identifying the relative importance of sediment sources, as shown in this paper, will provide valuable information for land management planning in the region. This study also reinforces the importance of testing model predictions before they are used to target investment in remedial action.

  4. Uncertainty in soil carbon accounting due to unrecognized soil erosion.

    Science.gov (United States)

    Sanderman, Jonathan; Chappell, Adrian

    2013-01-01

    The movement of soil organic carbon (SOC) during erosion and deposition events represents a major perturbation to the terrestrial carbon cycle. Despite the recognized impact soil redistribution can have on the carbon cycle, few major carbon accounting models currently allow for soil mass flux. Here, we modified a commonly used SOC model to include a soil redistribution term and then applied it to scenarios which explore the implications of unrecognized erosion and deposition for SOC accounting. We show that models that assume a static landscape may be calibrated incorrectly as erosion of SOC is hidden within the decay constants. This implicit inclusion of erosion then limits the predictive capacity of these models when applied to sites with different soil redistribution histories. Decay constants were found to be 15-50% slower when an erosion rate of 15 t soil ha(-1)  yr(-1) was explicitly included in the SOC model calibration. Static models cannot account for SOC change resulting from agricultural management practices focused on reducing erosion rates. Without accounting for soil redistribution, a soil sampling scheme which uses a fixed depth to support model development can create large errors in actual and relative changes in SOC stocks. When modest levels of erosion were ignored, the combined uncertainty in carbon sequestration rates was 0.3-1.0 t CO2  ha(-1)  yr(-1) . This range is similar to expected sequestration rates for many management options aimed at increasing SOC levels. It is evident from these analyses that explicit recognition of soil redistribution is critical to the success of a carbon monitoring or trading scheme which seeks to credit agricultural activities. © 2012 Blackwell Publishing Ltd.

  5. Modelling soil erosion at European scale: towards harmonization and reproducibility

    Science.gov (United States)

    Bosco, C.; de Rigo, D.; Dewitte, O.; Poesen, J.; Panagos, P.

    2015-02-01

    Soil erosion by water is one of the most widespread forms of soil degradation. The loss of soil as a result of erosion can lead to decline in organic matter and nutrient contents, breakdown of soil structure and reduction of the water-holding capacity. Measuring soil loss across the whole landscape is impractical and thus research is needed to improve methods of estimating soil erosion with computational modelling, upon which integrated assessment and mitigation strategies may be based. Despite the efforts, the prediction value of existing models is still limited, especially at regional and continental scale, because a systematic knowledge of local climatological and soil parameters is often unavailable. A new approach for modelling soil erosion at regional scale is here proposed. It is based on the joint use of low-data-demanding models and innovative techniques for better estimating model inputs. The proposed modelling architecture has at its basis the semantic array programming paradigm and a strong effort towards computational reproducibility. An extended version of the Revised Universal Soil Loss Equation (RUSLE) has been implemented merging different empirical rainfall-erosivity equations within a climatic ensemble model and adding a new factor for a better consideration of soil stoniness within the model. Pan-European soil erosion rates by water have been estimated through the use of publicly available data sets and locally reliable empirical relationships. The accuracy of the results is corroborated by a visual plausibility check (63% of a random sample of grid cells are accurate, 83% at least moderately accurate, bootstrap p ≤ 0.05). A comparison with country-level statistics of pre-existing European soil erosion maps is also provided.

  6. EFFECTS OF SLOPE SHAPES ON SOIL EROSION

    Directory of Open Access Journals (Sweden)

    Hüseyin ŞENSOY, Şahin PALTA

    2009-01-01

    Full Text Available Water is one of the most important erosive forces. A great number of factors also play a role in erosion process and slope characteristic is also one of them. The steepness and length of the slope are important factors for runoff and soil erosion. Another slope factor that has an effect on erosion is the shape of the slope. Generally, different erosion and runoff characteristics exist in different slopes which can be classified as uniform, concave, convex and complex shape. In this study, the effects of slope shape on erosion are stated and emphasized by taking similar researches into consideration.

  7. Water Erosion Prediction Using the Revised Universal Soil Loss Equation (RUSLE in a GIS Framework, Central Chile Estimación de la Erosión Hídrica Empleando la Ecuación Universal de Pérdida de Suelo Revisada (RUSLE y SIG en Chile Central

    Directory of Open Access Journals (Sweden)

    Carlos A Bonilla

    2010-03-01

    Full Text Available Soil erosion is a growing problem in Central Chile, particularly in coastal dry lands, where it can significantly decrease the productivity of rainfed agriculture and forestry. In this study, the Revised Universal Soil Loss Equation (RUSLE was integrated into a Geographic Information System (GIS, and used to evaluate the effects of different combinations of vegetative cover on soil erosion rates for Santo Domingo County in Central Chile. Implementing RUSLE in the GIS required a complete description of the county’s soils, climate, topography and current land use/land cover. This information was compiled in rasters of 25 x 25 m cells. RUSLE parameter values were assigned to each cell and annual soil loss estimates were generated on a cell by cell basis. Soil losses were estimated for the current and for three alternate scenarios of vegetative cover. Under current conditions, 39.7% of the county is predicted to have low erosion rates ( 1.1 t ha-1 yr-1. The remainder of the surface (10.2% is not subject to erosion. Under the recommended alternate scenario, 89.3% of the county is predicted to have low erosion rates, and no areas are affected by high soil loss, reducing soil erosion to a level that will not affect long term productivity. This paper describes how RUSLE was implemented in the GIS, and the methodology and equations used to evaluate the effects of the land use/land cover changes.La erosión hídrica es un problema creciente en la Zona Central de Chile, especialmente en el Secano Costero, donde reduce la productividad de los suelos agrícolas y forestales. En este trabajo se empleó la Ecuación Universal de Pérdida de Suelo Revisada (RUSLE integrada a un Sistema de Información Geográfica (GIS para evaluar el efecto de distintas combinaciones de cubierta vegetal en las tasas de erosión en la comuna de Santo Domingo, Chile. La implementación de RUSLE en el GIS requirió la caracterización de suelos, clima, relieve y uso actual del

  8. CFD simulations of flow erosion and flow-induced deformation of needle valve: Effects of operation, structure and fluid parameters

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Hongjun, E-mail: ticky863@126.com [State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu 610500, Sichuan (China); State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan (China); Pan, Qian; Zhang, Wenli; Feng, Guang; Li, Xue [State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu 610500, Sichuan (China)

    2014-07-01

    Highlights: • A combined FSI–CFD and DPM computational method is used to investigate flow erosion and deformation of needle valve. • The numerical model is validated with the comparison of measured and predicted erosion rate. • Effects of operation, structure and fluid parameters on flow erosion and flow-induced deformation are discussed. • Particle diameter has the most significant effect on flow erosion. • Inlet rate has the most obvious effect on flow-induced deformation. - Abstract: A three-dimensional fluid–structure interaction (FSI) computational model coupling with a combined continuum and discrete model has been used to predict the flow erosion rate and flow-induced deformation of needle valve. Comparisons with measured data demonstrate good agreement with the predictions of erosion rate. The flow field distribution of gas-particle flow and the erosion rate and deformation of valve core are captured under different operating and structural conditions with different fluid parameters. The effects of inlet velocity, valve opening and inlet valve channel size, particle concentration, particle diameter and particle phase components are discussed in detail. The results indicate that valve tip has the most severe erosion and deformation, and flow field, erosion rate and deformation of valve are all sensitive to inlet condition changes, structural changes and fluid properties changes. The effect of particle diameter on erosion is the most significant, while the influence of inlet rate on deformation is the greatest one.

  9. Water Erosion in Different Slope Lengths on Bare Soil

    Directory of Open Access Journals (Sweden)

    Bárbara Bagio

    Full Text Available ABSTRACT Water erosion degrades the soil and contaminates the environment, and one influential factor on erosion is slope length. The aim of this study was to quantify losses of soil (SL and water (WL in a Humic Cambisol in a field experiment under natural rainfall conditions from July 4, 2014 to June 18, 2015 in individual events of 41 erosive rains in the Southern Plateau of Santa Catarina and to estimate soil losses through the USLE and RUSLE models. The treatments consisted of slope lengths of 11, 22, 33, and 44 m, with an average degree of slope of 8 %, on bare and uncropped soil that had been cultivated with corn prior to the study. At the end of the corn cycle, the stalk residue was removed from the surface, leaving the roots of the crop in the soil. Soil loss by water erosion is related linearly and positively to the increase in slope length in the span between 11 and 44 m. Soil losses were related to water losses and the Erosivity Index (EI30, while water losses were related to rain depth. Soil losses estimated by the USLE and RUSLE model showed lower values than the values observed experimentally in the field, especially the values estimated by the USLE. The values of factor L calculated for slope length of 11, 22, 33, and 44 m for the two versions (USLE and RUSLE of the soil loss prediction model showed satisfactory results in relation to the values of soil losses observed.

  10. Integrated spatial assessment of wind erosion risk in Hungary

    Directory of Open Access Journals (Sweden)

    L. Pásztor

    2016-11-01

    Full Text Available Wind erosion susceptibility of Hungarian soils was mapped on the national level integrating three factors of the complex phenomenon of deflation (physical soil features, wind characteristics, and land use and land cover. Results of wind tunnel experiments on erodibility of representative soil samples were used for the parametrization of a countrywide map of soil texture compiled for the upper 5 cm layer of soil, which resulted in a map representing threshold wind velocity exceedance. Average wind velocity was spatially estimated with 0.5′ resolution using the Meteorological Interpolation based on Surface Homogenised Data Basis (MISH method elaborated for the spatial interpolation of surface meteorological elements. The probability of threshold wind velocity exceedance was determined based on values predicted by the soil texture map at the grid locations. Ratio values were further interpolated to a finer 1 ha resolution using sand and silt content of the uppermost (0–5 cm layer of soil as spatial co-variables. Land cover was also taken into account, excluding areas that are not relevant to wind erosion (forests, water bodies, settlements, etc., to spatially assess the risk of wind erosion. According to the resulting map of wind erosion susceptibility, about 10 % of the total area of Hungary can be identified as susceptible to wind erosion. The map gives more detailed insight into the spatial distribution of wind-affected areas in Hungary compared to previous studies.

  11. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    Directory of Open Access Journals (Sweden)

    O'Gara Fergal

    2010-11-01

    Full Text Available Abstract Background Catabolite repression control (CRC is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas

  12. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    Science.gov (United States)

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  13. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  14. A model for hydrolytic degradation and erosion of biodegradable polymers.

    Science.gov (United States)

    Sevim, Kevser; Pan, Jingzhe

    2018-01-15

    For aliphatic polyesters such as PLAs and PGAs, there is a strong interplay between the hydrolytic degradation and erosion - degradation leads to a critically low molecular weight at which erosion starts. This paper considers the underlying physical and chemical processes of hydrolytic degradation and erosion. Several kinetic mechanisms are incorporated into a mathematical model in an attempt to explain different behaviours of mass loss observed in experiments. In the combined model, autocatalytic hydrolysis, oligomer production and their diffusion are considered together with surface and interior erosion using a set of differential equations and Monte Carlo technique. Oligomer and drug diffusion are modelled using Fick's law with the diffusion coefficients dependent on porosity. The porosity is due to the formation of cavities which are a result of polymer erosion. The model can follow mass loss and drug release up to 100%, which cannot be explained using a simple reaction-diffusion. The model is applied to two case studies from the literature to demonstrate its validity. The case studies show that a critical molecular weight for the onset of polymer erosion and an incubation period for the polymer dissolution are two critical factors that need to be considered when predicting mass loss and drug release. In order to design bioresorbable implants, it is important to have a mathematical model to predict polymer degradation and corresponding drug release. However, very different behaviours of polymer degradation have been observed and there is no single model that can capture all these behaviours. For the first time, the model presented in this paper is capable of capture all these observed behaviours by switching on and off different underlying mechanisms. Unlike the existing reaction-diffusion models, the model presented here can follow the degradation and drug release all the way to the full disappearance of an implant. Crown Copyright © 2017. Published by