Science.gov

Sample records for accurately predict ice

  1. Arctic Sea Ice Predictability and the Sea Ice Prediction Network

    NASA Astrophysics Data System (ADS)

    Wiggins, H. V.; Stroeve, J. C.

    2014-12-01

    Drastic reductions in Arctic sea ice cover have increased the demand for Arctic sea ice predictions by a range of stakeholders, including local communities, resource managers, industry and the public. The science of sea-ice prediction has been challenged to keep up with these developments. Efforts such as the SEARCH Sea Ice Outlook (SIO; http://www.arcus.org/sipn/sea-ice-outlook) and the Sea Ice for Walrus Outlook have provided a forum for the international sea-ice prediction and observing community to explore and compare different approaches. The SIO, originally organized by the Study of Environmental Change (SEARCH), is now managed by the new Sea Ice Prediction Network (SIPN), which is building a collaborative network of scientists and stakeholders to improve arctic sea ice prediction. The SIO synthesizes predictions from a variety of methods, including heuristic and from a statistical and/or dynamical model. In a recent study, SIO data from 2008 to 2013 were analyzed. The analysis revealed that in some years the predictions were very successful, in other years they were not. Years that were anomalous compared to the long-term trend have proven more difficult to predict, regardless of which method was employed. This year, in response to feedback from users and contributors to the SIO, several enhancements have been made to the SIO reports. One is to encourage contributors to provide spatial probability maps of sea ice cover in September and the first day each location becomes ice-free; these are an example of subseasonal to seasonal, local-scale predictions. Another enhancement is a separate analysis of the modeling contributions. In the June 2014 SIO report, 10 of 28 outlooks were produced from models that explicitly simulate sea ice from dynamic-thermodynamic sea ice models. Half of the models included fully-coupled (atmosphere, ice, and ocean) models that additionally employ data assimilation. Both of these subsets (models and coupled models with data

  2. Predicting September sea ice: Ensemble skill of the SEARCH Sea Ice Outlook 2008-2013

    NASA Astrophysics Data System (ADS)

    Stroeve, Julienne; Hamilton, Lawrence C.; Bitz, Cecilia M.; Blanchard-Wrigglesworth, Edward

    2014-04-01

    Since 2008, the Study of Environmental Arctic Change Sea Ice Outlook has solicited predictions of September sea-ice extent from the Arctic research community. Individuals and teams employ a variety of modeling, statistical, and heuristic approaches to make these predictions. Viewed as monthly ensembles each with one or two dozen individual predictions, they display a bimodal pattern of success. In years when observed ice extent is near its trend, the median predictions tend to be accurate. In years when the observed extent is anomalous, the median and most individual predictions are less accurate. Statistical analysis suggests that year-to-year variability, rather than methods, dominate the variation in ensemble prediction success. Furthermore, ensemble predictions do not improve as the season evolves. We consider the role of initial ice, atmosphere and ocean conditions, and summer storms and weather in contributing to the challenge of sea-ice prediction.

  3. DRA/NASA/ONERA Collaboration on Icing Research. Part 2; Prediction of Airfoil Ice Accretion

    NASA Technical Reports Server (NTRS)

    Wright, William B.; Gent, R. W.; Guffond, Didier

    1997-01-01

    This report presents results from a joint study by DRA, NASA, and ONERA for the purpose of comparing, improving, and validating the aircraft icing computer codes developed by each agency. These codes are of three kinds: (1) water droplet trajectory prediction, (2) ice accretion modeling, and (3) transient electrothermal deicer analysis. In this joint study, the agencies compared their code predictions with each other and with experimental results. These comparison exercises were published in three technical reports, each with joint authorship. DRA published and had first authorship of Part 1 - Droplet Trajectory Calculations, NASA of Part 2 - Ice Accretion Prediction, and ONERA of Part 3 - Electrothermal Deicer Analysis. The results cover work done during the period from August 1986 to late 1991. As a result, all of the information in this report is dated. Where necessary, current information is provided to show the direction of current research. In this present report on ice accretion, each agency predicted ice shapes on two dimensional airfoils under icing conditions for which experimental ice shapes were available. In general, all three codes did a reasonable job of predicting the measured ice shapes. For any given experimental condition, one of the three codes predicted the general ice features (i.e., shape, impingement limits, mass of ice) somewhat better than did the other two. However, no single code consistently did better than the other two over the full range of conditions examined, which included rime, mixed, and glaze ice conditions. In several of the cases, DRA showed that the user's knowledge of icing can significantly improve the accuracy of the code prediction. Rime ice predictions were reasonably accurate and consistent among the codes, because droplets freeze on impact and the freezing model is simple. Glaze ice predictions were less accurate and less consistent among the codes, because the freezing model is more complex and is critically

  4. Analytical ice shape predictions for flight in natural icing conditions

    NASA Technical Reports Server (NTRS)

    Berkowitz, Brian M.; Riley, James T.

    1988-01-01

    LEWICE is an analytical ice prediction code that has been evaluated against icing tunnel data, but on a more limited basis against flight data. Ice shapes predicted by LEWICE is compared with experimental ice shapes accreted on the NASA Lewis Icing Research Aircraft. The flight data selected for comparison includes liquid water content recorded using a hot wire device and droplet distribution data from a laser spectrometer; the ice shape is recorded using stereo photography. The main findings are as follows: (1) An equivalent sand grain roughness correlation different from that used for LEWICE tunnel comparisons must be employed to obtain satisfactory results for flight; (2) Using this correlation and making no other changes in the code, the comparisons to ice shapes accreted in flight are in general as good as the comparisons to ice shapes accreted in the tunnel (as in the case of tunnel ice shapes, agreement is least reliable for large glaze ice shapes at high angles of attack); (3) In some cases comparisons can be somewhat improved by utilizing the code so as to take account of the variation of parameters such as liquid water content, which may vary significantly in flight.

  5. New model accurately predicts reformate composition

    SciTech Connect

    Ancheyta-Juarez, J.; Aguilar-Rodriguez, E. )

    1994-01-31

    Although naphtha reforming is a well-known process, the evolution of catalyst formulation, as well as new trends in gasoline specifications, have led to rapid evolution of the process, including: reactor design, regeneration mode, and operating conditions. Mathematical modeling of the reforming process is an increasingly important tool. It is fundamental to the proper design of new reactors and revamp of existing ones. Modeling can be used to optimize operating conditions, analyze the effects of process variables, and enhance unit performance. Instituto Mexicano del Petroleo has developed a model of the catalytic reforming process that accurately predicts reformate composition at the higher-severity conditions at which new reformers are being designed. The new AA model is more accurate than previous proposals because it takes into account the effects of temperature and pressure on the rate constants of each chemical reaction.

  6. Predictability of the Arctic sea ice edge

    NASA Astrophysics Data System (ADS)

    Goessling, H. F.; Tietsche, S.; Day, J. J.; Hawkins, E.; Jung, T.

    2016-02-01

    Skillful sea ice forecasts from days to years ahead are becoming increasingly important for the operation and planning of human activities in the Arctic. Here we analyze the potential predictability of the Arctic sea ice edge in six climate models. We introduce the integrated ice-edge error (IIEE), a user-relevant verification metric defined as the area where the forecast and the "truth" disagree on the ice concentration being above or below 15%. The IIEE lends itself to decomposition into an absolute extent error, corresponding to the common sea ice extent error, and a misplacement error. We find that the often-neglected misplacement error makes up more than half of the climatological IIEE. In idealized forecast ensembles initialized on 1 July, the IIEE grows faster than the absolute extent error. This means that the Arctic sea ice edge is less predictable than sea ice extent, particularly in September, with implications for the potential skill of end-user relevant forecasts.

  7. On the Predictability of Sea Ice

    NASA Astrophysics Data System (ADS)

    Blanchard-Wrigglesworth, Edward

    We investigate the persistence and predictability of sea ice in numerical models and observations. We first use the 3rd generation Community Climate System Model (CCSM3) General Circulation Model (GCM) to investigate the inherent persistence of sea-ice area and thickness. We find that sea-ice area anomalies have a seasonal decay timescale, exhibiting an initial decorrelation similar to a first order auto-regressive (AR1, or red noise) process. Beyond this initial loss of memory, there is a re-emergence of memory at certain times of the year. There are two distinct modes of re-emergence in the model, one driven by the seasonal coupling of area and thickness anomalies in the summer, the other by the persistence of upper ocean temperature anomalies that originate from ice anomalies in the melt season and then influence ice anomalies in the growth season. Comparison with satellite observations where available indicate these processes appear in nature. We then use the 4th generation CCSM (CCSM4) to investigate the partition of Arctic sea-ice predictability into its initial-value and boundary forced components under present day forcing conditions. We find that initial-value predictability lasts for 1-2 years for sea-ice area, and 3-4 years for sea-ice volume. Forced predictability arises after just 4-5 years for both area and volume. Initial-value predictability of sea-ice area during the summer hinges on the coupling between thickness and area anomalies during that season. We find that the loss of initial-value predictability with time is not uniform --- there is a rapid loss of predictability of sea-ice volume during the late spring early summer associated with snow melt and albedo feedbacks. At the same time, loss of predictability is not uniform across different regions. Given the usefulness of ice thickness as a predictor of summer sea-ice area, we obtain a hindcast of September sea-ice area initializing the GCM on May 1with an estimate of observed sea-ice thickness

  8. A Comparative Study Using CFD to Predict Iced Airfoil Aerodynamics

    NASA Technical Reports Server (NTRS)

    Chi, x.; Li, Y.; Chen, H.; Addy, H. E.; Choo, Y. K.; Shih, T. I-P.

    2005-01-01

    WIND, Fluent, and PowerFLOW were used to predict the lift, drag, and moment coefficients of a business-jet airfoil with a rime ice (rough and jagged, but no protruding horns) and with a glaze ice (rough and jagged end has two or more protruding horns) for angles of attack from zero to and after stall. The performance of the following turbulence models were examined by comparing predictions with available experimental data. Spalart-Allmaras (S-A), RNG k-epsilon, shear-stress transport, v(sup 2)-f, and a differential Reynolds stress model with and without non-equilibrium wall functions. For steady RANS simulations, WIND and FLUENT were found to give nearly identical results if the grid about the iced airfoil, the turbulence model, and the order of accuracy of the numerical schemes used are the same. The use of wall functions was found to be acceptable for the rime ice configuration and the flow conditions examined. For rime ice, the S-A model was found to predict accurately until near the stall angle. For glaze ice, the CFD predictions were much less satisfactory for all turbulence models and codes investigated because of the large separated region produced by the horns. For unsteady RANS, WIND and FLUENT did not provide better results. PowerFLOW, based on the Lattice Boltzmann method, gave excellent results for the lift coefficient at and near stall for the rime ice, where the flow is inherently unsteady.

  9. How to measure the wind accurately in icing conditions

    SciTech Connect

    Kenyon, P.R.; Blittersdorf, D.C.

    1995-12-31

    Atmospheric icing occurs frequently in the northwestern, Midwestern and northeastern United States from early October through April at locations with high average wind speeds. It has caused wind data recovery problems at sites as far south as Texas. Icing slows anemometers used to assess the wind resource. Data recovered from sites prone to icing will show lower average wind speeds than actual, undervaluing them. The assessment of a wind site must present the actual wind potential. Anemometers used at these sites must remain free of ice. This report presents a description of icing types and the data distortion they cause based on NRG field experience. A brief history of anti-icing anemometers available today for remote site and turbine site monitoring follows. Comparative data of NRG`s IceFree anemometers and the industry standard unheated anemometer is included.

  10. Sea Ice Prediction Has Easy and Difficult Years

    NASA Technical Reports Server (NTRS)

    Hamilton, Lawrence C.; Bitz, Cecilia M.; Blanchard-Wrigglesworth, Edward; Cutler, Matthew; Kay, Jennifer; Meier, Walter N.; Stroeve, Julienne; Wiggins, Helen

    2014-01-01

    Arctic sea ice follows an annual cycle, reaching its low point in September each year. The extent of sea ice remaining at this low point has been trending downwards for decades as the Arctic warms. Around the long-term downward trend, however, there is significant variation in the minimum extent from one year to the next. Accurate forecasts of yearly conditions would have great value to Arctic residents, shipping companies, and other stakeholders and are the subject of much current research. Since 2008 the Sea Ice Outlook (SIO) (http://www.arcus.org/search-program/seaiceoutlook) organized by the Study of Environmental Arctic Change (SEARCH) (http://www.arcus.org/search-program) has invited predictions of the September Arctic sea ice minimum extent, which are contributed from the Arctic research community. Individual predictions, based on a variety of approaches, are solicited in three cycles each year in early June, July, and August. (SEARCH 2013).

  11. Navy Sea Ice Prediction Systems

    DTIC Science & Technology

    2002-01-01

    ANSI Std Z39-18 45 Oceanography • Vol. 15 • No. 1/2002 part of the International Arctic Buoy Program ( IABP ). These data have been used to support...real-time opera- tions in the Arctic as well as meteorological and oceanographic research of the Arctic basin. More infor- mation on the IABP is...ice thickness. Figure 5a represents the observed ice motion derived from the available IABP drifting buoys. Figures 5a and 5b show the qualitative

  12. Predicting Accumulations of Ice on Aerodynamic Surfaces

    NASA Technical Reports Server (NTRS)

    Bidwell, Colin; Potapczuk, Mark; Addy, Gene; Wright, William

    2003-01-01

    LEWICE is a computer program that predicts the accumulation of ice on two-dimensional aerodynamic surfaces under conditions representative of the flight of an aircraft through an icing cloud. The software first calculates the airflow surrounding the body of interest, then uses the airflow to compute the trajectories of water droplets that impinge on the surface of the body. The droplet trajectories are also used to compute impingement limits and local collection efficiencies, which are used in subsequent ice-growth calculations and are also useful for designing systems to protect against icing. Next, the software predicts the shape of accumulating ice by modeling transfers of mass and energy in small control volumes. The foregoing computations are repeated over several computational time steps until the total icing exposure time is reached. Results of computations by LEWICE have been compared with an extensive database of measured ice shapes obtained from experiments, and have been shown to closely approximate those shapes under most conditions of interest to the aviation community.

  13. A gene expression biomarker accurately predicts estrogen ...

    EPA Pesticide Factsheets

    The EPA’s vision for the Endocrine Disruptor Screening Program (EDSP) in the 21st Century (EDSP21) includes utilization of high-throughput screening (HTS) assays coupled with computational modeling to prioritize chemicals with the goal of eventually replacing current Tier 1 screening tests. The ToxCast program currently includes 18 HTS in vitro assays that evaluate the ability of chemicals to modulate estrogen receptor α (ERα), an important endocrine target. We propose microarray-based gene expression profiling as a complementary approach to predict ERα modulation and have developed computational methods to identify ERα modulators in an existing database of whole-genome microarray data. The ERα biomarker consisted of 46 ERα-regulated genes with consistent expression patterns across 7 known ER agonists and 3 known ER antagonists. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression data sets from experiments in MCF-7 cells. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% or 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) OECD ER reference chemicals including “very weak” agonists and replicated predictions based on 18 in vitro ER-associated HTS assays. For 114 chemicals present in both the HTS data and the MCF-7 c

  14. You Can Accurately Predict Land Acquisition Costs.

    ERIC Educational Resources Information Center

    Garrigan, Richard

    1967-01-01

    Land acquisition costs were tested for predictability based upon the 1962 assessed valuations of privately held land acquired for campus expansion by the University of Wisconsin from 1963-1965. By correlating the land acquisition costs of 108 properties acquired during the 3 year period with--(1) the assessed value of the land, (2) the assessed…

  15. Gravel transport by ice in a subarctic river from accurate laser scanning

    NASA Astrophysics Data System (ADS)

    Lotsari, Eliisa; Wang, Yunsheng; Kaartinen, Harri; Jaakkola, Anttoni; Kukko, Antero; Vaaja, Matti; Hyyppä, Hannu; Hyyppä, Juha; Alho, Petteri

    2015-10-01

    For decades the importance of ice and the effects of cold-region processes on river channel morphology have been discussed, with a general consensus as to their importance emerging only recently. River ice cover, anchor ice, frazil ice, and ice jams may not only scour the channel bed and banks but also pick up, transport, and deposit fine sediments and gravels during winter, especially during the spring ice breakup period. However, knowledge of the interactions between coarse sediment transport and ice processes remains insufficient, particularly in rockier river reaches, with a lack of accurate and sufficiently extensive data hindering their quantification. The aim of this study was to quantify and analyse the impact of river ice on gravel transport in a subarctic river during one winter via the acquisition of laser scanning data for the river channel and ice surface. Terrestrial and mobile laser scanning were performed in 2012-2013 on the Tana River in northern Finland. Both of these techniques are considered accurate and applicable for detecting elevation and volumetric changes in river bed, defining gravel clast sizes, and detecting the movement of individual clasts. More importantly, ice surface, thickness, and decay during spring were also captured via laser scanning. In the winter of 2012-2013, a period characterised by an absence of ice jams and mid-winter ice-decay periods, with spring ice breakup discharges close to average yearly conditions, ice had the most significant role, greater than that of flowing water, in erosion and transport of coarse sediment from the channel bed and gently sloping banks. Changes in river bed elevation and volume were recorded throughout the study site, and erosion predominated. In addition to broader scale erosion, the movement of single clasts up to 2 m in size occurred. However, the observed overall channel change patterns did not coincide with the areas of fastest ice decay. The obtained results could also be applied to

  16. Towards more accurate vegetation mortality predictions

    DOE PAGES

    Sevanto, Sanna Annika; Xu, Chonggang

    2016-09-26

    Predicting the fate of vegetation under changing climate is one of the major challenges of the climate modeling community. Here, terrestrial vegetation dominates the carbon and water cycles over land areas, and dramatic changes in vegetation cover resulting from stressful environmental conditions such as drought feed directly back to local and regional climate, potentially leading to a vicious cycle where vegetation recovery after a disturbance is delayed or impossible.

  17. Accurate and stable time stepping in ice sheet modeling

    NASA Astrophysics Data System (ADS)

    Cheng, Gong; Lötstedt, Per; von Sydow, Lina

    2017-01-01

    In this paper we introduce adaptive time step control for simulation of the evolution of ice sheets. The discretization error in the approximations is estimated using "Milne's device" by comparing the result from two different methods in a predictor-corrector pair. Using a predictor-corrector pair the expensive part of the procedure, the solution of the velocity and pressure equations, is performed only once per time step and an estimate of the local error is easily obtained. The stability of the numerical solution is maintained and the accuracy is controlled by keeping the local error below a given threshold using PI-control. Depending on the threshold, the time step Δt is bound by stability requirements or accuracy requirements. Our method takes a shorter Δt than an implicit method but with less work in each time step and the solver is simpler. The method is analyzed theoretically with respect to stability and applied to the simulation of a 2D ice slab and a 3D circular ice sheet. The stability bounds in the experiments are explained by and agree well with the theoretical results.

  18. A prediction method of ice breaking resistance using a multiple regression analysis

    NASA Astrophysics Data System (ADS)

    Cho, Seong-Rak; Lee, Sungsu

    2015-07-01

    The two most important tasks of icebreakers are first to secure a sailing route by breaking the thick sea ice and second to sail efficiently herself for purposes of exploration and transportation in the polar seas. The resistance of icebreakers is a priority factor at the preliminary design stage; not only must their sailing efficiency be satisfied, but the design of the propulsion system will be directly affected. Therefore, the performance of icebreakers must be accurately calculated and evaluated through the use of model tests in an ice tank before construction starts. In this paper, a new procedure is developed, based on model tests, to estimate a ship's ice breaking resistance during continuous ice-breaking in ice. Some of the factors associated with crushing failures are systematically considered in order to correctly estimate her ice-breaking resistance. This study is intended to contribute to the improvement of the techniques for ice resistance prediction with ice breaking ships.

  19. A predictable and accurate technique with elastomeric impression materials.

    PubMed

    Barghi, N; Ontiveros, J C

    1999-08-01

    A method for obtaining more predictable and accurate final impressions with polyvinylsiloxane impression materials in conjunction with stock trays is proposed and tested. Heavy impression material is used in advance for construction of a modified custom tray, while extra-light material is used for obtaining a more accurate final impression.

  20. Accurate torque-speed performance prediction for brushless dc motors

    NASA Astrophysics Data System (ADS)

    Gipper, Patrick D.

    Desirable characteristics of the brushless dc motor (BLDCM) have resulted in their application for electrohydrostatic (EH) and electromechanical (EM) actuation systems. But to effectively apply the BLDCM requires accurate prediction of performance. The minimum necessary performance characteristics are motor torque versus speed, peak and average supply current and efficiency. BLDCM nonlinear simulation software specifically adapted for torque-speed prediction is presented. The capability of the software to quickly and accurately predict performance has been verified on fractional to integral HP motor sizes, and is presented. Additionally, the capability of torque-speed prediction with commutation angle advance is demonstrated.

  1. Prediction of ice skating performance with off-ice testing in women's ice hockey players.

    PubMed

    Bracko, M R; George, J D

    2001-02-01

    Off-ice predictors of skating performance have not been investigated for women's hockey players. The purpose of this study was to identify the off-ice variables associated with high-performance skating acceleration, speed, agility, and on-ice anaerobic capacity and power in women's ice hockey players. Sixty-one women's ice hockey players between the ages of 8 and 16 years (x age = 12.18 +/- 2.05 years, x playing experience = 4.68 +/- 2.69 years) participated in the study. Subjects were 1-4 months postseason. Some players were continuing to play once per week during the off-season. Skating tests (ST) included (a) 6.10-m acceleration, (b) 47.85-m speed, (c) agility cornering S turn, and (d) modified repeat skate test (MRS). Two trials of each ST were measured with a photoelectric timing system (except MRS, which was measured with 1 trial). The off-ice variables that were evaluated included age, years of playing experience, height, body mass, predicted fat percentage, sit-and-reach flexibility, vertical jump height, 40-yd dash time, and 1-minute timed sit-ups and push-ups. The results of this study show that 40-yd dash time is the strongest predictor of skating speed in women's hockey players ages 8-16 years old. From the regression procedure the best prediction equation was speed = 4.913 - (0.0107 x kilograms) + (0.4356 x 40-yd dash time).

  2. Impact of sea ice initialization on sea ice and atmosphere prediction skill on seasonal timescales

    NASA Astrophysics Data System (ADS)

    Guemas, V.; Chevallier, M.; Déqué, M.; Bellprat, O.; Doblas-Reyes, F.

    2016-04-01

    We present a robust assessment of the impact of sea ice initialization from reconstructions of the real state on the sea ice and atmosphere prediction skill. We ran two ensemble seasonal prediction experiments from 1979 to 2012 : one using realistic sea ice initial conditions and another where sea ice is initialized from a climatology, with two forecast systems. During the melting season in the Arctic Ocean, sea ice forecasts become skilful with sea ice initialization until 3-5 months ahead, thanks to the memory held by sea ice thickness. During the freezing season in both the Arctic and Antarctic Oceans, sea ice forecasts are skilful for 7 and 2 months, respectively, with negligible differences between the two experiments, the memory being held by the ocean heat content. A weak impact on the atmosphere prediction skill is obtained.

  3. Off-Ice Anaerobic Power Does Not Predict On-Ice Repeated Shift Performance in Hockey.

    PubMed

    Peterson, Ben J; Fitzgerald, John S; Dietz, Calvin C; Ziegler, Kevin S; Baker, Sarah E; Snyder, Eric M

    2016-09-01

    Peterson, BJ, Fitzgerald, JS, Dietz, CC, Ziegler, KS, Baker, SE, and Snyder, EM. Off-ice anaerobic power does not predict on-ice repeated shift performance in hockey. J Strength Cond Res 30(9): 2375-2381, 2016-Anaerobic power is a significant predictor of acceleration and top speed in team sport athletes. Historically, these findings have been applied to ice hockey although recent research has brought their validity for this sport into question. As ice hockey emphasizes the ability to repeatedly produce power, single bout anaerobic power tests should be examined to determine their ability to predict on-ice performance. We tested whether conventional off-ice anaerobic power tests could predict on-ice acceleration, top speed, and repeated shift performance. Forty-five hockey players, aged 18-24 years, completed anthropometric, off-ice, and on-ice tests. Anthropometric and off-ice testing included height, weight, body composition, vertical jump, and Wingate tests. On-ice testing consisted of acceleration, top speed, and repeated shift fatigue tests. Vertical jump (VJ) (r = -0.42; r = -0.58), Wingate relative peak power (WRPP) (r = -0.32; r = -0.43), and relative mean power (WRMP) (r = -0.34; r = -0.48) were significantly correlated (p ≤ 0.05) to on-ice acceleration and top speed, respectively. Conversely, none of the off-ice tests correlated with on-ice repeated shift performance, as measured by first gate, second gate, or total course fatigue; VJ (r = 0.06; r = 0.13; r = 0.09), WRPP (r = 0.06; r = 0.14; r = 0.10), or WRMP (r = -0.10; r = -0.01; r = -0.01). Although conventional off-ice anaerobic power tests predict single bout on-ice acceleration and top speed, they neither predict the repeated shift ability of the player, nor are good markers for performance in ice hockey.

  4. On the Accurate Prediction of CME Arrival At the Earth

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Hess, Phillip

    2016-07-01

    We will discuss relevant issues regarding the accurate prediction of CME arrival at the Earth, from both observational and theoretical points of view. In particular, we clarify the importance of separating the study of CME ejecta from the ejecta-driven shock in interplanetary CMEs (ICMEs). For a number of CME-ICME events well observed by SOHO/LASCO, STEREO-A and STEREO-B, we carry out the 3-D measurements by superimposing geometries onto both the ejecta and sheath separately. These measurements are then used to constrain a Drag-Based Model, which is improved through a modification of including height dependence of the drag coefficient into the model. Combining all these factors allows us to create predictions for both fronts at 1 AU and compare with actual in-situ observations. We show an ability to predict the sheath arrival with an average error of under 4 hours, with an RMS error of about 1.5 hours. For the CME ejecta, the error is less than two hours with an RMS error within an hour. Through using the best observations of CMEs, we show the power of our method in accurately predicting CME arrival times. The limitation and implications of our accurate prediction method will be discussed.

  5. Predicting uncertainty in future marine ice sheet volume using Bayesian statistical methods

    NASA Astrophysics Data System (ADS)

    Davis, A. D.

    2015-12-01

    The marine ice instability can trigger rapid retreat of marine ice streams. Recent observations suggest that marine ice systems in West Antarctica have begun retreating. However, unknown ice dynamics, computationally intensive mathematical models, and uncertain parameters in these models make predicting retreat rate and ice volume difficult. In this work, we fuse current observational data with ice stream/shelf models to develop probabilistic predictions of future grounded ice sheet volume. Given observational data (e.g., thickness, surface elevation, and velocity) and a forward model that relates uncertain parameters (e.g., basal friction and basal topography) to these observations, we use a Bayesian framework to define a posterior distribution over the parameters. A stochastic predictive model then propagates uncertainties in these parameters to uncertainty in a particular quantity of interest (QoI)---here, the volume of grounded ice at a specified future time. While the Bayesian approach can in principle characterize the posterior predictive distribution of the QoI, the computational cost of both the forward and predictive models makes this effort prohibitively expensive. To tackle this challenge, we introduce a new Markov chain Monte Carlo method that constructs convergent approximations of the QoI target density in an online fashion, yielding accurate characterizations of future ice sheet volume at significantly reduced computational cost.Our second goal is to attribute uncertainty in these Bayesian predictions to uncertainties in particular parameters. Doing so can help target data collection, for the purpose of constraining the parameters that contribute most strongly to uncertainty in the future volume of grounded ice. For instance, smaller uncertainties in parameters to which the QoI is highly sensitive may account for more variability in the prediction than larger uncertainties in parameters to which the QoI is less sensitive. We use global sensitivity

  6. Accelerated Prediction of the Polar Ice and Global Ocean (APPIGO)

    DTIC Science & Technology

    2013-09-30

    SEP 2013 2. REPORT TYPE 3. DATES COVERED 00-00-2013 to 00-00-2013 4. TITLE AND SUBTITLE Accelerated Prediction of the Polar Ice and Global...the Polar Ice and Global Ocean (APPIGO) Eric P. Chassignet Center for Ocean-Atmospheric Prediction Studies Florida State University phone: (850...architectures. These codes form the ocean and sea ice components of the Navy’s Arctic Cap Nowcast/Forecast System (ACNFS) and the Navy Global Ocean

  7. Stochastic sea ice parameterizations and impacts on polar predictability

    NASA Astrophysics Data System (ADS)

    Juricke, Stephan; Goessling, Helge; Jung, Thomas

    2015-04-01

    Stochastic sea ice parameterizations are implemented in a global coupled model to include first estimates of model uncertainty in the assessment of sea ice predictability. The impact of incorporating estimates of model uncertainty in the sea ice dynamics is compared to the impact of atmospheric initial condition uncertainty. In this context a set of ensembles with stochastic sea ice strength perturbations and a set of ensembles with atmospheric initial condition perturbations are investigated. Seasonal integrations show that especially during the first weeks the incorporation of model uncertainty estimates in the sea ice dynamics leads to a significant increase in ensemble spread of sea ice thickness in the central Arctic and along coastlines when compared to the ensembles with atmospheric initial perturbations. The latter, in contrast, produce significantly larger variability along the ice edge. During the first weeks of the integration, applying the combined perturbations leads to an accumulation of spread from both uncertainties pointing at the importance of including estimates of model uncertainty for subseasonal sea ice predictions. After the first few weeks, however, the differences between ensemble spreads become mostly insignificant so that estimates of seasonal potential sea ice predictability for the Arctic remain largely unaffected by uncertainty estimates in the sea ice dynamics. For the Antarctic sea ice, differences in sea ice thickness spread between the different ensemble configurations are less pronounced throughout the year. Stochastic perturbations are also applied to the sea ice thermodynamics, namely the sea ice albedo parameterization, to investigate the diverse impacts of the incorporation of uncertainty estimates in different parts of the sea ice model, affecting different regions of the polar regions and at different times during the annual cycle.

  8. Land-ice modeling for sea-level prediction

    SciTech Connect

    Lipscomb, William H

    2010-06-11

    There has been major progress in ice sheet modeling since IPCC AR4. We will soon have efficient higherorder ice sheet models that can run at ",1 km resolution for entire ice sheets, either standalone or coupled to GeMs. These models should significantly reduce uncertainties in sea-level predictions. However, the least certain and potentially greatest contributions to 21st century sea-level rise may come from ice-ocean interactions, especially in West Antarctica. This is a coupled modeling problem that requires collaboration among ice, ocean and atmosphere modelers.

  9. Ice Accretion Prediction on Wind Turbines and Consequent Power Losses

    NASA Astrophysics Data System (ADS)

    Yirtici, Ozcan; Tuncer, Ismail H.; Ozgen, Serkan

    2016-09-01

    Ice accretion on wind turbine blades modifies the sectional profiles and causes alteration in the aerodynamic characteristic of the blades. The objective of this study is to determine performance losses on wind turbines due to the formation of ice in cold climate regions and mountainous areas where wind energy resources are found. In this study, the Blade Element Momentum method is employed together with an ice accretion prediction tool in order to estimate the ice build-up on wind turbine blades and the energy production for iced and clean blades. The predicted ice shapes of the various airfoil profiles are validated with the experimental data and it is shown that the tool developed is promising to be used in the prediction of power production losses of wind turbines.

  10. How predictable is a summer-ice free Arctic?

    NASA Astrophysics Data System (ADS)

    Jahn, Alexandra

    2016-04-01

    There is large interest from different stakeholders in when we will first see a summer ice-free Arctic Ocean. However, while the CMIP5 models agree that we will see a further decline of the Arctic sea ice cover over the 21st century, their projections of when an ice-free Arctic will occur has a range of over 100 years for even the strongest forcing scenario, the RCP8.5. A large part of this uncertainty stems from model biases in the simulation of Arctic sea ice in some models. But apart from this bias, how predictable is the Arctic sea ice extent and the timing of the first ice-free Arctic summer in general? Using the Community Earth System Model (CESM) large ensemble with 40+ members for RCP8.5 and the CESM medium ensemble with 15 members for RCP4.5, we will show that internal variability leads to a range of ~20 years for predictions of threshold crossing of Arctic sea ice, limiting the long-term predictability of when an ice-free Arctic Ocean can first be expected. A detailed analysis of the trajectories of the individual ensemble members will reveal whether there are features of the climate system that allow an improvement of this predictability as we get closer to a summer ice-free Arctic.

  11. Passive samplers accurately predict PAH levels in resident crayfish.

    PubMed

    Paulik, L Blair; Smith, Brian W; Bergmann, Alan J; Sower, Greg J; Forsberg, Norman D; Teeguarden, Justin G; Anderson, Kim A

    2016-02-15

    Contamination of resident aquatic organisms is a major concern for environmental risk assessors. However, collecting organisms to estimate risk is often prohibitively time and resource-intensive. Passive sampling accurately estimates resident organism contamination, and it saves time and resources. This study used low density polyethylene (LDPE) passive water samplers to predict polycyclic aromatic hydrocarbon (PAH) levels in signal crayfish, Pacifastacus leniusculus. Resident crayfish were collected at 5 sites within and outside of the Portland Harbor Superfund Megasite (PHSM) in the Willamette River in Portland, Oregon. LDPE deployment was spatially and temporally paired with crayfish collection. Crayfish visceral and tail tissue, as well as water-deployed LDPE, were extracted and analyzed for 62 PAHs using GC-MS/MS. Freely-dissolved concentrations (Cfree) of PAHs in water were calculated from concentrations in LDPE. Carcinogenic risks were estimated for all crayfish tissues, using benzo[a]pyrene equivalent concentrations (BaPeq). ∑PAH were 5-20 times higher in viscera than in tails, and ∑BaPeq were 6-70 times higher in viscera than in tails. Eating only tail tissue of crayfish would therefore significantly reduce carcinogenic risk compared to also eating viscera. Additionally, PAH levels in crayfish were compared to levels in crayfish collected 10 years earlier. PAH levels in crayfish were higher upriver of the PHSM and unchanged within the PHSM after the 10-year period. Finally, a linear regression model predicted levels of 34 PAHs in crayfish viscera with an associated R-squared value of 0.52 (and a correlation coefficient of 0.72), using only the Cfree PAHs in water. On average, the model predicted PAH concentrations in crayfish tissue within a factor of 2.4 ± 1.8 of measured concentrations. This affirms that passive water sampling accurately estimates PAH contamination in crayfish. Furthermore, the strong predictive ability of this simple model suggests

  12. Inverter Modeling For Accurate Energy Predictions Of Tracking HCPV Installations

    NASA Astrophysics Data System (ADS)

    Bowman, J.; Jensen, S.; McDonald, Mark

    2010-10-01

    High efficiency high concentration photovoltaic (HCPV) solar plants of megawatt scale are now operational, and opportunities for expanded adoption are plentiful. However, effective bidding for sites requires reliable prediction of energy production. HCPV module nameplate power is rated for specific test conditions; however, instantaneous HCPV power varies due to site specific irradiance and operating temperature, and is degraded by soiling, protective stowing, shading, and electrical connectivity. These factors interact with the selection of equipment typically supplied by third parties, e.g., wire gauge and inverters. We describe a time sequence model accurately accounting for these effects that predicts annual energy production, with specific reference to the impact of the inverter on energy output and interactions between system-level design decisions and the inverter. We will also show two examples, based on an actual field design, of inverter efficiency calculations and the interaction between string arrangements and inverter selection.

  13. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    SciTech Connect

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

  14. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  15. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    PubMed Central

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel C.; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-01-01

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification. PMID:23499924

  16. Using reanalysis data for the prediction of seasonal wind turbine power losses due to icing

    NASA Astrophysics Data System (ADS)

    Burtch, Daniel G.

    The Northern Plains region of the United States is home to a significant amount of potential wind energy. However, in winter months capturing this potential power is severely impacted by the meteorological conditions, in the form of icing. Predicting the expected loss in power production due to icing is a valuable parameter that can be used in wind turbine operations, determination of wind turbine site locations and long-term energy estimates which are used for financing purposes. Currently, losses due to icing must be estimated when developing predictions for turbine feasibility and financing studies, while icing maps, a tool commonly used in Europe, are lacking in the United States. This study uses the Modern-Era Retrospective Analysis for Research and Applications (MERRA) dataset in conjunction with turbine production data and in-situ wind measurements to investigate six methods of predicting seasonal losses (October-March) due to icing at two sites located in Petersburg, ND and Valley City, ND. The prediction of icing losses is based on temperature and relative humidity thresholds and is accomplished using six methods. Three methods use a Measure-Correlate-Predict (MCP) and flow model (WAsP) analysis for the determination of wind speeds and MERRA for temperature and relative humidity, while three methods use MERRA for all three variables. For each season from 2002 to 2010, the predicted losses due to icing are determined for a range of relative humidity thresholds and compared with observed icing losses. An optimal relative humidity is then determined and tested on all seasons from 2002 to 2013. The prediction methods are then compared to a common practice used in the wind energy industry of assuming a constant percentage loss for icing over the same time period. The three methods using MERRA data alone show severe deficiencies in the accurate determination of wind speeds which leads to a large underprediction in accurate power output. Of the three MCP

  17. Mouse models of human AML accurately predict chemotherapy response

    PubMed Central

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S.; Zhao, Zhen; Rappaport, Amy R.; Luo, Weijun; McCurrach, Mila E.; Yang, Miao-Miao; Dolan, M. Eileen; Kogan, Scott C.; Downing, James R.; Lowe, Scott W.

    2009-01-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients. PMID:19339691

  18. Mouse models of human AML accurately predict chemotherapy response.

    PubMed

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S; Zhao, Zhen; Rappaport, Amy R; Luo, Weijun; McCurrach, Mila E; Yang, Miao-Miao; Dolan, M Eileen; Kogan, Scott C; Downing, James R; Lowe, Scott W

    2009-04-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients.

  19. Turbulence Models for Accurate Aerothermal Prediction in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang-Hong; Wu, Yi-Zao; Wang, Jiang-Feng

    Accurate description of the aerodynamic and aerothermal environment is crucial to the integrated design and optimization for high performance hypersonic vehicles. In the simulation of aerothermal environment, the effect of viscosity is crucial. The turbulence modeling remains a major source of uncertainty in the computational prediction of aerodynamic forces and heating. In this paper, three turbulent models were studied: the one-equation eddy viscosity transport model of Spalart-Allmaras, the Wilcox k-ω model and the Menter SST model. For the k-ω model and SST model, the compressibility correction, press dilatation and low Reynolds number correction were considered. The influence of these corrections for flow properties were discussed by comparing with the results without corrections. In this paper the emphasis is on the assessment and evaluation of the turbulence models in prediction of heat transfer as applied to a range of hypersonic flows with comparison to experimental data. This will enable establishing factor of safety for the design of thermal protection systems of hypersonic vehicle.

  20. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    PubMed Central

    Noecker, Cecilia; Schaefer, Krista; Zaccheo, Kelly; Yang, Yiding; Day, Judy; Ganusov, Vitaly V.

    2015-01-01

    Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results

  1. Arctic Sea Ice Predictability and Prediction on Seasonal-to-Decadal Timescales

    NASA Astrophysics Data System (ADS)

    Guemas, V.; Blanchard-Wrigglesworth, E.; Chevallier, M.; Déqué, M.; Doblas-Reyes, F.; Fuckar, N. S.; Volpi, D.; Salas y Mélia, D.

    2014-12-01

    Sea ice stands as a major component of the climate system through its key impact on the water and energy budgets and it substantially impacts local and remote atmospheric and oceanic circulations. The societal and economic perspectives of Arctic sea ice prediction on seasonal-to-decadal timescales have led to increasing efforts in the development of sea ice forecast systems. An overview of the potential sources of Arctic sea ice predictability on these timescales will be given. Then, current approaches to generate ensemble sea ice reconstructions and initialize climate predictions will be described. The performances over the satellite era of the EC-Earth and CNRM-CM coupled models in predicting the Arctic sea ice cover and its spatial characteristics on seasonal timescales will finally be presented.

  2. Cohesion predicts success in junior ice hockey.

    PubMed

    Salminen, S; Luhtanen, P

    1998-10-01

    This study examined the relationship between cohesion measured by the Group Environment Questionnaire and success measured by winning percentage with over 200 junior ice hockey players. The cohesion explained 29% of the variance of the success. Scores on task cohesion were better predictors of success than social cohesion.

  3. A parallel high-order accurate finite element nonlinear Stokes ice sheet model and benchmark experiments: A PARALLEL FEM STOKES ICE SHEET MODEL

    SciTech Connect

    Leng, Wei; Ju, Lili; Gunzburger, Max; Price, Stephen; Ringler, Todd

    2012-01-04

    The numerical modeling of glacier and ice sheet evolution is a subject of growing interest, in part because of the potential for models to inform estimates of global sea level change. This paper focuses on the development of a numerical model that determines the velocity and pressure fields within an ice sheet. Our numerical model features a high-fidelity mathematical model involving the nonlinear Stokes system and combinations of no-sliding and sliding basal boundary conditions, high-order accurate finite element discretizations based on variable resolution grids, and highly scalable parallel solution strategies, all of which contribute to a numerical model that can achieve accurate velocity and pressure approximations in a highly efficient manner. We demonstrate the accuracy and efficiency of our model by analytical solution tests, established ice sheet benchmark experiments, and comparisons with other well-established ice sheet models.

  4. Early Student Support to Investigate the Role of Sea Ice-Albedo Feedback in Sea Ice Predictions

    DTIC Science & Technology

    2014-09-30

    Ice-Albedo Feedback in Sea Ice Predictions Cecilia M. Bitz Atmospheric Sciences MS351640 University of Washington Seattle, WA 98196-1640 phone...TERM GOALS The overarching goals of this project are to understand the role of sea ice-albedo feedback on sea ice predictability, to improve how... feedback in models, and thereby directly relate feedback to predictability. We will use initial conditions from the model itself in idealized

  5. Fast and accurate predictions of covalent bonds in chemical space

    NASA Astrophysics Data System (ADS)

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  6. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-07

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  7. On using numerical sea-ice prediction and indigenous observations to improve operational sea-ice forecasts during spring in the bering sea

    NASA Astrophysics Data System (ADS)

    Deemer, Gregory Joseph

    Impacts of a rapidly changing climate are amplified in the Arctic. The most notorious change has come in the form of record-breaking summertime sea-ice retreat. Larger areas of open water and a prolonged ice-free season create opportunity for some industries, but bring new challenges to indigenous populations that rely on sea-ice cover for subsistence. Observed and projected increases in maritime activities require accurate sea-ice forecasts on the weather timescale, which are currently lacking. Motivated by this need, this study explores how new modeling developments and local-scale observations can contribute to improving sea-ice forecasts. The Arctic Cap Nowcast/Forecast System, a research sea-ice forecast model developed by the U.S. Navy, is evaluated for forecast skill. Forecasts of ice concentration, thickness, and drift speed produced by the model from April through June 2011 in the Bering Sea were investigated to determine how the model performs relative to persistence and climatology. Results show that model forecasts can outperform forecasts based on climatology or persistence. However, predictive skill is less consistent during powerful, synoptic-scale events and near the Bering Slope. Forecast case studies in Western Alaska were presented. Community-based observations from recognized indigenous sea-ice experts have been analyzed to gauge the prospect of using local observations in the operational sea-ice monitoring and prediction process. Local observations were discussed in the context of cross-validating model guidance, data sources used in operational ice monitoring, and public sea-ice information products issued by the U.S. National Weather Service. Instrumentation for observing sea-ice and weather at the local scale was supplied to key observers. The instrumentation shows utility in the field and may help translate the context of indigenous observations and provide ground-truth data for use by forecasters.

  8. Forecasting severe ice storms using numerical weather prediction: the March 2010 Newfoundland event

    NASA Astrophysics Data System (ADS)

    Hosek, J.; Musilek, P.; Lozowski, E.; Pytlak, P.

    2011-02-01

    The northeast coast of North America is frequently hit by severe ice storms. These freezing rain events can produce large ice accretions that damage structures, frequently power transmission and distribution infrastructure. For this reason, it is highly desirable to model and forecast such icing events, so that the consequent damages can be prevented or mitigated. The case study presented in this paper focuses on the March 2010 ice storm event that took place in eastern Newfoundland. We apply a combination of a numerical weather prediction model and an ice accretion algorithm to simulate a forecast of this event. The main goals of this study are to compare the simulated meteorological variables to observations, and to assess the ability of the model to accurately predict the ice accretion load for different forecast horizons. The duration and timing of the freezing rain event that occurred between the night of 4 March and the morning of 6 March was simulated well in all model runs. The total precipitation amounts in the model, however, differed by up to a factor of two from the observations. The accuracy of the model air temperature strongly depended on the forecast horizon, but it was acceptable for all simulation runs. The simulated accretion loads were also compared to the design values for power delivery structures in the region. The results indicated that the simulated values exceeded design criteria in the areas of reported damage and power outages.

  9. IRIS: Towards an Accurate and Fast Stage Weight Prediction Method

    NASA Astrophysics Data System (ADS)

    Taponier, V.; Balu, A.

    2002-01-01

    The knowledge of the structural mass fraction (or the mass ratio) of a given stage, which affects the performance of a rocket, is essential for the analysis of new or upgraded launchers or stages, whose need is increased by the quick evolution of the space programs and by the necessity of their adaptation to the market needs. The availability of this highly scattered variable, ranging between 0.05 and 0.15, is of primary importance at the early steps of the preliminary design studies. At the start of the staging and performance studies, the lack of frozen weight data (to be obtained later on from propulsion, trajectory and sizing studies) leads to rely on rough estimates, generally derived from printed sources and adapted. When needed, a consolidation can be acquired trough a specific analysis activity involving several techniques and implying additional effort and time. The present empirical approach allows thus to get approximated values (i.e. not necessarily accurate or consistent), inducing some result inaccuracy as well as, consequently, difficulties of performance ranking for a multiple option analysis, and an increase of the processing duration. This forms a classical harsh fact of the preliminary design system studies, insufficiently discussed to date. It appears therefore highly desirable to have, for all the evaluation activities, a reliable, fast and easy-to-use weight or mass fraction prediction method. Additionally, the latter should allow for a pre selection of the alternative preliminary configurations, making possible a global system approach. For that purpose, an attempt at modeling has been undertaken, whose objective was the determination of a parametric formulation of the mass fraction, to be expressed from a limited number of parameters available at the early steps of the project. It is based on the innovative use of a statistical method applicable to a variable as a function of several independent parameters. A specific polynomial generator

  10. Predicted slowdown in the rate of Atlantic sea ice loss

    NASA Astrophysics Data System (ADS)

    Yeager, Stephen G.; Karspeck, Alicia R.; Danabasoglu, Gokhan

    2015-12-01

    Coupled climate models initialized from historical climate states and subject to anthropogenic forcings can produce skillful decadal predictions of sea surface temperature change in the subpolar North Atlantic. The skill derives largely from initialization, which improves the representation of slow changes in ocean circulation and associated poleward heat transport. We show that skillful predictions of decadal trends in Arctic winter sea ice extent are also possible, particularly in the Atlantic sector. External radiative forcing contributes to the skill of retrospective decadal sea ice predictions, but the spatial and temporal accuracy is greatly enhanced by the more realistic representation of ocean heat transport anomalies afforded by initialization. Recent forecasts indicate that a spin-down of the thermohaline circulation that began near the turn of the century will continue, and this will result in near-neutral decadal trends in Atlantic winter sea ice extent in the coming years, with decadal growth in select regions.

  11. Evaluation of icing drag coefficient correlations applied to iced propeller performance prediction

    NASA Technical Reports Server (NTRS)

    Miller, Thomas L.; Shaw, R. J.; Korkan, K. D.

    1987-01-01

    Evaluation of three empirical icing drag coefficient correlations is accomplished through application to a set of propeller icing data. The various correlations represent the best means currently available for relating drag rise to various flight and atmospheric conditions for both fixed-wing and rotating airfoils, and the work presented here ilustrates and evaluates one such application of the latter case. The origins of each of the correlations are discussed, and their apparent capabilities and limitations are summarized. These correlations have been made to be an integral part of a computer code, ICEPERF, which has been designed to calculate iced propeller performance. Comparison with experimental propeller icing data shows generally good agreement, with the quality of the predicted results seen to be directly related to the radial icing extent of each case. The code's capability to properly predict thrust coefficient, power coefficient, and propeller efficiency is shown to be strongly dependent on the choice of correlation selected, as well as upon proper specificatioon of radial icing extent.

  12. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions

    PubMed Central

    Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin

    2015-01-01

    Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale. PMID:26198229

  13. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions.

    PubMed

    Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin

    2015-07-07

    Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale.

  14. Prediction of Preoperative Anxiety in Children: Who is Most Accurate?

    PubMed Central

    MacLaren, Jill E.; Thompson, Caitlin; Weinberg, Megan; Fortier, Michelle A.; Morrison, Debra E.; Perret, Danielle; Kain, Zeev N.

    2009-01-01

    Background In this investigation, we sought to assess the ability of pediatric attending anesthesiologists, resident anesthesiologists and mothers to predict anxiety during induction of anesthesia in 2 to 16-year-old children (n=125). Methods Anesthesiologists and mothers provided predictions using a visual analog scale and children's anxiety was assessed using a valid behavior observation tool the Modified Yale Preoperative Anxiety Scale (mYPAS). All mothers were present during anesthetic induction and no child received sedative premedication. Correlational analyses were conducted. Results A total of 125 children aged 2 to 16 years, their mothers, and their attending pediatric anesthesiologists and resident anesthesiologists were studied. Correlational analyses revealed significant associations between attending predictions and child anxiety at induction (rs= 0.38, p<0.001). Resident anesthesiologist and mother predictions were not significantly related to children's anxiety during induction (rs = 0.01 and 0.001, respectively). In terms of accuracy of prediction, 47.2% of predictions made by attending anesthesiologists were within one standard deviation of the observed anxiety exhibited by the child, and 70.4% of predictions were within 2 standard deviations. Conclusions We conclude that attending anesthesiologists who practice in pediatric settings are better than mothers in predicting the anxiety of children during induction of anesthesia. While this finding has significant clinical implications, it is unclear if it can be extended to attending anesthesiologists whose practice is not mostly pediatric anesthesia. PMID:19448201

  15. A New Arctic Ice-Ocean Prediction System

    DTIC Science & Technology

    2016-06-07

    A New Arctic Ice-Ocean Prediction System Albert Semtner Oceanography Department Naval Postgraduate School Monterey, CA 93943 phone: (831) 656-3267...N0001499WR30136 http://www.oc.nps.navy.mil/~pips3 LONG-TERM GOALS The long term goal of the project is to produce a new operational Arctic ice...POP). What is new about the models is their higher resolution already with 18-km grid spacing, as well as their adaptation in advance to the new US

  16. Data-driven Analysis and Prediction of Arctic Sea Ice

    NASA Astrophysics Data System (ADS)

    Kondrashov, D. A.; Chekroun, M.; Ghil, M.; Yuan, X.; Ting, M.

    2015-12-01

    We present results of data-driven predictive analyses of sea ice over the main Arctic regions. Our approach relies on the Multilayer Stochastic Modeling (MSM) framework of Kondrashov, Chekroun and Ghil [Physica D, 2015] and it leads to prognostic models of sea ice concentration (SIC) anomalies on seasonal time scales.This approach is applied to monthly time series of leading principal components from the multivariate Empirical Orthogonal Function decomposition of SIC and selected climate variables over the Arctic. We evaluate the predictive skill of MSM models by performing retrospective forecasts with "no-look ahead" forup to 6-months ahead. It will be shown in particular that the memory effects included in our non-Markovian linear MSM models improve predictions of large-amplitude SIC anomalies in certain Arctic regions. Furtherimprovements allowed by the MSM framework will adopt a nonlinear formulation, as well as alternative data-adaptive decompositions.

  17. Is Three-Dimensional Soft Tissue Prediction by Software Accurate?

    PubMed

    Nam, Ki-Uk; Hong, Jongrak

    2015-11-01

    The authors assessed whether virtual surgery, performed with a soft tissue prediction program, could correctly simulate the actual surgical outcome, focusing on soft tissue movement. Preoperative and postoperative computed tomography (CT) data for 29 patients, who had undergone orthognathic surgery, were obtained and analyzed using the Simplant Pro software. The program made a predicted soft tissue image (A) based on presurgical CT data. After the operation, we obtained actual postoperative CT data and an actual soft tissue image (B) was generated. Finally, the 2 images (A and B) were superimposed and analyzed differences between the A and B. Results were grouped in 2 classes: absolute values and vector values. In the absolute values, the left mouth corner was the most significant error point (2.36 mm). The right mouth corner (2.28 mm), labrale inferius (2.08 mm), and the pogonion (2.03 mm) also had significant errors. In vector values, prediction of the right-left side had a left-sided tendency, the superior-inferior had a superior tendency, and the anterior-posterior showed an anterior tendency. As a result, with this program, the position of points tended to be located more left, anterior, and superior than the "real" situation. There is a need to improve the prediction accuracy for soft tissue images. Such software is particularly valuable in predicting craniofacial soft tissues landmarks, such as the pronasale. With this software, landmark positions were most inaccurate in terms of anterior-posterior predictions.

  18. Fast and accurate automatic structure prediction with HHpred.

    PubMed

    Hildebrand, Andrea; Remmert, Michael; Biegert, Andreas; Söding, Johannes

    2009-01-01

    Automated protein structure prediction is becoming a mainstream tool for biological research. This has been fueled by steady improvements of publicly available automated servers over the last decade, in particular their ability to build good homology models for an increasing number of targets by reliably detecting and aligning more and more remotely homologous templates. Here, we describe the three fully automated versions of the HHpred server that participated in the community-wide blind protein structure prediction competition CASP8. What makes HHpred unique is the combination of usability, short response times (typically under 15 min) and a model accuracy that is competitive with those of the best servers in CASP8.

  19. Accurate perception of negative emotions predicts functional capacity in schizophrenia.

    PubMed

    Abram, Samantha V; Karpouzian, Tatiana M; Reilly, James L; Derntl, Birgit; Habel, Ute; Smith, Matthew J

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration.

  20. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  1. Accurate Theoretical Prediction of the Properties of Energetic Materials

    DTIC Science & Technology

    2007-11-02

    calculations (e.g. Cheetah ). 8. Sensitivity. The structure prediction and lattice potential work will serve as a platform to examine impact/shock...nitromethane molecules. (In an extension of the present work, we will freeze the internal coordinates of the molecules and assess the extent to which the

  2. Learning regulatory programs that accurately predict differential expression with MEDUSA.

    PubMed

    Kundaje, Anshul; Lianoglou, Steve; Li, Xuejing; Quigley, David; Arias, Marta; Wiggins, Chris H; Zhang, Li; Leslie, Christina

    2007-12-01

    Inferring gene regulatory networks from high-throughput genomic data is one of the central problems in computational biology. In this paper, we describe a predictive modeling approach for studying regulatory networks, based on a machine learning algorithm called MEDUSA. MEDUSA integrates promoter sequence, mRNA expression, and transcription factor occupancy data to learn gene regulatory programs that predict the differential expression of target genes. Instead of using clustering or correlation of expression profiles to infer regulatory relationships, MEDUSA determines condition-specific regulators and discovers regulatory motifs that mediate the regulation of target genes. In this way, MEDUSA meaningfully models biological mechanisms of transcriptional regulation. MEDUSA solves the problem of predicting the differential (up/down) expression of target genes by using boosting, a technique from statistical learning, which helps to avoid overfitting as the algorithm searches through the high-dimensional space of potential regulators and sequence motifs. Experimental results demonstrate that MEDUSA achieves high prediction accuracy on held-out experiments (test data), that is, data not seen in training. We also present context-specific analysis of MEDUSA regulatory programs for DNA damage and hypoxia, demonstrating that MEDUSA identifies key regulators and motifs in these processes. A central challenge in the field is the difficulty of validating reverse-engineered networks in the absence of a gold standard. Our approach of learning regulatory programs provides at least a partial solution for the problem: MEDUSA's prediction accuracy on held-out data gives a concrete and statistically sound way to validate how well the algorithm performs. With MEDUSA, statistical validation becomes a prerequisite for hypothesis generation and network building rather than a secondary consideration.

  3. Standardized EEG interpretation accurately predicts prognosis after cardiac arrest

    PubMed Central

    Rossetti, Andrea O.; van Rootselaar, Anne-Fleur; Wesenberg Kjaer, Troels; Horn, Janneke; Ullén, Susann; Friberg, Hans; Nielsen, Niklas; Rosén, Ingmar; Åneman, Anders; Erlinge, David; Gasche, Yvan; Hassager, Christian; Hovdenes, Jan; Kjaergaard, Jesper; Kuiper, Michael; Pellis, Tommaso; Stammet, Pascal; Wanscher, Michael; Wetterslev, Jørn; Wise, Matt P.; Cronberg, Tobias

    2016-01-01

    Objective: To identify reliable predictors of outcome in comatose patients after cardiac arrest using a single routine EEG and standardized interpretation according to the terminology proposed by the American Clinical Neurophysiology Society. Methods: In this cohort study, 4 EEG specialists, blinded to outcome, evaluated prospectively recorded EEGs in the Target Temperature Management trial (TTM trial) that randomized patients to 33°C vs 36°C. Routine EEG was performed in patients still comatose after rewarming. EEGs were classified into highly malignant (suppression, suppression with periodic discharges, burst-suppression), malignant (periodic or rhythmic patterns, pathological or nonreactive background), and benign EEG (absence of malignant features). Poor outcome was defined as best Cerebral Performance Category score 3–5 until 180 days. Results: Eight TTM sites randomized 202 patients. EEGs were recorded in 103 patients at a median 77 hours after cardiac arrest; 37% had a highly malignant EEG and all had a poor outcome (specificity 100%, sensitivity 50%). Any malignant EEG feature had a low specificity to predict poor prognosis (48%) but if 2 malignant EEG features were present specificity increased to 96% (p < 0.001). Specificity and sensitivity were not significantly affected by targeted temperature or sedation. A benign EEG was found in 1% of the patients with a poor outcome. Conclusions: Highly malignant EEG after rewarming reliably predicted poor outcome in half of patients without false predictions. An isolated finding of a single malignant feature did not predict poor outcome whereas a benign EEG was highly predictive of a good outcome. PMID:26865516

  4. How Accurately Can We Predict Eclipses for Algol? (Poster abstract)

    NASA Astrophysics Data System (ADS)

    Turner, D.

    2016-06-01

    (Abstract only) beta Persei, or Algol, is a very well known eclipsing binary system consisting of a late B-type dwarf that is regularly eclipsed by a GK subgiant every 2.867 days. Eclipses, which last about 8 hours, are regular enough that predictions for times of minima are published in various places, Sky & Telescope magazine and The Observer's Handbook, for example. But eclipse minimum lasts for less than a half hour, whereas subtle mistakes in the current ephemeris for the star can result in predictions that are off by a few hours or more. The Algol system is fairly complex, with the Algol A and Algol B eclipsing system also orbited by Algol C with an orbital period of nearly 2 years. Added to that are complex long-term O-C variations with a periodicity of almost two centuries that, although suggested by Hoffmeister to be spurious, fit the type of light travel time variations expected for a fourth star also belonging to the system. The AB sub-system also undergoes mass transfer events that add complexities to its O-C behavior. Is it actually possible to predict precise times of eclipse minima for Algol months in advance given such complications, or is it better to encourage ongoing observations of the star so that O-C variations can be tracked in real time?

  5. Predictive rendering for accurate material perception: modeling and rendering fabrics

    NASA Astrophysics Data System (ADS)

    Bala, Kavita

    2012-03-01

    In computer graphics, rendering algorithms are used to simulate the appearance of objects and materials in a wide range of applications. Designers and manufacturers rely entirely on these rendered images to previsualize scenes and products before manufacturing them. They need to differentiate between different types of fabrics, paint finishes, plastics, and metals, often with subtle differences, for example, between silk and nylon, formaica and wood. Thus, these applications need predictive algorithms that can produce high-fidelity images that enable such subtle material discrimination.

  6. Accelerated Prediction of the Polar Ice and Global Ocean (APPIGO)

    DTIC Science & Technology

    2015-09-30

    optimizations, to tune the standard 0.04 degree global HYCOM benchmark case described above for the Cray XC40 and the Intel fortran compiler. At Navy...then transferred with MPI, and copied back to the device memory on the recipient host. A new approach called GPUDirect now provides a mechanism that...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Accelerated Prediction of the Polar Ice and Global Ocean

  7. Can numerical simulations accurately predict hydrodynamic instabilities in liquid films?

    NASA Astrophysics Data System (ADS)

    Denner, Fabian; Charogiannis, Alexandros; Pradas, Marc; van Wachem, Berend G. M.; Markides, Christos N.; Kalliadasis, Serafim

    2014-11-01

    Understanding the dynamics of hydrodynamic instabilities in liquid film flows is an active field of research in fluid dynamics and non-linear science in general. Numerical simulations offer a powerful tool to study hydrodynamic instabilities in film flows and can provide deep insights into the underlying physical phenomena. However, the direct comparison of numerical results and experimental results is often hampered by several reasons. For instance, in numerical simulations the interface representation is problematic and the governing equations and boundary conditions may be oversimplified, whereas in experiments it is often difficult to extract accurate information on the fluid and its behavior, e.g. determine the fluid properties when the liquid contains particles for PIV measurements. In this contribution we present the latest results of our on-going, extensive study on hydrodynamic instabilities in liquid film flows, which includes direct numerical simulations, low-dimensional modelling as well as experiments. The major focus is on wave regimes, wave height and wave celerity as a function of Reynolds number and forcing frequency of a falling liquid film. Specific attention is paid to the differences in numerical and experimental results and the reasons for these differences. The authors are grateful to the EPSRC for their financial support (Grant EP/K008595/1).

  8. Prediction of sea ice thickness cluster in the Northern Hemisphere

    NASA Astrophysics Data System (ADS)

    Fuckar, Neven-Stjepan; Guemas, Virginie; Johnson, Nathaniel; Doblas-Reyes, Francisco

    2016-04-01

    Sea ice thickness (SIT) has a potential to contain substantial climate memory and predictability in the northern hemisphere (NH) sea ice system. We use 5-member NH SIT, reconstructed with an ocean-sea-ice general circulation model (NEMOv3.3 with LIM2) with a simple data assimilation routine, to determine NH SIT modes of variability disentangled from the long-term climate change. Specifically, we apply the K-means cluster analysis - one of nonhierarchical clustering methods that partition data into modes or clusters based on their distances in the physical - to determine optimal number of NH SIT clusters (K=3) and their historical variability. To examine prediction skill of NH SIT clusters in EC-Earth2.3, a state-of-the-art coupled climate forecast system, we use 5-member ocean and sea ice initial conditions (IC) from the same ocean-sea-ice historical reconstruction and atmospheric IC from ERA-Interim reanalysis. We focus on May 1st and Nov 1st start dates from 1979 to 2010. Common skill metrics of probability forecast, such as rank probability skill core and ROC (relative operating characteristics - hit rate versus false alarm rate) and reliability diagrams show that our dynamical model predominately perform better than the 1st order Marko chain forecast (that beats climatological forecast) over the first forecast year. On average May 1st start dates initially have lower skill than Nov 1st start dates, but their skill is degraded at slower rate than skill of forecast started on Nov 1st.

  9. Data-Driven Modeling and Prediction of Arctic Sea Ice

    NASA Astrophysics Data System (ADS)

    Kondrashov, Dmitri; Chekroun, Mickael; Ghil, Michael

    2016-04-01

    We present results of data-driven predictive analyses of sea ice over the main Arctic regions. Our approach relies on the Multilayer Stochastic Modeling (MSM) framework of Kondrashov, Chekroun and Ghil [Physica D, 2015] and it leads to probabilistic prognostic models of sea ice concentration (SIC) anomalies on seasonal time scales. This approach is applied to monthly time series of state-of-the-art data-adaptive decompositions of SIC and selected climate variables over the Arctic. We evaluate the predictive skill of MSM models by performing retrospective forecasts with "no-look ahead" for up to 6-months ahead. It will be shown in particular that the memory effects included intrinsically in the formulation of our non-Markovian MSM models allow for improvements of the prediction skill of large-amplitude SIC anomalies in certain Arctic regions on the one hand, and of September Sea Ice Extent, on the other. Further improvements allowed by the MSM framework will adopt a nonlinear formulation and explore next-generation data-adaptive decompositions, namely modification of Principal Oscillation Patterns (POPs) and rotated Multichannel Singular Spectrum Analysis (M-SSA).

  10. Objective criteria accurately predict amputation following lower extremity trauma.

    PubMed

    Johansen, K; Daines, M; Howey, T; Helfet, D; Hansen, S T

    1990-05-01

    MESS (Mangled Extremity Severity Score) is a simple rating scale for lower extremity trauma, based on skeletal/soft-tissue damage, limb ischemia, shock, and age. Retrospective analysis of severe lower extremity injuries in 25 trauma victims demonstrated a significant difference between MESS values for 17 limbs ultimately salvaged (mean, 4.88 +/- 0.27) and nine requiring amputation (mean, 9.11 +/- 0.51) (p less than 0.01). A prospective trial of MESS in lower extremity injuries managed at two trauma centers again demonstrated a significant difference between MESS values of 14 salvaged (mean, 4.00 +/- 0.28) and 12 doomed (mean, 8.83 +/- 0.53) limbs (p less than 0.01). In both the retrospective survey and the prospective trial, a MESS value greater than or equal to 7 predicted amputation with 100% accuracy. MESS may be useful in selecting trauma victims whose irretrievably injured lower extremities warrant primary amputation.

  11. Improved Ecosystem Predictions of the California Current System via Accurate Light Calculations

    DTIC Science & Technology

    2011-09-30

    System via Accurate Light Calculations Curtis D. Mobley Sequoia Scientific, Inc. 2700 Richards Road, Suite 107 Bellevue, WA 98005 phone: 425...incorporate extremely fast but accurate light calculations into coupled physical-biological-optical ocean ecosystem models as used for operational three...dimensional ecosystem predictions. Improvements in light calculations lead to improvements in predictions of chlorophyll concentrations and other

  12. Generating highly accurate prediction hypotheses through collaborative ensemble learning

    PubMed Central

    Arsov, Nino; Pavlovski, Martin; Basnarkov, Lasko; Kocarev, Ljupco

    2017-01-01

    Ensemble generation is a natural and convenient way of achieving better generalization performance of learning algorithms by gathering their predictive capabilities. Here, we nurture the idea of ensemble-based learning by combining bagging and boosting for the purpose of binary classification. Since the former improves stability through variance reduction, while the latter ameliorates overfitting, the outcome of a multi-model that combines both strives toward a comprehensive net-balancing of the bias-variance trade-off. To further improve this, we alter the bagged-boosting scheme by introducing collaboration between the multi-model’s constituent learners at various levels. This novel stability-guided classification scheme is delivered in two flavours: during or after the boosting process. Applied among a crowd of Gentle Boost ensembles, the ability of the two suggested algorithms to generalize is inspected by comparing them against Subbagging and Gentle Boost on various real-world datasets. In both cases, our models obtained a 40% generalization error decrease. But their true ability to capture details in data was revealed through their application for protein detection in texture analysis of gel electrophoresis images. They achieve improved performance of approximately 0.9773 AUROC when compared to the AUROC of 0.9574 obtained by an SVM based on recursive feature elimination. PMID:28304378

  13. Accurate predictions for the production of vaporized water

    SciTech Connect

    Morin, E.; Montel, F.

    1995-12-31

    The production of water vaporized in the gas phase is controlled by the local conditions around the wellbore. The pressure gradient applied to the formation creates a sharp increase of the molar water content in the hydrocarbon phase approaching the well; this leads to a drop in the pore water saturation around the wellbore. The extent of the dehydrated zone which is formed is the key controlling the bottom-hole content of vaporized water. The maximum water content in the hydrocarbon phase at a given pressure, temperature and salinity is corrected by capillarity or adsorption phenomena depending on the actual water saturation. Describing the mass transfer of the water between the hydrocarbon phases and the aqueous phase into the tubing gives a clear idea of vaporization effects on the formation of scales. Field example are presented for gas fields with temperatures ranging between 140{degrees}C and 180{degrees}C, where water vaporization effects are significant. Conditions for salt plugging in the tubing are predicted.

  14. Generating highly accurate prediction hypotheses through collaborative ensemble learning

    NASA Astrophysics Data System (ADS)

    Arsov, Nino; Pavlovski, Martin; Basnarkov, Lasko; Kocarev, Ljupco

    2017-03-01

    Ensemble generation is a natural and convenient way of achieving better generalization performance of learning algorithms by gathering their predictive capabilities. Here, we nurture the idea of ensemble-based learning by combining bagging and boosting for the purpose of binary classification. Since the former improves stability through variance reduction, while the latter ameliorates overfitting, the outcome of a multi-model that combines both strives toward a comprehensive net-balancing of the bias-variance trade-off. To further improve this, we alter the bagged-boosting scheme by introducing collaboration between the multi-model’s constituent learners at various levels. This novel stability-guided classification scheme is delivered in two flavours: during or after the boosting process. Applied among a crowd of Gentle Boost ensembles, the ability of the two suggested algorithms to generalize is inspected by comparing them against Subbagging and Gentle Boost on various real-world datasets. In both cases, our models obtained a 40% generalization error decrease. But their true ability to capture details in data was revealed through their application for protein detection in texture analysis of gel electrophoresis images. They achieve improved performance of approximately 0.9773 AUROC when compared to the AUROC of 0.9574 obtained by an SVM based on recursive feature elimination.

  15. Change in BMI Accurately Predicted by Social Exposure to Acquaintances

    PubMed Central

    Oloritun, Rahman O.; Ouarda, Taha B. M. J.; Moturu, Sai; Madan, Anmol; Pentland, Alex (Sandy); Khayal, Inas

    2013-01-01

    Research has mostly focused on obesity and not on processes of BMI change more generally, although these may be key factors that lead to obesity. Studies have suggested that obesity is affected by social ties. However these studies used survey based data collection techniques that may be biased toward select only close friends and relatives. In this study, mobile phone sensing techniques were used to routinely capture social interaction data in an undergraduate dorm. By automating the capture of social interaction data, the limitations of self-reported social exposure data are avoided. This study attempts to understand and develop a model that best describes the change in BMI using social interaction data. We evaluated a cohort of 42 college students in a co-located university dorm, automatically captured via mobile phones and survey based health-related information. We determined the most predictive variables for change in BMI using the least absolute shrinkage and selection operator (LASSO) method. The selected variables, with gender, healthy diet category, and ability to manage stress, were used to build multiple linear regression models that estimate the effect of exposure and individual factors on change in BMI. We identified the best model using Akaike Information Criterion (AIC) and R2. This study found a model that explains 68% (p<0.0001) of the variation in change in BMI. The model combined social interaction data, especially from acquaintances, and personal health-related information to explain change in BMI. This is the first study taking into account both interactions with different levels of social interaction and personal health-related information. Social interactions with acquaintances accounted for more than half the variation in change in BMI. This suggests the importance of not only individual health information but also the significance of social interactions with people we are exposed to, even people we may not consider as close friends. PMID

  16. Three dimensional numerical prediction of icing related power and energy losses on a wind turbine

    NASA Astrophysics Data System (ADS)

    Sagol, Ece

    , while the latter performs all the steps in the 3D domain. The Fully-3D method yields more accurate predictions for a clean blade. For icing conditions, a validation is not possible, owing to the lack of experimental data. However, the two methods produce quite different results for the performance of the ice shape and the iced blade. A critical analysis of the results shows that, although the computational cost of the Fully-3D method is much higher, icing analyses in 2D may lack accuracy, because the ice shape and the related power loss are compromised by not considering the 3D features of rotational flow. While performing the CFD computations on the iced blade, the rough surface of the ice is smoothed to a degree, in order to prevent numerical instability and to keep the mesh size within a reasonable limit. However, roughness effects cannot be excluded altogether, as they contribute significantly to performance reduction. We consider roughness through a modification in the CFD code, and assess its effect on performance for the clean blade.

  17. Temperature and Runback Ice Prediction Method for Three-Dimensional Hot Air Anti-Icing System

    NASA Astrophysics Data System (ADS)

    Zhou, Ying; Lin, Guiping; Bu, Xueqin; Mu, Zuodong; Pan, Rui; Ge, Qimo; Qiao, Xudong

    2017-03-01

    A prediction method of surface temperature and runback ice for a three-dimensional hot air anti-icing system was proposed. Computational approach to realize this method was introduced. Both the external and internal flows were separately calculated, results of which were set as boundary conditions of heat conduction computation in airfoil skin. The results of external and internal flow calculations show that the effect of surface temperature on convective heat transfer coefficients and local droplet collection efficiency is negligible and the calculations can be decoupled. The prediction method based on heat flux was used to calculate surface temperature and runback ice results. The results show that, the effects of LWC and Mach number are much more significant than the effect of external flow temperature. The surface temperature at impinging interaction point is more sensitive to the change of external conditions than that at stagnation point. The surface temperature changes significantly with changing Mach number because both the mass rate of droplet and the impact limit are changed.

  18. US Navy Operational Global Ocean and Arctic Ice Prediction Systems

    DTIC Science & Technology

    2014-09-01

    Wallcraft, L. Zamudio, D.S. Franklin, P.G. Posey, M.W. Phelps, P.J. Hogan, F.L. Bub, and C.J. DeHaan. 2014. US Navy operational global ocean and...P E C I A L I S S U E O N N AV Y O P E R AT I O N A L M O D E L S US Navy Operational Global Ocean and Arctic Ice Prediction Systems B Y E...operational Global Ocean Forecast System that shows the proper placement of the Kuroshio (the strongly inertial western boundary current in the North

  19. A constitutive framework for predicting weakening and reduced buttressing of ice shelves based on observations of the progressive deterioration of the remnant Larsen B Ice Shelf

    NASA Astrophysics Data System (ADS)

    Borstad, Chris; Khazendar, Ala; Scheuchl, Bernd; Morlighem, Mathieu; Larour, Eric; Rignot, Eric

    2016-03-01

    The increasing contribution of the Antarctic Ice Sheet to sea level rise is linked to reductions in ice shelf buttressing, driven in large part by basal melting of ice shelves. These ocean-driven buttressing losses are being compounded as ice shelves weaken and fracture. To date, model projections of ice sheet evolution have not accounted for weakening ice shelves. Here we present the first constitutive framework for ice deformation that explicitly includes mechanical weakening, based on observations of the progressive degradation of the remnant Larsen B Ice Shelf from 2000 to 2015. We implement this framework in an ice sheet model and are able to reproduce most of the observed weakening of the ice shelf. In addition to predicting ice shelf weakening and reduced buttressing, this new framework opens the door for improved understanding and predictions of iceberg calving, meltwater routing and hydrofracture, and ice shelf collapse.

  20. Prospects for improved seasonal Arctic sea ice predictions from multivariate data assimilation

    NASA Astrophysics Data System (ADS)

    Massonnet, François; Fichefet, Thierry; Goosse, Hugues

    2015-04-01

    Predicting the summer Arctic sea ice conditions a few months in advance has become a challenging priority. Seasonal prediction is partly an initial condition problem; therefore, a good knowledge of the initial sea ice state is necessary to hopefully produce reliable forecasts. Most of the intrinsic memory of sea ice lies in its thickness, but consistent and homogeneous observational networks of sea ice thickness are still limited in space and time. To overcome this problem, we constrain the ocean-sea ice model NEMO-LIM3 with gridded sea ice concentration retrievals from satellite observations using the ensemble Kalman filter. No sea ice thickness products are assimilated. However, thanks to the multivariate formalism of the data assimilation method used, sea ice thickness is globally updated in a consistent way whenever observations of concentration are available. We compare in this paper the skill of 27 pairs of initialized and uninitialized seasonal Arctic sea ice hindcasts spanning 1983-2009, driven by the same atmospheric forcing as to isolate the pure role of initial conditions on the prediction skill. The results exhibit the interest of multivariate sea ice initialization for the seasonal predictions of the September ice concentration and are particularly encouraging for hindcasts in the 2000s. In line with previous studies showing the interest of data assimilation for sea ice thickness reconstruction, our results thus show that sea ice data assimilation is also a promising tool for short-term prediction, and that current seasonal sea ice forecast systems could gain predictive skill from a more realistic sea ice initialization.

  1. Assessing the predictability of a coupled climate-ice sheet model system for the response of the Greenland Ice Sheet

    NASA Astrophysics Data System (ADS)

    Adalgeirsdottir, G.; Stendel, M.; Bueler, E.; Christensen, J. H.; Drews, M.; Mottram, R.

    2009-04-01

    The wild card for reliable sea level rise prediction is the contribution of the Greenland Ice Sheet. There is an urgent need to determine the predictability of models that simulate the response of Greenland Ice Sheet to rising temperatures and the amount of freshwater flux that can be expected into the ocean. Modelling efforts have been limited by poorly known boundary and initial conditions, low resolution and lack of presentation of fast flowing ice streams. We address these limitations by building a model system consisting of a high resolution regional climate model (HIRHAM4), that has been run for the period 1950-2080 at 25 km, and Parallel Ice Sheet Model (PISM), which simulates spatially and temporally varying ice streams by combining the solutions of the Shallow Shelf and Shallow Ice Approximations. The surface mass balance is simulated with a positive-degree-day method. The important and poorly constrained model component is the past climate forcing, which serves the purpose of initializing the model by simulating the present ice sheet and observed rate of mass changes. Simulated gradients of mass loss due to warming trends of past decade and prediction for the future are presented as well as estimated sensitivities due to the various model component uncertainties.

  2. Predictions of depth-to-ice on asteroids based on an asynchronous model of temperature, impact stirring, and ice loss

    NASA Astrophysics Data System (ADS)

    Schorghofer, Norbert

    2016-09-01

    Water ice near the surface of main belt asteroids is gradually lost to space. A mantle of low thermal conductivity causes large surface temperature amplitudes, and thus increased cooling by thermal re-radiation, lowering temperatures well below the fast-rotator limit. A computational barrier for modeling this ice loss is the multi-scale character of the problem: accurate temperatures require many time steps within a solar day, but ice retreats slowly over billions of years. This barrier is overcome with asynchronous coupling: Models of temperature, ice loss, and impact stirring each use their own time steps and are coupled with one another. The model is applied to 1 Ceres and 7968 Elst-Pizarro. On Ceres, ice can be expected in the top half meter poleward of 60° latitude on both hemispheres, even if excursions of the axis tilt took place, and even in the presence of impact gardening. At the poles, ice can be expected within a centimeter of the surface. The retreating ice crust leads to emission of water from the surface, mainly at the equator; the gradually retreating ice supplies a water exosphere less dense than has been observed by the Herschel telescope. For Main Belt Comet Elst-Pizarro, depths to ice depend on the properties of the surface mantle. For a dust mantle estimated depths are on the order of a decimeter; for a rocky surface the depth at the pole is on the order of one meter. Hence, it could have been activated by a small impact that exposed buried ice.

  3. Early Student Support to Investigate the Role of Sea Ice-Albedo Feedback in Sea Ice Predictions

    DTIC Science & Technology

    2013-09-30

    CESM1 in all its versions employs the Los Alamos National Laboratory ( LANL ) sea ice model, known as CICE. The sea ice in CESM1 has been... documented in a series of papers (e.g., Jahn et al, 2012; Kay Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the...collaborator Dr. Elizabeth Hunke from LANL , who is the chief developer of CICE. Dr. Hunke is a partner with the sea ice prediction network and has a

  4. Accurate determination of surface reference data in digital photographs in ice-free surfaces of Maritime Antarctica.

    PubMed

    Pina, Pedro; Vieira, Gonçalo; Bandeira, Lourenço; Mora, Carla

    2016-12-15

    The ice-free areas of Maritime Antarctica show complex mosaics of surface covers, with wide patches of diverse bare soils and rock, together with various vegetation communities dominated by lichens and mosses. The microscale variability is difficult to characterize and quantify, but is essential for ground-truthing and for defining classifiers for large areas using, for example high resolution satellite imagery, or even ultra-high resolution unmanned aerial vehicle (UAV) imagery. The main objective of this paper is to verify the ability and robustness of an automated approach to discriminate the variety of surface types in digital photographs acquired at ground level in ice-free regions of Maritime Antarctica. The proposed method is based on an object-based classification procedure built in two main steps: first, on the automated delineation of homogeneous regions (the objects) of the images through the watershed transform with adequate filtering to avoid an over-segmentation, and second, on labelling each identified object with a supervised decision classifier trained with samples of representative objects of ice-free surface types (bare rock, bare soil, moss and lichen formations). The method is evaluated with images acquired in summer campaigns in Fildes and Barton peninsulas (King George Island, South Shetlands). The best performances for the datasets of the two peninsulas are achieved with a SVM classifier with overall accuracies of about 92% and kappa values around 0.89. The excellent performances allow validating the adequacy of the approach for obtaining accurate surface reference data at the complete pixel scale (sub-metric) of current very high resolution (VHR) satellite images, instead of a common single point sampling.

  5. Diagnostic sea ice predictability in the pan-Arctic and U.S. Arctic regional seas

    NASA Astrophysics Data System (ADS)

    Cheng, Wei; Blanchard-Wrigglesworth, Edward; Bitz, Cecilia M.; Ladd, Carol; Stabeno, Phyllis J.

    2016-11-01

    This study assesses sea ice predictability in the pan-Arctic and U.S. Arctic regional (Bering, Chukchi, and Beaufort) seas with a purpose of understanding regional differences from the pan-Arctic perspective and how predictability might change under changing climate. Lagged correlation is derived using existing output from the Community Earth System Model Large Ensemble (CESM-LE), Pan-Arctic Ice-Ocean Modeling and Assimilation System, and NOAA Coupled Forecast System Reanalysis models. While qualitatively similar, quantitative differences exist in Arctic ice area lagged correlation in models with or without data assimilation. On regional scales, modeled ice area lagged correlations are strongly location and season dependent. A robust feature in the CESM-LE is that the pan-Arctic melt-to-freeze season ice area memory intensifies, whereas the freeze-to-melt season memory weakens as climate warms, but there are across-region variations in the sea ice predictability changes with changing climate.

  6. Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

    PubMed

    Faraggi, Eshel; Kloczkowski, Andrzej

    2017-01-01

    Accurate prediction of protein secondary structure and other one-dimensional structure features is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. SPINE-X is a software package to predict secondary structure as well as accessible surface area and dihedral angles ϕ and ψ. For secondary structure SPINE-X achieves an accuracy of between 81 and 84 % depending on the dataset and choice of tests. The Pearson correlation coefficient for accessible surface area prediction is 0.75 and the mean absolute error from the ϕ and ψ dihedral angles are 20(∘) and 33(∘), respectively. The source code and a Linux executables for SPINE-X are available from Research and Information Systems at http://mamiris.com .

  7. A hydrologically inspired approach to predicting fjord bedrock elevation at the ice-ocean interface of the Greenland Ice Sheet

    NASA Astrophysics Data System (ADS)

    Williams, Chris; Bamber, Jonathan; Cochran, James; Cornford, Stephen; Dowdeswell, Julian; Jordan, Tom; Morlighem, Mathieu; Palmer, Steven; Siegert, Martin; Tinto, Kirsty; Paden, John

    2016-04-01

    Measurements of ice sheet basal topography provide vital boundary conditions for numerical modelling of ice sheet evolution and are key to understanding observations of ice sheet dynamics. A consistent issue with existing bed topography products for the Greenland Ice Sheet - developed using ice thickness observations from ice penetrating radar, interpolation, and mass conservation (Bamber et al., 2013, Morlighem et al., 2014) - is the poor quantification of near coastal bathymetry. Accurate mapping of bedrock elevation in these areas is important as glaciers local to these regions have been observed to have the largest velocities, greatest associated mass changes, and are therefore most sensitive to uncertainties in basal boundary conditions when modelling ice motion (e.g. Nick et al., 2013). Sparse data availability and resultant coarse rendering of digital elevation products at the edges of existing ice sheet bed elevation products poses issues, particularly when integrating models over longer periods of time (e.g. Vieli and Nick, 2011). Improving data coverage in these regions is a further priority as fjord bathymetry is known to provide a strong control on ocean circulation and ice-ocean forcing (e.g. Straneo et al., 2011) which have been related to changes observed in tidewater glacier systems (e.g. Murray et al., 2010). We have developed a method that improves existing products of the Greenland Ice Sheet bed rock and surrounding bathymetry through [1] the addition of new bathymetric and ice thickness data where available and [2] the integration of generalised fjord structures in data sparse regions to better inform interpolation routines. Following the release of the last Greenland bed topography-bathymetry product (Bamber et al., 2013), new data acquired through gravity inversion as well as single and multi-beam echo sounding are included, improving bed elevation data density and coverage. In fjords which remain data sparse, idealised fjord geometry is

  8. Broad-scale predictability of carbohydrates and exopolymers in Antarctic and Arctic sea ice.

    PubMed

    Underwood, Graham J C; Aslam, Shazia N; Michel, Christine; Niemi, Andrea; Norman, Louiza; Meiners, Klaus M; Laybourn-Parry, Johanna; Paterson, Harriet; Thomas, David N

    2013-09-24

    Sea ice can contain high concentrations of dissolved organic carbon (DOC), much of which is carbohydrate-rich extracellular polymeric substances (EPS) produced by microalgae and bacteria inhabiting the ice. Here we report the concentrations of dissolved carbohydrates (dCHO) and dissolved EPS (dEPS) in relation to algal standing stock [estimated by chlorophyll (Chl) a concentrations] in sea ice from six locations in the Southern and Arctic Oceans. Concentrations varied substantially within and between sampling sites, reflecting local ice conditions and biological content. However, combining all data revealed robust statistical relationships between dCHO concentrations and the concentrations of different dEPS fractions, Chl a, and DOC. These relationships were true for whole ice cores, bottom ice (biomass rich) sections, and colder surface ice. The distribution of dEPS was strongly correlated to algal biomass, with the highest concentrations of both dEPS and non-EPS carbohydrates in the bottom horizons of the ice. Complex EPS was more prevalent in colder surface sea ice horizons. Predictive models (validated against independent data) were derived to enable the estimation of dCHO concentrations from data on ice thickness, salinity, and vertical position in core. When Chl a data were included a higher level of prediction was obtained. The consistent patterns reflected in these relationships provide a strong basis for including estimates of regional and seasonal carbohydrate and dEPS carbon budgets in coupled physical-biogeochemical models, across different types of sea ice from both polar regions.

  9. Multivariable time series prediction for the icing process on overhead power transmission line.

    PubMed

    Li, Peng; Zhao, Na; Zhou, Donghua; Cao, Min; Li, Jingjie; Shi, Xinling

    2014-01-01

    The design of monitoring and predictive alarm systems is necessary for successful overhead power transmission line icing. Given the characteristics of complexity, nonlinearity, and fitfulness in the line icing process, a model based on a multivariable time series is presented here to predict the icing load of a transmission line. In this model, the time effects of micrometeorology parameters for the icing process have been analyzed. The phase-space reconstruction theory and machine learning method were then applied to establish the prediction model, which fully utilized the history of multivariable time series data in local monitoring systems to represent the mapping relationship between icing load and micrometeorology factors. Relevant to the characteristic of fitfulness in line icing, the simulations were carried out during the same icing process or different process to test the model's prediction precision and robustness. According to the simulation results for the Tao-Luo-Xiong Transmission Line, this model demonstrates a good accuracy of prediction in different process, if the prediction length is less than two hours, and would be helpful for power grid departments when deciding to take action in advance to address potential icing disasters.

  10. Multivariable Time Series Prediction for the Icing Process on Overhead Power Transmission Line

    PubMed Central

    Li, Peng; Zhao, Na; Zhou, Donghua; Cao, Min; Li, Jingjie; Shi, Xinling

    2014-01-01

    The design of monitoring and predictive alarm systems is necessary for successful overhead power transmission line icing. Given the characteristics of complexity, nonlinearity, and fitfulness in the line icing process, a model based on a multivariable time series is presented here to predict the icing load of a transmission line. In this model, the time effects of micrometeorology parameters for the icing process have been analyzed. The phase-space reconstruction theory and machine learning method were then applied to establish the prediction model, which fully utilized the history of multivariable time series data in local monitoring systems to represent the mapping relationship between icing load and micrometeorology factors. Relevant to the characteristic of fitfulness in line icing, the simulations were carried out during the same icing process or different process to test the model's prediction precision and robustness. According to the simulation results for the Tao-Luo-Xiong Transmission Line, this model demonstrates a good accuracy of prediction in different process, if the prediction length is less than two hours, and would be helpful for power grid departments when deciding to take action in advance to address potential icing disasters. PMID:25136653

  11. Impact of the initialisation on the predictability of the Southern Ocean sea ice at interannual to multi-decadal timescales

    NASA Astrophysics Data System (ADS)

    Zunz, Violette; Goosse, Hugues; Dubinkina, Svetlana

    2015-04-01

    In this study, we assess systematically the impact of different initialisation procedures on the predictability of the sea ice in the Southern Ocean. These initialisation strategies are based on three data assimilation methods: the nudging, the particle filter with sequential importance resampling and the nudging proposal particle filter. An Earth system model of intermediate complexity is used to perform hindcast simulations in a perfect model approach. The predictability of the Antarctic sea ice at interannual to multi-decadal timescales is estimated through two aspects: the spread of the hindcast ensemble, indicating the uncertainty of the ensemble, and the correlation between the ensemble mean and the pseudo-observations, used to assess the accuracy of the prediction. Our results show that at decadal timescales more sophisticated data assimilation methods as well as denser pseudo-observations used to initialise the hindcasts decrease the spread of the ensemble. However, our experiments did not clearly demonstrate that one of the initialisation methods systematically provides with a more accurate prediction of the sea ice in the Southern Ocean than the others. Overall, the predictability at interannual timescales is limited to 3 years ahead at most. At multi-decadal timescales, the trends in sea ice extent computed over the time period just after the initialisation are clearly better correlated between the hindcasts and the pseudo-observations if the initialisation takes into account the pseudo-observations. The correlation reaches values larger than 0.5 in winter. This high correlation has likely its origin in the slow evolution of the ocean ensured by its strong thermal inertia, showing the importance of the quality of the initialisation below the sea ice.

  12. Assessment of Arctic and Antarctic Sea Ice Predictability in CMIP5 Decadal Hindcasts

    NASA Technical Reports Server (NTRS)

    Yang, Chao-Yuan; Liu, Jiping (Inventor); Hu, Yongyun; Horton, Radley M.; Chen, Liqi; Cheng, Xiao

    2016-01-01

    This paper examines the ability of coupled global climate models to predict decadal variability of Arctic and Antarctic sea ice. We analyze decadal hindcasts/predictions of 11 Coupled Model Intercomparison Project Phase 5 (CMIP5) models. Decadal hindcasts exhibit a large multimodel spread in the simulated sea ice extent, with some models deviating significantly from the observations as the predicted ice extent quickly drifts away from the initial constraint. The anomaly correlation analysis between the decadal hindcast and observed sea ice suggests that in the Arctic, for most models, the areas showing significant predictive skill become broader associated with increasing lead times. This area expansion is largely because nearly all the models are capable of predicting the observed decreasing Arctic sea ice cover. Sea ice extent in the North Pacific has better predictive skill than that in the North Atlantic (particularly at a lead time of 3-7 years), but there is a reemerging predictive skill in the North Atlantic at a lead time of 6-8 years. In contrast to the Arctic, Antarctic sea ice decadal hindcasts do not show broad predictive skill at any timescales, and there is no obvious improvement linking the areal extent of significant predictive skill to lead time increase. This might be because nearly all the models predict a retreating Antarctic sea ice cover, opposite to the observations. For the Arctic, the predictive skill of the multi-model ensemble mean outperforms most models and the persistence prediction at longer timescales, which is not the case for the Antarctic. Overall, for the Arctic, initialized decadal hindcasts show improved predictive skill compared to uninitialized simulations, although this improvement is not present in the Antarctic.

  13. Assessment of Arctic and Antarctic sea ice predictability in CMIP5 decadal hindcasts

    NASA Astrophysics Data System (ADS)

    Yang, Chao-Yuan; Liu, Jiping; Hu, Yongyun; Horton, Radley M.; Chen, Liqi; Cheng, Xiao

    2016-10-01

    This paper examines the ability of coupled global climate models to predict decadal variability of Arctic and Antarctic sea ice. We analyze decadal hindcasts/predictions of 11 Coupled Model Intercomparison Project Phase 5 (CMIP5) models. Decadal hindcasts exhibit a large multi-model spread in the simulated sea ice extent, with some models deviating significantly from the observations as the predicted ice extent quickly drifts away from the initial constraint. The anomaly correlation analysis between the decadal hindcast and observed sea ice suggests that in the Arctic, for most models, the areas showing significant predictive skill become broader associated with increasing lead times. This area expansion is largely because nearly all the models are capable of predicting the observed decreasing Arctic sea ice cover. Sea ice extent in the North Pacific has better predictive skill than that in the North Atlantic (particularly at a lead time of 3-7 years), but there is a re-emerging predictive skill in the North Atlantic at a lead time of 6-8 years. In contrast to the Arctic, Antarctic sea ice decadal hindcasts do not show broad predictive skill at any timescales, and there is no obvious improvement linking the areal extent of significant predictive skill to lead time increase. This might be because nearly all the models predict a retreating Antarctic sea ice cover, opposite to the observations. For the Arctic, the predictive skill of the multi-model ensemble mean outperforms most models and the persistence prediction at longer timescales, which is not the case for the Antarctic. Overall, for the Arctic, initialized decadal hindcasts show improved predictive skill compared to uninitialized simulations, although this improvement is not present in the Antarctic.

  14. Accurate prediction of adsorption energies on graphene, using a dispersion-corrected semiempirical method including solvation.

    PubMed

    Vincent, Mark A; Hillier, Ian H

    2014-08-25

    The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can predict the adsorption energies of unsaturated hydrocarbons and the effect of substitution on these values to an accuracy comparable to DFT values and in good agreement with the experiment. The adsorption energies of TCNE, TCNQ, and a number of sulfonated pyrenes are also predicted, along with the effect of hydration using the COSMO model.

  15. Accurately predicting copper interconnect topographies in foundry design for manufacturability flows

    NASA Astrophysics Data System (ADS)

    Lu, Daniel; Fan, Zhong; Tak, Ki Duk; Chang, Li-Fu; Zou, Elain; Jiang, Jenny; Yang, Josh; Zhuang, Linda; Chen, Kuang Han; Hurat, Philippe; Ding, Hua

    2011-04-01

    This paper presents a model-based Chemical Mechanical Polishing (CMP) Design for Manufacturability (DFM) () methodology that includes an accurate prediction of post-CMP copper interconnect topographies at the advanced process technology nodes. Using procedures of extensive model calibration and validation, the CMP process model accurately predicts post-CMP dimensions, such as erosion, dishing, and copper thickness with excellent correlation to silicon measurements. This methodology provides an efficient DFM flow to detect and fix physical manufacturing hotspots related to copper pooling and Depth of Focus (DOF) failures at both block- and full chip level designs. Moreover, the predicted thickness output is used in the CMP-aware RC extraction and Timing analysis flows for better understanding of performance yield and timing impact. In addition, the CMP model can be applied to the verification of model-based dummy fill flows.

  16. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

    PubMed Central

    Singh, Ritambhara; Kuscu, Cem; Quinlan, Aaron; Qi, Yanjun; Adli, Mazhar

    2015-01-01

    The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CRISPR/Cas9 Off-target Prediction and Identification Tool (CROP-IT) that performs improved off-target binding and cleavage site predictions. Unlike existing prediction programs that solely use DNA sequence information; CROP-IT integrates whole genome level biological information from existing Cas9 binding and cleavage data sets. Utilizing whole-genome chromatin state information from 125 human cell types further enhances its computational prediction power. Comparative analyses on experimentally validated datasets show that CROP-IT outperforms existing computational algorithms in predicting both Cas9 binding as well as cleavage sites. With a user-friendly web-interface, CROP-IT outputs scored and ranked list of potential off-targets that enables improved guide RNA design and more accurate prediction of Cas9 binding or cleavage sites. PMID:26032770

  17. Multiple Off-Ice Performance Variables Predict On-Ice Skating Performance in Male and Female Division III Ice Hockey Players.

    PubMed

    Janot, Jeffrey M; Beltz, Nicholas M; Dalleck, Lance D

    2015-09-01

    The purpose of this study was to determine if off-ice performance variables could predict on-ice skating performance in Division III collegiate hockey players. Both men (n = 15) and women (n = 11) hockey players (age = 20.5 ± 1.4 years) participated in the study. The skating tests were agility cornering S-turn, 6.10 m acceleration, 44.80 m speed, modified repeat skate, and 15.20 m full speed. Off-ice variables assessed were years of playing experience, height, weight and percent body fat and off-ice performance variables included vertical jump (VJ), 40-yd dash (36.58m), 1-RM squat, pro-agility, Wingate peak power and peak power percentage drop (% drop), and 1.5 mile (2.4km) run. Results indicated that 40-yd dash (36.58m), VJ, 1.5 mile (2.4km) run, and % drop were significant predictors of skating performance for repeat skate (slowest, fastest, and average time) and 44.80 m speed time, respectively. Four predictive equations were derived from multiple regression analyses: 1) slowest repeat skate time = 2.362 + (1.68 x 40-yd dash time) + (0.005 x 1.5 mile run), 2) fastest repeat skate time = 9.762 - (0.089 x VJ) - (0.998 x 40-yd dash time), 3) average repeat skate time = 7.770 + (1.041 x 40-yd dash time) - (0.63 x VJ) + (0.003 x 1.5 mile time), and 4) 47.85 m speed test = 7.707 - (0.050 x VJ) - (0.01 x % drop). It was concluded that selected off-ice tests could be used to predict on-ice performance regarding speed and recovery ability in Division III male and female hockey players. Key pointsThe 40-yd dash (36.58m) and vertical jump tests are significant predictors of on-ice skating performance specific to speed.In addition to 40-yd dash and vertical jump, the 1.5 mile (2.4km) run for time and percent power drop from the Wingate anaerobic power test were also significant predictors of skating performance that incorporates the aspect of recovery from skating activity.Due to the specificity of selected off-ice variables as predictors of on-ice performance, coaches can

  18. Multiple Off-Ice Performance Variables Predict On-Ice Skating Performance in Male and Female Division III Ice Hockey Players

    PubMed Central

    Janot, Jeffrey M.; Beltz, Nicholas M.; Dalleck, Lance D.

    2015-01-01

    The purpose of this study was to determine if off-ice performance variables could predict on-ice skating performance in Division III collegiate hockey players. Both men (n = 15) and women (n = 11) hockey players (age = 20.5 ± 1.4 years) participated in the study. The skating tests were agility cornering S-turn, 6.10 m acceleration, 44.80 m speed, modified repeat skate, and 15.20 m full speed. Off-ice variables assessed were years of playing experience, height, weight and percent body fat and off-ice performance variables included vertical jump (VJ), 40-yd dash (36.58m), 1-RM squat, pro-agility, Wingate peak power and peak power percentage drop (% drop), and 1.5 mile (2.4km) run. Results indicated that 40-yd dash (36.58m), VJ, 1.5 mile (2.4km) run, and % drop were significant predictors of skating performance for repeat skate (slowest, fastest, and average time) and 44.80 m speed time, respectively. Four predictive equations were derived from multiple regression analyses: 1) slowest repeat skate time = 2.362 + (1.68 x 40-yd dash time) + (0.005 x 1.5 mile run), 2) fastest repeat skate time = 9.762 - (0.089 x VJ) - (0.998 x 40-yd dash time), 3) average repeat skate time = 7.770 + (1.041 x 40-yd dash time) - (0.63 x VJ) + (0.003 x 1.5 mile time), and 4) 47.85 m speed test = 7.707 - (0.050 x VJ) - (0.01 x % drop). It was concluded that selected off-ice tests could be used to predict on-ice performance regarding speed and recovery ability in Division III male and female hockey players. Key points The 40-yd dash (36.58m) and vertical jump tests are significant predictors of on-ice skating performance specific to speed. In addition to 40-yd dash and vertical jump, the 1.5 mile (2.4km) run for time and percent power drop from the Wingate anaerobic power test were also significant predictors of skating performance that incorporates the aspect of recovery from skating activity. Due to the specificity of selected off-ice variables as predictors of on-ice performance, coaches

  19. Quiet eye predicts goaltender success in deflected ice hockey shots.

    PubMed

    Panchuk, Derek; Vickers, Joan N; Hopkins, Will G

    2017-02-01

    In interceptive timing tasks, long quiet eye (QE) durations at the release point, along with early tracking on the object, allow performers to couple their actions to the kinematics of their opponent and regulate their movements based on emergent information from the object's trajectory. We used a mobile eye tracker to record the QE of eight university-level ice hockey goaltenders of an equivalent skill level as they responded to shots that deflected off a board placed to their left or right, resulting in a trajectory with low predictability. QE behaviour was assessed using logistic regression and magnitude-based inference. We found that when QE onset occurred later in the shot (950 ± 580 ms, mean ± SD) there was an increase in the proportion of goals allowed (41% vs. 22%) compared to when QE onset occurred earlier. A shorter QE duration (1260 ± 630 ms) predicted a large increase in the proportion of goals scored (38% vs. 14%). More saves occurred when QE duration (2074 ± 47 ms) was longer. An earlier QE offset (2004 ± 66 ms) also resulted in a large increase in the number of goals allowed (37% vs. 11%) compared to a later offset (2132 ± 41 ms). Since an early, sustained QE duration contributed to a higher percentage of saves, it is important that coaches develop practice activities that challenge the goaltender's ability to fixate the puck early, as well as sustain a long QE fixation on the puck until after it is released from the stick.

  20. Evaluating Antarctic sea ice predictability at seasonal to interannual timescales in global climate models

    NASA Astrophysics Data System (ADS)

    Marchi, Sylvain; Fichefet, Thierry; Goosse, Hugues; Zunz, Violette; Tietsche, Steffen; Day, Jonny; Hawkins, Ed

    2016-04-01

    Unlike the rapid sea ice losses reported in the Arctic, satellite observations show an overall increase in Antarctic sea ice extent over recent decades. Although many processes have already been suggested to explain this positive trend, it remains the subject of current investigations. Understanding the evolution of the Antarctic sea ice turns out to be more complicated than for the Arctic for two reasons: the lack of observations and the well-known biases of climate models in the Southern Ocean. Irrespective of those issues, another one is to determine whether the positive trend in sea ice extent would have been predictable if adequate observations and models were available some decades ago. This study of Antarctic sea ice predictability is carried out using 6 global climate models (HadGEM1.2, MPI-ESM-LR, GFDL CM3, EC-Earth V2, MIROC 5.2 and ECHAM 6-FESOM) which are all part of the APPOSITE project. These models are used to perform hindcast simulations in a perfect model approach. The predictive skill is estimated thanks to the PPP (Potential Prognostic Predictability) and the ACC (Anomaly Correlation Coefficient). The former is a measure of the uncertainty of the ensemble while the latter assesses the accuracy of the prediction. These two indicators are applied to different variables related to sea ice, in particular the total sea ice extent and the ice edge location. This first model intercomparison study about sea ice predictability in the Southern Ocean aims at giving a general overview of Antarctic sea ice predictability in current global climate models.

  1. Modeling methodology for the accurate and prompt prediction of symptomatic events in chronic diseases.

    PubMed

    Pagán, Josué; Risco-Martín, José L; Moya, José M; Ayala, José L

    2016-08-01

    Prediction of symptomatic crises in chronic diseases allows to take decisions before the symptoms occur, such as the intake of drugs to avoid the symptoms or the activation of medical alarms. The prediction horizon is in this case an important parameter in order to fulfill the pharmacokinetics of medications, or the time response of medical services. This paper presents a study about the prediction limits of a chronic disease with symptomatic crises: the migraine. For that purpose, this work develops a methodology to build predictive migraine models and to improve these predictions beyond the limits of the initial models. The maximum prediction horizon is analyzed, and its dependency on the selected features is studied. A strategy for model selection is proposed to tackle the trade off between conservative but robust predictive models, with respect to less accurate predictions with higher horizons. The obtained results show a prediction horizon close to 40min, which is in the time range of the drug pharmacokinetics. Experiments have been performed in a realistic scenario where input data have been acquired in an ambulatory clinical study by the deployment of a non-intrusive Wireless Body Sensor Network. Our results provide an effective methodology for the selection of the future horizon in the development of prediction algorithms for diseases experiencing symptomatic crises.

  2. Early Student Support to Investigate the Role of Sea Ice Albedo Feedback in Sea Ice Predictions

    DTIC Science & Technology

    2015-09-30

    Earth System Model version 1 (CESM1), which can be run in various configurations, such as fully-coupled, with slab-ocean, or ice-ocean only. We are...climate feedbacks using ra- diative kernels. J. Climate, 21, 3504–3520. 7 PUBLICATIONS Notz, D. and C.M. Bitz, Sea Ice in Earth System

  3. An effective method for accurate prediction of the first hyperpolarizability of alkalides.

    PubMed

    Wang, Jia-Nan; Xu, Hong-Liang; Sun, Shi-Ling; Gao, Ting; Li, Hong-Zhi; Li, Hui; Su, Zhong-Min

    2012-01-15

    The proper theoretical calculation method for nonlinear optical (NLO) properties is a key factor to design the excellent NLO materials. Yet it is a difficult task to obatin the accurate NLO property of large scale molecule. In present work, an effective intelligent computing method, as called extreme learning machine-neural network (ELM-NN), is proposed to predict accurately the first hyperpolarizability (β(0)) of alkalides from low-accuracy first hyperpolarizability. Compared with neural network (NN) and genetic algorithm neural network (GANN), the root-mean-square deviations of the predicted values obtained by ELM-NN, GANN, and NN with their MP2 counterpart are 0.02, 0.08, and 0.17 a.u., respectively. It suggests that the predicted values obtained by ELM-NN are more accurate than those calculated by NN and GANN methods. Another excellent point of ELM-NN is the ability to obtain the high accuracy level calculated values with less computing cost. Experimental results show that the computing time of MP2 is 2.4-4 times of the computing time of ELM-NN. Thus, the proposed method is a potentially powerful tool in computational chemistry, and it may predict β(0) of the large scale molecules, which is difficult to obtain by high-accuracy theoretical method due to dramatic increasing computational cost.

  4. On the possibility and predictability of rapid Arctic winter sea-ice loss

    NASA Astrophysics Data System (ADS)

    Bathiany, Sebastian; Notz, Dirk; Mauritsen, Thorsten; Raedel, Gaby; Brovkin, Victor; van der Bolt, Bregje; Scheffer, Marten; van Nes, Egbert; Williamson, Mark; Lenton, Tim

    2016-04-01

    We examine the transition from a seasonally ice-covered Arctic to an Arctic Ocean that is sea-ice free all year round under increasing atmospheric CO2 levels. Using two column models and nine Earth System Models, we investigate how rapid such Arctic winter sea-ice loss can be, and whether an abrupt ice loss can be predicted from observed trends in variance or autocorrelation. Such statistical indicators have been proposed as early warning signals of abrupt shifts that are caused by positive feedbacks. We show that in comprehensive climate models, the loss of winter sea-ice area is faster than the preceding loss of summer sea-ice area for the same rate of warming. In two of the models, several million km2 of winter sea ice are lost within only one decade. Their behaviour resembles the catastrophic winter ice loss in a column model where the stable ice-covered state suddenly disappears at a bifurcation point, implying an irreversible and abrupt shift to the ice-free solution. However, we argue that winter sea-ice loss in comprehensive models is reversible and not associated with the existence of multiple steady states. The large sensitivity of winter sea-ice area in complex models is caused by the asymmetry between melting and freezing: An ice-free summer requires the complete melt of even the thickest sea ice, which is why the perennial ice coverage decreases only gradually as more and more of the thinner ice melts away. In winter, however, sea-ice areal coverage remains high as long as sea ice still forms, and then drops to zero wherever the ocean warms sufficiently to no longer form ice during winter. As this mechanism occurs in every model we analyse and is independent of any specific parameterisation, it is likely to be relevant in the real world. We also find that expected trends in variance and autocorrelation of sea-ice area and thickness are not specific to the existence or the mechanism of abrupt ice loss. For example, natural fluctuations of ice volume

  5. Hash: a Program to Accurately Predict Protein Hα Shifts from Neighboring Backbone Shifts3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2012-01-01

    Chemical shifts provide not only peak identities for analyzing NMR data, but also an important source of conformational information for studying protein structures. Current structural studies requiring Hα chemical shifts suffer from the following limitations. (1) For large proteins, the Hα chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of Cα that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict Hα chemical shifts. Predicting accurate Hα chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict Hα chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate Hα chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins. PMID:23242797

  6. Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter

    PubMed Central

    Samsudin, Firdaus; Parker, Joanne L.; Sansom, Mark S.P.; Newstead, Simon; Fowler, Philip W.

    2016-01-01

    Summary Membrane transporters are critical modulators of drug pharmacokinetics, efficacy, and safety. One example is the proton-dependent oligopeptide transporter PepT1, also known as SLC15A1, which is responsible for the uptake of the β-lactam antibiotics and various peptide-based prodrugs. In this study, we modeled the binding of various peptides to a bacterial homolog, PepTSt, and evaluated a range of computational methods for predicting the free energy of binding. Our results show that a hybrid approach (endpoint methods to classify peptides into good and poor binders and a theoretically exact method for refinement) is able to accurately predict affinities, which we validated using proteoliposome transport assays. Applying the method to a homology model of PepT1 suggests that the approach requires a high-quality structure to be accurate. Our study provides a blueprint for extending these computational methodologies to other pharmaceutically important transporter families. PMID:27028887

  7. Fast and Accurate Prediction of Stratified Steel Temperature During Holding Period of Ladle

    NASA Astrophysics Data System (ADS)

    Deodhar, Anirudh; Singh, Umesh; Shukla, Rishabh; Gautham, B. P.; Singh, Amarendra K.

    2017-04-01

    Thermal stratification of liquid steel in a ladle during the holding period and the teeming operation has a direct bearing on the superheat available at the caster and hence on the caster set points such as casting speed and cooling rates. The changes in the caster set points are typically carried out based on temperature measurements at the end of tundish outlet. Thermal prediction models provide advance knowledge of the influence of process and design parameters on the steel temperature at various stages. Therefore, they can be used in making accurate decisions about the caster set points in real time. However, this requires both fast and accurate thermal prediction models. In this work, we develop a surrogate model for the prediction of thermal stratification using data extracted from a set of computational fluid dynamics (CFD) simulations, pre-determined using design of experiments technique. Regression method is used for training the predictor. The model predicts the stratified temperature profile instantaneously, for a given set of process parameters such as initial steel temperature, refractory heat content, slag thickness, and holding time. More than 96 pct of the predicted values are within an error range of ±5 K (±5 °C), when compared against corresponding CFD results. Considering its accuracy and computational efficiency, the model can be extended for thermal control of casting operations. This work also sets a benchmark for developing similar thermal models for downstream processes such as tundish and caster.

  8. Fast and Accurate Prediction of Stratified Steel Temperature During Holding Period of Ladle

    NASA Astrophysics Data System (ADS)

    Deodhar, Anirudh; Singh, Umesh; Shukla, Rishabh; Gautham, B. P.; Singh, Amarendra K.

    2016-12-01

    Thermal stratification of liquid steel in a ladle during the holding period and the teeming operation has a direct bearing on the superheat available at the caster and hence on the caster set points such as casting speed and cooling rates. The changes in the caster set points are typically carried out based on temperature measurements at the end of tundish outlet. Thermal prediction models provide advance knowledge of the influence of process and design parameters on the steel temperature at various stages. Therefore, they can be used in making accurate decisions about the caster set points in real time. However, this requires both fast and accurate thermal prediction models. In this work, we develop a surrogate model for the prediction of thermal stratification using data extracted from a set of computational fluid dynamics (CFD) simulations, pre-determined using design of experiments technique. Regression method is used for training the predictor. The model predicts the stratified temperature profile instantaneously, for a given set of process parameters such as initial steel temperature, refractory heat content, slag thickness, and holding time. More than 96 pct of the predicted values are within an error range of ±5 K (±5 °C), when compared against corresponding CFD results. Considering its accuracy and computational efficiency, the model can be extended for thermal control of casting operations. This work also sets a benchmark for developing similar thermal models for downstream processes such as tundish and caster.

  9. Can phenological models predict tree phenology accurately under climate change conditions?

    NASA Astrophysics Data System (ADS)

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2014-05-01

    The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay

  10. How predictable is the timing of a summer ice-free Arctic?

    NASA Astrophysics Data System (ADS)

    Jahn, Alexandra; Kay, Jennifer E.; Holland, Marika M.; Hall, David M.

    2016-09-01

    Climate model simulations give a large range of over 100 years for predictions of when the Arctic could first become ice free in the summer, and many studies have attempted to narrow this uncertainty range. However, given the chaotic nature of the climate system, what amount of spread in the prediction of an ice-free summer Arctic is inevitable? Based on results from large ensemble simulations with the Community Earth System Model, we show that internal variability alone leads to a prediction uncertainty of about two decades, while scenario uncertainty between the strong (Representative Concentration Pathway (RCP) 8.5) and medium (RCP4.5) forcing scenarios adds at least another 5 years. Common metrics of the past and present mean sea ice state (such as ice extent, volume, and thickness) as well as global mean temperatures do not allow a reduction of the prediction uncertainty from internal variability.

  11. Arctic Sea ice model sensitivities.

    SciTech Connect

    Peterson, Kara J.; Bochev, Pavel Blagoveston; Paskaleva, Biliana Stefanova

    2010-12-01

    Arctic sea ice is an important component of the global climate system and, due to feedback effects, the Arctic ice cover is changing rapidly. Predictive mathematical models are of paramount importance for accurate estimates of the future ice trajectory. However, the sea ice components of Global Climate Models (GCMs) vary significantly in their prediction of the future state of Arctic sea ice and have generally underestimated the rate of decline in minimum sea ice extent seen over the past thirty years. One of the contributing factors to this variability is the sensitivity of the sea ice state to internal model parameters. A new sea ice model that holds some promise for improving sea ice predictions incorporates an anisotropic elastic-decohesive rheology and dynamics solved using the material-point method (MPM), which combines Lagrangian particles for advection with a background grid for gradient computations. We evaluate the variability of this MPM sea ice code and compare it with the Los Alamos National Laboratory CICE code for a single year simulation of the Arctic basin using consistent ocean and atmospheric forcing. Sensitivities of ice volume, ice area, ice extent, root mean square (RMS) ice speed, central Arctic ice thickness,and central Arctic ice speed with respect to ten different dynamic and thermodynamic parameters are evaluated both individually and in combination using the Design Analysis Kit for Optimization and Terascale Applications (DAKOTA). We find similar responses for the two codes and some interesting seasonal variability in the strength of the parameters on the solution.

  12. Rapid and Highly Accurate Prediction of Poor Loop Diuretic Natriuretic Response in Patients With Heart Failure

    PubMed Central

    Testani, Jeffrey M.; Hanberg, Jennifer S.; Cheng, Susan; Rao, Veena; Onyebeke, Chukwuma; Laur, Olga; Kula, Alexander; Chen, Michael; Wilson, F. Perry; Darlington, Andrew; Bellumkonda, Lavanya; Jacoby, Daniel; Tang, W. H. Wilson; Parikh, Chirag R.

    2015-01-01

    Background Removal of excess sodium and fluid is a primary therapeutic objective in acute decompensated heart failure (ADHF) and commonly monitored with fluid balance and weight loss. However, these parameters are frequently inaccurate or not collected and require a delay of several hours after diuretic administration before they are available. Accessible tools for rapid and accurate prediction of diuretic response are needed. Methods and Results Based on well-established renal physiologic principles an equation was derived to predict net sodium output using a spot urine sample obtained one or two hours following loop diuretic administration. This equation was then prospectively validated in 50 ADHF patients using meticulously obtained timed 6-hour urine collections to quantitate loop diuretic induced cumulative sodium output. Poor natriuretic response was defined as a cumulative sodium output of <50 mmol, a threshold that would result in a positive sodium balance with twice-daily diuretic dosing. Following a median dose of 3 mg (2–4 mg) of intravenous bumetanide, 40% of the population had a poor natriuretic response. The correlation between measured and predicted sodium output was excellent (r=0.91, p<0.0001). Poor natriuretic response could be accurately predicted with the sodium prediction equation (AUC=0.95, 95% CI 0.89–1.0, p<0.0001). Clinically recorded net fluid output had a weaker correlation (r=0.66, p<0.001) and lesser ability to predict poor natriuretic response (AUC=0.76, 95% CI 0.63–0.89, p=0.002). Conclusions In patients being treated for ADHF, poor natriuretic response can be predicted soon after diuretic administration with excellent accuracy using a spot urine sample. PMID:26721915

  13. Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions

    PubMed Central

    2015-01-01

    Background Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorithms on specific biological tasks. We hypothesize that conditional co-regulation of genes is a key factor in determining cell phenotype and that accurately segregating conditions in biclusters will improve such predictions. Thus, we developed a bicluster sampled coherence metric (BSCM) for determining which conditions and signals should be included in a bicluster. Results Our BSCM calculates condition and cluster size specific p-values, and we incorporated these into the popular integrated biclustering algorithm cMonkey. We demonstrate that incorporation of our new algorithm significantly improves bicluster co-regulation scores (p-value = 0.009) and GO annotation scores (p-value = 0.004). Additionally, we used a bicluster based signal to predict whether a given experimental condition will result in yeast peroxisome induction. Using the new algorithm, the classifier accuracy improves from 41.9% to 76.1% correct. Conclusions We demonstrate that the proposed BSCM helps determine which signals ought to be co-clustered, resulting in more accurately assigned bicluster membership. Furthermore, we show that BSCM can be extended to more accurately detect under which experimental conditions the genes are co-clustered. Features derived from this more accurate analysis of conditional regulation results in a dramatic improvement in the ability to predict a cellular phenotype in yeast. The latest cMonkey is available for download at https://github.com/baliga-lab/cmonkey2. The experimental data and source code featured in this paper is available http://AitchisonLab.com/BSCM. BSCM has been incorporated in the official cMonkey release. PMID:25881257

  14. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    PubMed

    Kieslich, Chris A; Tamamis, Phanourios; Guzman, Yannis A; Onel, Melis; Floudas, Christodoulos A

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.

  15. Accurate similarity index based on activity and connectivity of node for link prediction

    NASA Astrophysics Data System (ADS)

    Li, Longjie; Qian, Lvjian; Wang, Xiaoping; Luo, Shishun; Chen, Xiaoyun

    2015-05-01

    Recent years have witnessed the increasing of available network data; however, much of those data is incomplete. Link prediction, which can find the missing links of a network, plays an important role in the research and analysis of complex networks. Based on the assumption that two unconnected nodes which are highly similar are very likely to have an interaction, most of the existing algorithms solve the link prediction problem by computing nodes' similarities. The fundamental requirement of those algorithms is accurate and effective similarity indices. In this paper, we propose a new similarity index, namely similarity based on activity and connectivity (SAC), which performs link prediction more accurately. To compute the similarity between two nodes, this index employs the average activity of these two nodes in their common neighborhood and the connectivities between them and their common neighbors. The higher the average activity is and the stronger the connectivities are, the more similar the two nodes are. The proposed index not only commendably distinguishes the contributions of paths but also incorporates the influence of endpoints. Therefore, it can achieve a better predicting result. To verify the performance of SAC, we conduct experiments on 10 real-world networks. Experimental results demonstrate that SAC outperforms the compared baselines.

  16. Accurate prediction of the linear viscoelastic properties of highly entangled mono and bidisperse polymer melts.

    PubMed

    Stephanou, Pavlos S; Mavrantzas, Vlasis G

    2014-06-07

    We present a hierarchical computational methodology which permits the accurate prediction of the linear viscoelastic properties of entangled polymer melts directly from the chemical structure, chemical composition, and molecular architecture of the constituent chains. The method entails three steps: execution of long molecular dynamics simulations with moderately entangled polymer melts, self-consistent mapping of the accumulated trajectories onto a tube model and parameterization or fine-tuning of the model on the basis of detailed simulation data, and use of the modified tube model to predict the linear viscoelastic properties of significantly higher molecular weight (MW) melts of the same polymer. Predictions are reported for the zero-shear-rate viscosity η0 and the spectra of storage G'(ω) and loss G″(ω) moduli for several mono and bidisperse cis- and trans-1,4 polybutadiene melts as well as for their MW dependence, and are found to be in remarkable agreement with experimentally measured rheological data.

  17. Predicting Clear-Sky Reflectance Over Snow/Ice in Polar Regions

    NASA Technical Reports Server (NTRS)

    Chen, Yan; Sun-Mack, Sunny; Arduini, Robert F.; Hong, Gang; Minnis, Patrick

    2015-01-01

    Satellite remote sensing of clouds requires an accurate estimate of the clear-sky radiances for a given scene to detect clouds and aerosols and to retrieve their microphysical properties. Knowing the spatial and angular variability of clear-sky albedo is essential for predicting clear-sky radiance at solar wavelengths. The Clouds and the Earth's Radiant Energy System (CERES) Project uses the nearinfrared (NIR; 1.24, 1.6 or 2.13 micrometers), visible (VIS; 0.63 micrometers) and vegetation (VEG; 0.86 micrometers) channels available on the Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) to help identify clouds and retrieve their properties in both snow-free and snow-covered conditions. Thus, it is critical to have reliable distributions of clear-sky albedo for all of these channels. In CERES Edition 4 (Ed4), the 1.24-micrometer channel is used to retrieve cloud optical depth over snow/ice-covered surfaces. Thus, it is especially critical to accurately predict the 1.24-micrometer clear-sky albedo alpha and reflectance rho for a given location and time. Snow albedo and reflectance patterns are very complex due to surface texture, particle shapes and sizes, melt water, and vegetation protrusions from the snow surface. To minimize those effects, this study focuses on the permanent snow cover of Antarctica where vegetation is absent and melt water is minimal. Clear-sky albedos are determined as a function of solar zenith angle (SZA) from observations over all scenes determined to be cloud-free to produce a normalized directional albedo model (DRM). The DRM is used to develop alpha(SZA=0 degrees) on 10 foot grid for each season. These values provide the basis for predicting r at any location and set of viewing & illumination conditions. This paper examines the accuracy of this approach for two theoretical snow surface reflectance models.

  18. Prediction of Accurate Thermochemistry of Medium and Large Sized Radicals Using Connectivity-Based Hierarchy (CBH).

    PubMed

    Sengupta, Arkajyoti; Raghavachari, Krishnan

    2014-10-14

    Accurate modeling of the chemical reactions in many diverse areas such as combustion, photochemistry, or atmospheric chemistry strongly depends on the availability of thermochemical information of the radicals involved. However, accurate thermochemical investigations of radical systems using state of the art composite methods have mostly been restricted to the study of hydrocarbon radicals of modest size. In an alternative approach, systematic error-canceling thermochemical hierarchy of reaction schemes can be applied to yield accurate results for such systems. In this work, we have extended our connectivity-based hierarchy (CBH) method to the investigation of radical systems. We have calibrated our method using a test set of 30 medium sized radicals to evaluate their heats of formation. The CBH-rad30 test set contains radicals containing diverse functional groups as well as cyclic systems. We demonstrate that the sophisticated error-canceling isoatomic scheme (CBH-2) with modest levels of theory is adequate to provide heats of formation accurate to ∼1.5 kcal/mol. Finally, we predict heats of formation of 19 other large and medium sized radicals for which the accuracy of available heats of formation are less well-known.

  19. Sea ice occurrence predicts genetic isolation in the Arctic fox.

    PubMed

    Geffen, Eli; Waidyaratne, Sitara; Dalén, Love; Angerbjörn, Anders; Vila, Carles; Hersteinsson, Pall; Fuglei, Eva; White, Paula A; Goltsman, Michael; Kapel, Christian M O; Wayne, Robert K

    2007-10-01

    Unlike Oceanic islands, the islands of the Arctic Sea are not completely isolated from migration by terrestrial vertebrates. The pack ice connects many Arctic Sea islands to the mainland during winter months. The Arctic fox (Alopex lagopus), which has a circumpolar distribution, populates numerous islands in the Arctic Sea. In this study, we used genetic data from 20 different populations, spanning the entire distribution of the Arctic fox, to identify barriers to dispersal. Specifically, we considered geographical distance, occurrence of sea ice, winter temperature, ecotype, and the presence of red fox and polar bear as nonexclusive factors that influence the dispersal behaviour of individuals. Using distance-based redundancy analysis and the BIOENV procedure, we showed that occurrence of sea ice is the key predictor and explained 40-60% of the genetic distance among populations. In addition, our analysis identified the Commander and Pribilof Islands Arctic populations as genetically unique suggesting they deserve special attention from a conservation perspective.

  20. Seasonal sea ice predictions for the Arctic based on assimilation of remotely sensed observations

    NASA Astrophysics Data System (ADS)

    Kauker, F.; Kaminski, T.; Ricker, R.; Toudal-Pedersen, L.; Dybkjaer, G.; Melsheimer, C.; Eastwood, S.; Sumata, H.; Karcher, M.; Gerdes, R.

    2015-10-01

    The recent thinning and shrinking of the Arctic sea ice cover has increased the interest in seasonal sea ice forecasts. Typical tools for such forecasts are numerical models of the coupled ocean sea ice system such as the North Atlantic/Arctic Ocean Sea Ice Model (NAOSIM). The model uses as input the initial state of the system and the atmospheric boundary condition over the forecasting period. This study investigates the potential of remotely sensed ice thickness observations in constraining the initial model state. For this purpose it employs a variational assimilation system around NAOSIM and the Alfred Wegener Institute's CryoSat-2 ice thickness product in conjunction with the University of Bremen's snow depth product and the OSI SAF ice concentration and sea surface temperature products. We investigate the skill of predictions of the summer ice conditions starting in March for three different years. Straightforward assimilation of the above combination of data streams results in slight improvements over some regions (especially in the Beaufort Sea) but degrades the over-all fit to independent observations. A considerable enhancement of forecast skill is demonstrated for a bias correction scheme for the CryoSat-2 ice thickness product that uses a spatially varying scaling factor.

  1. Impact of the assimilated sea ice data product on seasonal climate predictions with MPI-ESM

    NASA Astrophysics Data System (ADS)

    Bunzel, Felix; Notz, Dirk; Baehr, Johanna; Müller, Wolfgang; Fröhlich, Kristina

    2015-04-01

    We examine the impact of choosing a particular satellite record of sea ice for the initialisation of a seasonal prediction system. Such systems have in the past usually only been initialised with data describing the state of the ocean and of the atmosphere. However, also sea ice yields a substantial source of predictability, as it plays an important role for the Earth's energy and water budget. Therefore, recent studies started to incorporate sea ice into the initialisation of seasonal forecasts. For our study, we performed two assimilation runs with MPI-ESM from 1979 to 2012, where atmospheric and oceanic parameters as well as sea ice concentration were assimilated using Newtonian relaxation. The two assimilation runs differ only in the sea ice concentration dataset used for assimilating sea ice. In the first run, sea ice concentrations as derived by the NASA-Team algorithm are used, while in the second run sea ice concentrations computed from the Bootstrap algorithm are assimilated. A major difference between the two sea ice concentration data products involves the treatment of melt ponds. While for both products melt ponds appear as open water in the raw satellite data, the Bootstrap algorithm more strongly attempts to offset this systematic bias by synthetically increasing the retrieved ice concentration during summer months. For each year of the two assimilation runs we performed a 10-member ensemble of hindcast experiments starting on 1 May. We find the anomaly correlation coefficient for Arctic sea ice area at 2-3 months lead time to be substantially larger for Bootstrap initialisation compared to NASA-Team initialisation. The root mean square error reveals that in the central Arctic the Bootstrap initialisation produces better predictions, whereas the NASA-Team initialisation outperforms the Bootstrap initialisation in the vicinity of the ice edge. We investigate causes and mechanisms behind the dependence of the obtained prediction skill on the sea ice

  2. Planar Near-Field Phase Retrieval Using GPUs for Accurate THz Far-Field Prediction

    NASA Astrophysics Data System (ADS)

    Junkin, Gary

    2013-04-01

    With a view to using Phase Retrieval to accurately predict Terahertz antenna far-field from near-field intensity measurements, this paper reports on three fundamental advances that achieve very low algorithmic error penalties. The first is a new Gaussian beam analysis that provides accurate initial complex aperture estimates including defocus and astigmatic phase errors, based only on first and second moment calculations. The second is a powerful noise tolerant near-field Phase Retrieval algorithm that combines Anderson's Plane-to-Plane (PTP) with Fienup's Hybrid-Input-Output (HIO) and Successive Over-Relaxation (SOR) to achieve increased accuracy at reduced scan separations. The third advance employs teraflop Graphical Processing Units (GPUs) to achieve practically real time near-field phase retrieval and to obtain the optimum aperture constraint without any a priori information.

  3. Users Manual for the NASA Lewis Ice Accretion Prediction Code (LEWICE)

    NASA Technical Reports Server (NTRS)

    Ruff, Gary A.; Berkowitz, Brian M.

    1990-01-01

    LEWICE is an ice accretion prediction code that applies a time-stepping procedure to calculate the shape of an ice accretion. The potential flow field is calculated in LEWICE using the Douglas Hess-Smith 2-D panel code (S24Y). This potential flow field is then used to calculate the trajectories of particles and the impingement points on the body. These calculations are performed to determine the distribution of liquid water impinging on the body, which then serves as input to the icing thermodynamic code. The icing thermodynamic model is based on the work of Messinger, but contains several major modifications and improvements. This model is used to calculate the ice growth rate at each point on the surface of the geometry. By specifying an icing time increment, the ice growth rate can be interpreted as an ice thickness which is added to the body, resulting in the generation of new coordinates. This procedure is repeated, beginning with the potential flow calculations, until the desired icing time is reached. The operation of LEWICE is illustrated through the use of five examples. These examples are representative of the types of applications expected for LEWICE. All input and output is discussed, along with many of the diagnostic messages contained in the code. Several error conditions that may occur in the code for certain icing conditions are identified, and a course of action is recommended. LEWICE has been used to calculate a variety of ice shapes, but should still be considered a research code. The code should be exercised further to identify any shortcomings and inadequacies. Any modifications identified as a result of these cases, or of additional experimental results, should be incorporated into the model. Using it as a test bed for improvements to the ice accretion model is one important application of LEWICE.

  4. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-06-18

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  5. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  6. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  7. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

    SciTech Connect

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; Arkin, Adam P.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

  8. Development and Validation of a Multidisciplinary Tool for Accurate and Efficient Rotorcraft Noise Prediction (MUTE)

    NASA Technical Reports Server (NTRS)

    Liu, Yi; Anusonti-Inthra, Phuriwat; Diskin, Boris

    2011-01-01

    A physics-based, systematically coupled, multidisciplinary prediction tool (MUTE) for rotorcraft noise was developed and validated with a wide range of flight configurations and conditions. MUTE is an aggregation of multidisciplinary computational tools that accurately and efficiently model the physics of the source of rotorcraft noise, and predict the noise at far-field observer locations. It uses systematic coupling approaches among multiple disciplines including Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and high fidelity acoustics. Within MUTE, advanced high-order CFD tools are used around the rotor blade to predict the transonic flow (shock wave) effects, which generate the high-speed impulsive noise. Predictions of the blade-vortex interaction noise in low speed flight are also improved by using the Particle Vortex Transport Method (PVTM), which preserves the wake flow details required for blade/wake and fuselage/wake interactions. The accuracy of the source noise prediction is further improved by utilizing a coupling approach between CFD and CSD, so that the effects of key structural dynamics, elastic blade deformations, and trim solutions are correctly represented in the analysis. The blade loading information and/or the flow field parameters around the rotor blade predicted by the CFD/CSD coupling approach are used to predict the acoustic signatures at far-field observer locations with a high-fidelity noise propagation code (WOPWOP3). The predicted results from the MUTE tool for rotor blade aerodynamic loading and far-field acoustic signatures are compared and validated with a variation of experimental data sets, such as UH60-A data, DNW test data and HART II test data.

  9. The importance of spring atmospheric conditions for predictions of the Arctic summer sea ice extent

    NASA Astrophysics Data System (ADS)

    Kapsch, Marie-Luise; Graversen, Rune G.; Economou, Theodoros; Tjernström, Michael

    2014-07-01

    Recent studies have shown that atmospheric processes in spring play an important role for the initiation of the summer ice melt and therefore may strongly influence the September sea ice concentration (SSIC). Here a simple statistical regression model based on only atmospheric spring parameters is applied in order to predict the SSIC over the major part of the Arctic Ocean. By using spring anomalies of downwelling longwave radiation or atmospheric water vapor as predictor variables, correlation coefficients between observed and predicted SSIC of up to 0.5 are found. These skills of seasonal SSIC predictions are similar to those obtained using more complex dynamical forecast systems, despite the fact that the simple model applied here takes neither information of the sea ice state, oceanic conditions nor feedback mechanisms during summer into account. The results indicate that a realistic representation of spring atmospheric conditions in the prediction system plays an important role for the predictive skills of a model system.

  10. Accurate prediction of severe allergic reactions by a small set of environmental parameters (NDVI, temperature).

    PubMed

    Notas, George; Bariotakis, Michail; Kalogrias, Vaios; Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions.

  11. Microstructure-Dependent Gas Adsorption: Accurate Predictions of Methane Uptake in Nanoporous Carbons

    SciTech Connect

    Ihm, Yungok; Cooper, Valentino R; Gallego, Nidia C; Contescu, Cristian I; Morris, James R

    2014-01-01

    We demonstrate a successful, efficient framework for predicting gas adsorption properties in real materials based on first-principles calculations, with a specific comparison of experiment and theory for methane adsorption in activated carbons. These carbon materials have different pore size distributions, leading to a variety of uptake characteristics. Utilizing these distributions, we accurately predict experimental uptakes and heats of adsorption without empirical potentials or lengthy simulations. We demonstrate that materials with smaller pores have higher heats of adsorption, leading to a higher gas density in these pores. This pore-size dependence must be accounted for, in order to predict and understand the adsorption behavior. The theoretical approach combines: (1) ab initio calculations with a van der Waals density functional to determine adsorbent-adsorbate interactions, and (2) a thermodynamic method that predicts equilibrium adsorption densities by directly incorporating the calculated potential energy surface in a slit pore model. The predicted uptake at P=20 bar and T=298 K is in excellent agreement for all five activated carbon materials used. This approach uses only the pore-size distribution as an input, with no fitting parameters or empirical adsorbent-adsorbate interactions, and thus can be easily applied to other adsorbent-adsorbate combinations.

  12. Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

    PubMed Central

    Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

  13. Accurate bearing remaining useful life prediction based on Weibull distribution and artificial neural network

    NASA Astrophysics Data System (ADS)

    Ben Ali, Jaouher; Chebel-Morello, Brigitte; Saidi, Lotfi; Malinowski, Simon; Fnaiech, Farhat

    2015-05-01

    Accurate remaining useful life (RUL) prediction of critical assets is an important challenge in condition based maintenance to improve reliability and decrease machine's breakdown and maintenance's cost. Bearing is one of the most important components in industries which need to be monitored and the user should predict its RUL. The challenge of this study is to propose an original feature able to evaluate the health state of bearings and to estimate their RUL by Prognostics and Health Management (PHM) techniques. In this paper, the proposed method is based on the data-driven prognostic approach. The combination of Simplified Fuzzy Adaptive Resonance Theory Map (SFAM) neural network and Weibull distribution (WD) is explored. WD is used just in the training phase to fit measurement and to avoid areas of fluctuation in the time domain. SFAM training process is based on fitted measurements at present and previous inspection time points as input. However, the SFAM testing process is based on real measurements at present and previous inspections. Thanks to the fuzzy learning process, SFAM has an important ability and a good performance to learn nonlinear time series. As output, seven classes are defined; healthy bearing and six states for bearing degradation. In order to find the optimal RUL prediction, a smoothing phase is proposed in this paper. Experimental results show that the proposed method can reliably predict the RUL of rolling element bearings (REBs) based on vibration signals. The proposed prediction approach can be applied to prognostic other various mechanical assets.

  14. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    PubMed Central

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-01-01

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded. PMID:25979264

  15. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    SciTech Connect

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

  16. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    DOE PAGES

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  17. Accurate verification of the conserved-vector-current and standard-model predictions

    SciTech Connect

    Sirlin, A.; Zucchini, R.

    1986-10-20

    An approximate analytic calculation of O(Z..cap alpha../sup 2/) corrections to Fermi decays is presented. When the analysis of Koslowsky et al. is modified to take into account the new results, it is found that each of the eight accurately studied scrFt values differs from the average by approx. <1sigma, thus significantly improving the comparison of experiments with conserved-vector-current predictions. The new scrFt values are lower than before, which also brings experiments into very good agreement with the three-generation standard model, at the level of its quantum corrections.

  18. Special purpose hybrid transfinite elements and unified computational methodology for accurately predicting thermoelastic stress waves

    NASA Technical Reports Server (NTRS)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1988-01-01

    This paper represents an attempt to apply extensions of a hybrid transfinite element computational approach for accurately predicting thermoelastic stress waves. The applicability of the present formulations for capturing the thermal stress waves induced by boundary heating for the well known Danilovskaya problems is demonstrated. A unique feature of the proposed formulations for applicability to the Danilovskaya problem of thermal stress waves in elastic solids lies in the hybrid nature of the unified formulations and the development of special purpose transfinite elements in conjunction with the classical Galerkin techniques and transformation concepts. Numerical test cases validate the applicability and superior capability to capture the thermal stress waves induced due to boundary heating.

  19. The MIDAS touch for Accurately Predicting the Stress-Strain Behavior of Tantalum

    SciTech Connect

    Jorgensen, S.

    2016-03-02

    Testing the behavior of metals in extreme environments is not always feasible, so material scientists use models to try and predict the behavior. To achieve accurate results it is necessary to use the appropriate model and material-specific parameters. This research evaluated the performance of six material models available in the MIDAS database [1] to determine at which temperatures and strain-rates they perform best, and to determine to which experimental data their parameters were optimized. Additionally, parameters were optimized for the Johnson-Cook model using experimental data from Lassila et al [2].

  20. Accurate prediction of human drug toxicity: a major challenge in drug development.

    PubMed

    Li, Albert P

    2004-11-01

    Over the past decades, a number of drugs have been withdrawn or have required special labeling due to adverse effects observed post-marketing. Species differences in drug toxicity in preclinical safety tests and the lack of sensitive biomarkers and nonrepresentative patient population in clinical trials are probable reasons for the failures in predicting human drug toxicity. It is proposed that toxicology should evolve from an empirical practice to an investigative discipline. Accurate prediction of human drug toxicity requires resources and time to be spent in clearly defining key toxic pathways and corresponding risk factors, which hopefully, will be compensated by the benefits of a lower percentage of clinical failure due to toxicity and a decreased frequency of market withdrawal due to unacceptable adverse drug effects.

  1. Accurate prediction of the response of freshwater fish to a mixture of estrogenic chemicals.

    PubMed

    Brian, Jayne V; Harris, Catherine A; Scholze, Martin; Backhaus, Thomas; Booy, Petra; Lamoree, Marja; Pojana, Giulio; Jonkers, Niels; Runnalls, Tamsin; Bonfà, Angela; Marcomini, Antonio; Sumpter, John P

    2005-06-01

    Existing environmental risk assessment procedures are limited in their ability to evaluate the combined effects of chemical mixtures. We investigated the implications of this by analyzing the combined effects of a multicomponent mixture of five estrogenic chemicals using vitellogenin induction in male fathead minnows as an end point. The mixture consisted of estradiol, ethynylestradiol, nonylphenol, octylphenol, and bisphenol A. We determined concentration-response curves for each of the chemicals individually. The chemicals were then combined at equipotent concentrations and the mixture tested using fixed-ratio design. The effects of the mixture were compared with those predicted by the model of concentration addition using biomathematical methods, which revealed that there was no deviation between the observed and predicted effects of the mixture. These findings demonstrate that estrogenic chemicals have the capacity to act together in an additive manner and that their combined effects can be accurately predicted by concentration addition. We also explored the potential for mixture effects at low concentrations by exposing the fish to each chemical at one-fifth of its median effective concentration (EC50). Individually, the chemicals did not induce a significant response, although their combined effects were consistent with the predictions of concentration addition. This demonstrates the potential for estrogenic chemicals to act additively at environmentally relevant concentrations. These findings highlight the potential for existing environmental risk assessment procedures to underestimate the hazard posed by mixtures of chemicals that act via a similar mode of action, thereby leading to erroneous conclusions of absence of risk.

  2. Accurate Prediction of the Response of Freshwater Fish to a Mixture of Estrogenic Chemicals

    PubMed Central

    Brian, Jayne V.; Harris, Catherine A.; Scholze, Martin; Backhaus, Thomas; Booy, Petra; Lamoree, Marja; Pojana, Giulio; Jonkers, Niels; Runnalls, Tamsin; Bonfà, Angela; Marcomini, Antonio; Sumpter, John P.

    2005-01-01

    Existing environmental risk assessment procedures are limited in their ability to evaluate the combined effects of chemical mixtures. We investigated the implications of this by analyzing the combined effects of a multicomponent mixture of five estrogenic chemicals using vitellogenin induction in male fathead minnows as an end point. The mixture consisted of estradiol, ethynylestradiol, nonylphenol, octylphenol, and bisphenol A. We determined concentration–response curves for each of the chemicals individually. The chemicals were then combined at equipotent concentrations and the mixture tested using fixed-ratio design. The effects of the mixture were compared with those predicted by the model of concentration addition using biomathematical methods, which revealed that there was no deviation between the observed and predicted effects of the mixture. These findings demonstrate that estrogenic chemicals have the capacity to act together in an additive manner and that their combined effects can be accurately predicted by concentration addition. We also explored the potential for mixture effects at low concentrations by exposing the fish to each chemical at one-fifth of its median effective concentration (EC50). Individually, the chemicals did not induce a significant response, although their combined effects were consistent with the predictions of concentration addition. This demonstrates the potential for estrogenic chemicals to act additively at environmentally relevant concentrations. These findings highlight the potential for existing environmental risk assessment procedures to underestimate the hazard posed by mixtures of chemicals that act via a similar mode of action, thereby leading to erroneous conclusions of absence of risk. PMID:15929895

  3. IDSite: An accurate approach to predict P450-mediated drug metabolism

    PubMed Central

    Li, Jianing; Schneebeli, Severin T.; Bylund, Joseph; Farid, Ramy; Friesner, Richard A.

    2011-01-01

    Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets. PMID:22247702

  4. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    PubMed

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

  5. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    PubMed Central

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  6. Importance of initial conditions in seasonal predictions of Arctic sea ice extent

    NASA Astrophysics Data System (ADS)

    Msadek, R.; Vecchi, G. A.; Winton, M.; Gudgel, R. G.

    2014-07-01

    We present seasonal predictions of Arctic sea ice extent (SIE) over the 1982-2013 period using two suites of retrospective forecasts initialized from a fully coupled ocean-atmosphere-sea ice assimilation system. High skill scores are found in predicting year-to-year fluctuations of Arctic SIE, with significant correlations up to 7 month ahead for September detrended anomalies. Predictions over the recent era, which coincides with an improved observational coverage, outperform the earlier period for most target months. We find, however, a degradation of skill in September during the last decade, a period of sea ice thinning in observations. The two prediction models, Climate Model version 2.1 (CM2.1) and Forecast-oriented Low Ocean Resolution (FLOR), share very similar ocean and ice component and initialization but differ by their atmospheric component. FLOR has improved climatological atmospheric circulation and sea ice mean state, but its skill is overall similar to CM2.1 for most seasons, which suggests a key role for initial conditions in predicting seasonal SIE fluctuations.

  7. ILT based defect simulation of inspection images accurately predicts mask defect printability on wafer

    NASA Astrophysics Data System (ADS)

    Deep, Prakash; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2016-05-01

    At advanced technology nodes mask complexity has been increased because of large-scale use of resolution enhancement technologies (RET) which includes Optical Proximity Correction (OPC), Inverse Lithography Technology (ILT) and Source Mask Optimization (SMO). The number of defects detected during inspection of such mask increased drastically and differentiation of critical and non-critical defects are more challenging, complex and time consuming. Because of significant defectivity of EUVL masks and non-availability of actinic inspection, it is important and also challenging to predict the criticality of defects for printability on wafer. This is one of the significant barriers for the adoption of EUVL for semiconductor manufacturing. Techniques to decide criticality of defects from images captured using non actinic inspection images is desired till actinic inspection is not available. High resolution inspection of photomask images detects many defects which are used for process and mask qualification. Repairing all defects is not practical and probably not required, however it's imperative to know which defects are severe enough to impact wafer before repair. Additionally, wafer printability check is always desired after repairing a defect. AIMSTM review is the industry standard for this, however doing AIMSTM review for all defects is expensive and very time consuming. Fast, accurate and an economical mechanism is desired which can predict defect printability on wafer accurately and quickly from images captured using high resolution inspection machine. Predicting defect printability from such images is challenging due to the fact that the high resolution images do not correlate with actual mask contours. The challenge is increased due to use of different optical condition during inspection other than actual scanner condition, and defects found in such images do not have correlation with actual impact on wafer. Our automated defect simulation tool predicts

  8. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

    PubMed Central

    Li, Zhen; Zhang, Renyu

    2017-01-01

    Motivation Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. Method This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Results Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact

  9. A hierarchical approach to accurate predictions of macroscopic thermodynamic behavior from quantum mechanics and molecular simulations

    NASA Astrophysics Data System (ADS)

    Garrison, Stephen L.

    2005-07-01

    The combination of molecular simulations and potentials obtained from quantum chemistry is shown to be able to provide reasonably accurate thermodynamic property predictions. Gibbs ensemble Monte Carlo simulations are used to understand the effects of small perturbations to various regions of the model Lennard-Jones 12-6 potential. However, when the phase behavior and second virial coefficient are scaled by the critical properties calculated for each potential, the results obey a corresponding states relation suggesting a non-uniqueness problem for interaction potentials fit to experimental phase behavior. Several variations of a procedure collectively referred to as quantum mechanical Hybrid Methods for Interaction Energies (HM-IE) are developed and used to accurately estimate interaction energies from CCSD(T) calculations with a large basis set in a computationally efficient manner for the neon-neon, acetylene-acetylene, and nitrogen-benzene systems. Using these results and methods, an ab initio, pairwise-additive, site-site potential for acetylene is determined and then improved using results from molecular simulations using this initial potential. The initial simulation results also indicate that a limited range of energies important for accurate phase behavior predictions. Second virial coefficients calculated from the improved potential indicate that one set of experimental data in the literature is likely erroneous. This prescription is then applied to methanethiol. Difficulties in modeling the effects of the lone pair electrons suggest that charges on the lone pair sites negatively impact the ability of the intermolecular potential to describe certain orientations, but that the lone pair sites may be necessary to reasonably duplicate the interaction energies for several orientations. Two possible methods for incorporating the effects of three-body interactions into simulations within the pairwise-additivity formulation are also developed. A low density

  10. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    NASA Astrophysics Data System (ADS)

    Shvab, I.; Sadus, Richard J.

    2013-11-01

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm3 for a wide range of temperatures (298-650 K) and pressures (0.1-700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  11. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water.

    PubMed

    Shvab, I; Sadus, Richard J

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g∕cm(3) for a wide range of temperatures (298-650 K) and pressures (0.1-700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC∕E and TIP4P∕2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC∕E and TIP4P∕2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  12. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    SciTech Connect

    Shvab, I.; Sadus, Richard J.

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  13. Predicting Ice Sheet and Climate Evolution at Extreme Scales

    SciTech Connect

    Heimbach, Patrick

    2016-02-06

    A main research objectives of PISCEES is the development of formal methods for quantifying uncertainties in ice sheet modeling. Uncertainties in simulating and projecting mass loss from the polar ice sheets arise primarily from initial conditions, surface and basal boundary conditions, and model parameters. In general terms, two main chains of uncertainty propagation may be identified: 1. inverse propagation of observation and/or prior onto posterior control variable uncertainties; 2. forward propagation of prior or posterior control variable uncertainties onto those of target output quantities of interest (e.g., climate indices or ice sheet mass loss). A related goal is the development of computationally efficient methods for producing initial conditions for an ice sheet that are close to available present-day observations and essentially free of artificial model drift, which is required in order to be useful for model projections (“initialization problem”). To be of maximum value, such optimal initial states should be accompanied by “useful” uncertainty estimates that account for the different sources of uncerainties, as well as the degree to which the optimum state is constrained by available observations. The PISCEES proposal outlined two approaches for quantifying uncertainties. The first targets the full exploration of the uncertainty in model projections with sampling-based methods and a workflow managed by DAKOTA (the main delivery vehicle for software developed under QUEST). This is feasible for low-dimensional problems, e.g., those with a handful of global parameters to be inferred. This approach can benefit from derivative/adjoint information, but it is not necessary, which is why it often referred to as “non-intrusive”. The second approach makes heavy use of derivative information from model adjoints to address quantifying uncertainty in high-dimensions (e.g., basal boundary conditions in ice sheet models). The use of local gradient, or

  14. Predictability of winter temperature in China from previous autumn Arctic sea ice

    NASA Astrophysics Data System (ADS)

    Zuo, Jinqing; Ren, Hong-Li; Wu, Bingyi; Li, Weijing

    2016-10-01

    The potential predictability of winter temperature in China from autumn Arctic sea ice anomalies is studied by examining and statistically modeling the large-scale interannual covariability between them on the basis of singular value decomposition analysis. It is demonstrated that an intimate relationship exists between September and October sea ice anomalies in the Eurasian Arctic and following winter temperature anomalies in China, except in the Tibetan Plateau. When the autumn sea ice anomalies decline in the Eurasian Arctic, above-normal pressure anomalies appear to prevail over the region from the Eurasian Arctic to Eastern Europe and Mongolia, and below-normal anomalies prevail over the mid-latitudes of Asia and Northwestern Pacific in the following winter. Consequently, the winter Siberian High and East Asian trough are both strengthened, favoring the southward invasion of high-latitude cold air masses and thus cold temperature anomalies in China. It is found that the Siberian High plays a crucial role in delivering effects of the autumn Arctic sea ice anomalies on winter temperature variability in China. Based on this evidence, a statistical model is established to examine the potential predictability of winter temperature anomalies in China by taking the autumn Arctic sea ice signals as a predictor. Validation shows considerable skill in predicting winter temperature anomalies over a large part of China, indicating a significant potential for improving winter climate prediction in China.

  15. Acute Toxicity Prediction to Threatened and Endangered Species Using Interspecies Correlation Estimation (ICE) Models.

    PubMed

    Willming, Morgan M; Lilavois, Crystal R; Barron, Mace G; Raimondo, Sandy

    2016-10-04

    Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA's Internet application Web-ICE is a suite of Interspecies Correlation Estimation (ICE) models that can extrapolate species sensitivity to listed taxa using least-squares regressions of the sensitivity of a surrogate species and a predicted taxon (species, genus, or family). Web-ICE was expanded with new models that can predict toxicity to over 250 listed species. A case study was used to assess protectiveness of genus and family model estimates derived from either geometric mean or minimum taxa toxicity values for listed species. Models developed from the most sensitive value for each chemical were generally protective of the most sensitive species within predicted taxa, including listed species, and were more protective than geometric means models. ICE model estimates were compared to HC5 values derived from Species Sensitivity Distributions for the case study chemicals to assess protectiveness of the two approaches. ICE models provide robust toxicity predictions and can generate protective toxicity estimates for assessing contaminant risk to listed species.

  16. Distance scaling method for accurate prediction of slowly varying magnetic fields in satellite missions

    NASA Astrophysics Data System (ADS)

    Zacharias, Panagiotis P.; Chatzineofytou, Elpida G.; Spantideas, Sotirios T.; Capsalis, Christos N.

    2016-07-01

    In the present work, the determination of the magnetic behavior of localized magnetic sources from near-field measurements is examined. The distance power law of the magnetic field fall-off is used in various cases to accurately predict the magnetic signature of an equipment under test (EUT) consisting of multiple alternating current (AC) magnetic sources. Therefore, parameters concerning the location of the observation points (magnetometers) are studied towards this scope. The results clearly show that these parameters are independent of the EUT's size and layout. Additionally, the techniques developed in the present study enable the placing of the magnetometers close to the EUT, thus achieving high signal-to-noise ratio (SNR). Finally, the proposed method is verified by real measurements, using a mobile phone as an EUT.

  17. A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows

    NASA Astrophysics Data System (ADS)

    Bijleveld, H. A.; Veldman, A. E. P.

    2014-12-01

    A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.

  18. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  19. Predictions replaced by facts: a keystone species' behavioural responses to declining arctic sea-ice.

    PubMed

    Hamilton, Charmain D; Lydersen, Christian; Ims, Rolf A; Kovacs, Kit M

    2015-11-01

    Since the first documentation of climate-warming induced declines in arctic sea-ice, predictions have been made regarding the expected negative consequences for endemic marine mammals. But, several decades later, little hard evidence exists regarding the responses of these animals to the ongoing environmental changes. Herein, we report the first empirical evidence of a dramatic shift in movement patterns and foraging behaviour of the arctic endemic ringed seal (Pusa hispida), before and after a major collapse in sea-ice in Svalbard, Norway. Among other changes to the ice-regime, this collapse shifted the summer position of the marginal ice zone from over the continental shelf, northward to the deep Arctic Ocean Basin. Following this change, which is thought to be a 'tipping point', subadult ringed seals swam greater distances, showed less area-restricted search behaviour, dived for longer periods, exhibited shorter surface intervals, rested less on sea-ice and did less diving directly beneath the ice during post-moulting foraging excursions. In combination, these behavioural changes suggest increased foraging effort and thus also likely increases in the energetic costs of finding food. Continued declines in sea-ice are likely to result in distributional changes, range reductions and population declines in this keystone arctic species.

  20. Analysis and Prediction of Ice Shedding for a Full-Scale Heated Tail Rotor

    NASA Technical Reports Server (NTRS)

    Kreeger, Richard E.; Work, Andrew; Douglass, Rebekah; Gazella, Matthew; Koster, Zakery; Turk, Jodi

    2016-01-01

    When helicopters are to fly in icing conditions, it is necessary to consider the possibility of ice shed from the rotor blades. In 2013, a series of tests were conducted on a heated tail rotor at NASA Glenn's Icing Research Tunnel (IRT). The tests produced several shed events that were captured on camera. Three of these shed events were captured at a sufficiently high frame rate to obtain multiple images of the shed ice in flight that had a sufficiently long section of shed ice for analysis. Analysis of these shed events is presented and compared to an analytical Shedding Trajectory Model (STM). The STM is developed and assumes that the ice breaks off instantly as it reaches the end of the blade, while frictional and viscous forces are used as parameters to fit the STM. The trajectory of each shed is compared to that predicted by the STM, where the STM provides information of the shed group of ice as a whole. The limitations of the model's underlying assumptions are discussed in comparison to experimental shed events.

  1. Measuring solar reflectance Part I: Defining a metric that accurately predicts solar heat gain

    SciTech Connect

    Levinson, Ronnen; Akbari, Hashem; Berdahl, Paul

    2010-05-14

    Solar reflectance can vary with the spectral and angular distributions of incident sunlight, which in turn depend on surface orientation, solar position and atmospheric conditions. A widely used solar reflectance metric based on the ASTM Standard E891 beam-normal solar spectral irradiance underestimates the solar heat gain of a spectrally selective 'cool colored' surface because this irradiance contains a greater fraction of near-infrared light than typically found in ordinary (unconcentrated) global sunlight. At mainland U.S. latitudes, this metric RE891BN can underestimate the annual peak solar heat gain of a typical roof or pavement (slope {le} 5:12 [23{sup o}]) by as much as 89 W m{sup -2}, and underestimate its peak surface temperature by up to 5 K. Using R{sub E891BN} to characterize roofs in a building energy simulation can exaggerate the economic value N of annual cool-roof net energy savings by as much as 23%. We define clear-sky air mass one global horizontal ('AM1GH') solar reflectance R{sub g,0}, a simple and easily measured property that more accurately predicts solar heat gain. R{sub g,0} predicts the annual peak solar heat gain of a roof or pavement to within 2 W m{sup -2}, and overestimates N by no more than 3%. R{sub g,0} is well suited to rating the solar reflectances of roofs, pavements and walls. We show in Part II that R{sub g,0} can be easily and accurately measured with a pyranometer, a solar spectrophotometer or version 6 of the Solar Spectrum Reflectometer.

  2. Accurate prediction of wall shear stress in a stented artery: newtonian versus non-newtonian models.

    PubMed

    Mejia, Juan; Mongrain, Rosaire; Bertrand, Olivier F

    2011-07-01

    A significant amount of evidence linking wall shear stress to neointimal hyperplasia has been reported in the literature. As a result, numerical and experimental models have been created to study the influence of stent design on wall shear stress. Traditionally, blood has been assumed to behave as a Newtonian fluid, but recently that assumption has been challenged. The use of a linear model; however, can reduce computational cost, and allow the use of Newtonian fluids (e.g., glycerine and water) instead of a blood analog fluid in an experimental setup. Therefore, it is of interest whether a linear model can be used to accurately predict the wall shear stress caused by a non-Newtonian fluid such as blood within a stented arterial segment. The present work compares the resulting wall shear stress obtained using two linear and one nonlinear model under the same flow waveform. All numerical models are fully three-dimensional, transient, and incorporate a realistic stent geometry. It is shown that traditional linear models (based on blood's lowest viscosity limit, 3.5 Pa s) underestimate the wall shear stress within a stented arterial segment, which can lead to an overestimation of the risk of restenosis. The second linear model, which uses a characteristic viscosity (based on an average strain rate, 4.7 Pa s), results in higher wall shear stress levels, but which are still substantially below those of the nonlinear model. It is therefore shown that nonlinear models result in more accurate predictions of wall shear stress within a stented arterial segment.

  3. Point-of-care cardiac troponin test accurately predicts heat stroke severity in rats.

    PubMed

    Audet, Gerald N; Quinn, Carrie M; Leon, Lisa R

    2015-11-15

    Heat stroke (HS) remains a significant public health concern. Despite the substantial threat posed by HS, there is still no field or clinical test of HS severity. We suggested previously that circulating cardiac troponin (cTnI) could serve as a robust biomarker of HS severity after heating. In the present study, we hypothesized that (cTnI) point-of-care test (ctPOC) could be used to predict severity and organ damage at the onset of HS. Conscious male Fischer 344 rats (n = 16) continuously monitored for heart rate (HR), blood pressure (BP), and core temperature (Tc) (radiotelemetry) were heated to maximum Tc (Tc,Max) of 41.9 ± 0.1°C and recovered undisturbed for 24 h at an ambient temperature of 20°C. Blood samples were taken at Tc,Max and 24 h after heat via submandibular bleed and analyzed on ctPOC test. POC cTnI band intensity was ranked using a simple four-point scale via two blinded observers and compared with cTnI levels measured by a clinical blood analyzer. Blood was also analyzed for biomarkers of systemic organ damage. HS severity, as previously defined using HR, BP, and recovery Tc profile during heat exposure, correlated strongly with cTnI (R(2) = 0.69) at Tc,Max. POC cTnI band intensity ranking accurately predicted cTnI levels (R(2) = 0.64) and HS severity (R(2) = 0.83). Five markers of systemic organ damage also correlated with ctPOC score (albumin, alanine aminotransferase, blood urea nitrogen, cholesterol, and total bilirubin; R(2) > 0.4). This suggests that cTnI POC tests can accurately determine HS severity and could serve as simple, portable, cost-effective HS field tests.

  4. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

    PubMed Central

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research. PMID:27571061

  5. Validation of the FAST skating protocol to predict aerobic power in ice hockey players.

    PubMed

    Petrella, Nicholas J; Montelpare, William J; Nystrom, Murray; Plyley, Michael; Faught, Brent E

    2007-08-01

    Few studies have reported a sport-specific protocol to measure the aerobic power of ice hockey players using a predictive process. The purpose of our study was to validate an ice hockey aerobic field test on players of varying ages, abilities, and levels. The Faught Aerobic Skating Test (FAST) uses an on-ice continuous skating protocol on a course measuring 160 feet (48.8 m) using a CD to pace the skater with a beep signal to cross the starting line at each end of the course. The FAST incorporates the principle of increasing workload at measured time intervals during a continuous skating exercise. Step-wise multiple regression modelling was used to determine the estimate of aerobic power. Participants completed a maximal aerobic power test using a modified Bruce incremental treadmill protocol, as well as the on-ice FAST. Normative data were collected on 406 ice hockey players (291 males, 115 females) ranging in age from 9 to 25 y. A regression to predict maximum aerobic power was developed using body mass (kg), height (m), age (y), and maximum completed lengths of the FAST as the significant predictors of skating aerobic power (adjusted R2 = 0.387, SEE = 7.25 mL.kg-1.min-1, p < 0.0001). These results support the application of the FAST in estimating aerobic power among male and female competitive ice hockey players between the ages of 9 and 25 years.

  6. Predicting and evaluating the performance of ice harvesting thermal energy storage systems

    SciTech Connect

    Knebel, D.E.

    1995-05-01

    The author describes a model for predicting the net rated ice making capacity of thermal energy storage systems. Harvesting ice generators are a simple application of a direct expansion, flooded or pumped overfeed refrigeration system. Single refrigeration circuits over 300 tons (1,056 kW) have been predominantly pumped overfeed. The evaporator consists of a series of vertical plate heat exchangers mounted above a storage tank. Water is pumped from the storage tank at low head and distributed over the evaporator surface where it flows in a thin film down the surface and returns to the storage tank by gravity. If the water temperature is warm, the evaporator functions as a chiller. If the water temperature is low, some of the water is frozen into sheets of ice about 3/16 in. to 3/8 in. (5 to 9 mm) thick. Periodically, the ice is released from the evaporator surface by reversing the refrigerant flow to the evaporator.

  7. Assessment of Lightning Transients on a De-Iced Rotor Blade with Predictive Tools and Coaxial Return Measurements

    NASA Astrophysics Data System (ADS)

    Guillet, S.; Gosmain, A.; Ducoux, W.; Ponçon, M.; Fontaine, G.; Desseix, P.; Perraud, P.

    2012-05-01

    The increasing use of composite materials in aircrafts primary structures has led to different problematics in the field of safety of flight in lightning conditions. The consequences of this technological mutation, which occurs in a parallel context of extension of electrified critical functions, are addressed by aircraft manufacturers through the enhancement of their available assessment means of lightning transient. On the one hand, simulation tools, provided an accurate description of aircraft design, are today valuable assessment tools, in both predictive and operative terms. On the other hand, in-house test means allow confirmation and consolidation of design office hardening solutions. The combined use of predictive simulation tools and in- house test means offers an efficient and reliable support for all aircraft developments in their various life-time stages. The present paper provides PREFACE research project results that illustrate the above introduced strategy on the de-icing system of the NH90 composite main rotor blade.

  8. A Critical Review for Developing Accurate and Dynamic Predictive Models Using Machine Learning Methods in Medicine and Health Care.

    PubMed

    Alanazi, Hamdan O; Abdullah, Abdul Hanan; Qureshi, Kashif Naseer

    2017-04-01

    Recently, Artificial Intelligence (AI) has been used widely in medicine and health care sector. In machine learning, the classification or prediction is a major field of AI. Today, the study of existing predictive models based on machine learning methods is extremely active. Doctors need accurate predictions for the outcomes of their patients' diseases. In addition, for accurate predictions, timing is another significant factor that influences treatment decisions. In this paper, existing predictive models in medicine and health care have critically reviewed. Furthermore, the most famous machine learning methods have explained, and the confusion between a statistical approach and machine learning has clarified. A review of related literature reveals that the predictions of existing predictive models differ even when the same dataset is used. Therefore, existing predictive models are essential, and current methods must be improved.

  9. Seasonal Ice loss in the Beaufort Sea: Toward Synchronicity and Prediction

    NASA Astrophysics Data System (ADS)

    Steele, M.; Dickinson, S.; Zhang, J.; Lindsay, R. W.

    2014-12-01

    The seasonal evolution of sea ice loss in the Beaufort Sea during 1979-2012 is examined, focusing on spatial differences between eastern and western sectors. Two stages in ice loss are identified: "opening" is defined as the spring decrease in ice concentration from its winter maximum below a value of 80% areal concentration; "retreat" is the summer decrease below 15% concentration. We consider three aspects of the problem, i.e. (i) the long-term mean, (ii) long-term linear trends, and (iii) year-to-year variability. We find that in the mean, ice opening occurs earliest in the southeast Beaufort Sea (SEB), forced by atmospheric heating acting on particularly thin ice relative to the southwestern Beaufort Sea (SWB). This thin SEB ice arises from divergence forced by easterly winds in fall and spring. There is no significant long-term trend in the date of SEB ice opening, although ice opening in the SWB is in fact trending toward earlier dates. This means that spatial differences in opening dates across the Beaufort Sea have been shrinking over the past 33 years, i.e., these dates are becoming more synchronous, a situation which may impact human and marine mammal activity in the area. Synchronicity in ice retreat dates is also increasing, although with no statistical significance at this time. Finally, we find that in any given year, an increase in monthly mean easterly winds of ~ 1 m/s during spring is associated with earlier summer retreat of 9-15 days, offering predictive capability with 1-2 months lead time.

  10. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina.

    PubMed

    Maturana, Matias I; Apollo, Nicholas V; Hadjinicolaou, Alex E; Garrett, David J; Cloherty, Shaun L; Kameneva, Tatiana; Grayden, David B; Ibbotson, Michael R; Meffin, Hamish

    2016-04-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron's electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy.

  11. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

    SciTech Connect

    Visel, Axel; Blow, Matthew J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Ren, Bing; Rubin, Edward M.; Pennacchio, Len A.

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

  12. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina

    PubMed Central

    Maturana, Matias I.; Apollo, Nicholas V.; Hadjinicolaou, Alex E.; Garrett, David J.; Cloherty, Shaun L.; Kameneva, Tatiana; Grayden, David B.; Ibbotson, Michael R.; Meffin, Hamish

    2016-01-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron’s electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  13. Fast and accurate pressure-drop prediction in straightened atherosclerotic coronary arteries.

    PubMed

    Schrauwen, Jelle T C; Koeze, Dion J; Wentzel, Jolanda J; van de Vosse, Frans N; van der Steen, Anton F W; Gijsen, Frank J H

    2015-01-01

    Atherosclerotic disease progression in coronary arteries is influenced by wall shear stress. To compute patient-specific wall shear stress, computational fluid dynamics (CFD) is required. In this study we propose a method for computing the pressure-drop in regions proximal and distal to a plaque, which can serve as a boundary condition in CFD. As a first step towards exploring the proposed method we investigated ten straightened coronary arteries. First, the flow fields were calculated with CFD and velocity profiles were fitted on the results. Second, the Navier-Stokes equation was simplified and solved with the found velocity profiles to obtain a pressure-drop estimate (Δp (1)). Next, Δp (1) was compared to the pressure-drop from CFD (Δp CFD) as a validation step. Finally, the velocity profiles, and thus the pressure-drop were predicted based on geometry and flow, resulting in Δp geom. We found that Δp (1) adequately estimated Δp CFD with velocity profiles that have one free parameter β. This β was successfully related to geometry and flow, resulting in an excellent agreement between Δp CFD and Δp geom: 3.9 ± 4.9% difference at Re = 150. We showed that this method can quickly and accurately predict pressure-drop on the basis of geometry and flow in straightened coronary arteries that are mildly diseased.

  14. Accurate load prediction by BEM with airfoil data from 3D RANS simulations

    NASA Astrophysics Data System (ADS)

    Schneider, Marc S.; Nitzsche, Jens; Hennings, Holger

    2016-09-01

    In this paper, two methods for the extraction of airfoil coefficients from 3D CFD simulations of a wind turbine rotor are investigated, and these coefficients are used to improve the load prediction of a BEM code. The coefficients are extracted from a number of steady RANS simulations, using either averaging of velocities in annular sections, or an inverse BEM approach for determination of the induction factors in the rotor plane. It is shown that these 3D rotor polars are able to capture the rotational augmentation at the inner part of the blade as well as the load reduction by 3D effects close to the blade tip. They are used as input to a simple BEM code and the results of this BEM with 3D rotor polars are compared to the predictions of BEM with 2D airfoil coefficients plus common empirical corrections for stall delay and tip loss. While BEM with 2D airfoil coefficients produces a very different radial distribution of loads than the RANS simulation, the BEM with 3D rotor polars manages to reproduce the loads from RANS very accurately for a variety of load cases, as long as the blade pitch angle is not too different from the cases from which the polars were extracted.

  15. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  16. Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning

    PubMed Central

    Abraham, Gad; Tye-Din, Jason A.; Bhalala, Oneil G.; Kowalczyk, Adam; Zobel, Justin; Inouye, Michael

    2014-01-01

    Practical application of genomic-based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European cohorts, we provide a proof-of-concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models of CD based on genome-wide SNP profiles. The high predictive capacity replicated both in cross-validation within each cohort (AUC of 0.87–0.89) and in independent replication across cohorts (AUC of 0.86–0.9), despite differences in ethnicity. The models explained 30–35% of disease variance and up to ∼43% of heritability. The GRS's utility was assessed in different clinically relevant settings. Comparable to HLA typing, the GRS can be used to identify individuals without CD with ≥99.6% negative predictive value however, unlike HLA typing, fine-scale stratification of individuals into categories of higher-risk for CD can identify those that would benefit from more invasive and costly definitive testing. The GRS is flexible and its performance can be adapted to the clinical situation by adjusting the threshold cut-off. Despite explaining a minority of disease heritability, our findings indicate a genomic risk score provides clinically relevant information to improve upon current diagnostic pathways for CD and support further studies evaluating the clinical utility of this approach in CD and other complex diseases. PMID:24550740

  17. Energy expenditure during level human walking: seeking a simple and accurate predictive solution.

    PubMed

    Ludlow, Lindsay W; Weyand, Peter G

    2016-03-01

    Accurate prediction of the metabolic energy that walking requires can inform numerous health, bodily status, and fitness outcomes. We adopted a two-step approach to identifying a concise, generalized equation for predicting level human walking metabolism. Using literature-aggregated values we compared 1) the predictive accuracy of three literature equations: American College of Sports Medicine (ACSM), Pandolf et al., and Height-Weight-Speed (HWS); and 2) the goodness-of-fit possible from one- vs. two-component descriptions of walking metabolism. Literature metabolic rate values (n = 127; speed range = 0.4 to 1.9 m/s) were aggregated from 25 subject populations (n = 5-42) whose means spanned a 1.8-fold range of heights and a 4.2-fold range of weights. Population-specific resting metabolic rates (V̇o2 rest) were determined using standardized equations. Our first finding was that the ACSM and Pandolf et al. equations underpredicted nearly all 127 literature-aggregated values. Consequently, their standard errors of estimate (SEE) were nearly four times greater than those of the HWS equation (4.51 and 4.39 vs. 1.13 ml O2·kg(-1)·min(-1), respectively). For our second comparison, empirical best-fit relationships for walking metabolism were derived from the data set in one- and two-component forms for three V̇o2-speed model types: linear (∝V(1.0)), exponential (∝V(2.0)), and exponential/height (∝V(2.0)/Ht). We found that the proportion of variance (R(2)) accounted for, when averaged across the three model types, was substantially lower for one- vs. two-component versions (0.63 ± 0.1 vs. 0.90 ± 0.03) and the predictive errors were nearly twice as great (SEE = 2.22 vs. 1.21 ml O2·kg(-1)·min(-1)). Our final analysis identified the following concise, generalized equation for predicting level human walking metabolism: V̇o2 total = V̇o2 rest + 3.85 + 5.97·V(2)/Ht (where V is measured in m/s, Ht in meters, and V̇o2 in ml O2·kg(-1)·min(-1)).

  18. Predicting Land-Ice Retreat and Sea-Level Rise with the Community Earth System Model

    SciTech Connect

    Lipscomb, William

    2012-06-19

    Coastal stakeholders need defensible predictions of 21st century sea-level rise (SLR). IPCC assessments suggest 21st century SLR of {approx}0.5 m under aggressive emission scenarios. Semi-empirical models project SLR of {approx}1 m or more by 2100. Although some sea-level contributions are fairly well constrained by models, others are highly uncertain. Recent studies suggest a potential large contribution ({approx}0.5 m/century) from the marine-based West Antarctic Ice Sheet, linked to changes in Southern Ocean wind stress. To assess the likelihood of fast retreat of marine ice sheets, we need coupled ice-sheet/ocean models that do not yet exist (but are well under way). CESM is uniquely positioned to provide integrated, physics based sea-level predictions.

  19. Can radiation therapy treatment planning system accurately predict surface doses in postmastectomy radiation therapy patients?

    SciTech Connect

    Wong, Sharon; Back, Michael; Tan, Poh Wee; Lee, Khai Mun; Baggarley, Shaun; Lu, Jaide Jay

    2012-07-01

    Skin doses have been an important factor in the dose prescription for breast radiotherapy. Recent advances in radiotherapy treatment techniques, such as intensity-modulated radiation therapy (IMRT) and new treatment schemes such as hypofractionated breast therapy have made the precise determination of the surface dose necessary. Detailed information of the dose at various depths of the skin is also critical in designing new treatment strategies. The purpose of this work was to assess the accuracy of surface dose calculation by a clinically used treatment planning system and those measured by thermoluminescence dosimeters (TLDs) in a customized chest wall phantom. This study involved the construction of a chest wall phantom for skin dose assessment. Seven TLDs were distributed throughout each right chest wall phantom to give adequate representation of measured radiation doses. Point doses from the CMS Xio Registered-Sign treatment planning system (TPS) were calculated for each relevant TLD positions and results correlated. There were no significant difference between measured absorbed dose by TLD and calculated doses by the TPS (p > 0.05 (1-tailed). Dose accuracy of up to 2.21% was found. The deviations from the calculated absorbed doses were overall larger (3.4%) when wedges and bolus were used. 3D radiotherapy TPS is a useful and accurate tool to assess the accuracy of surface dose. Our studies have shown that radiation treatment accuracy expressed as a comparison between calculated doses (by TPS) and measured doses (by TLD dosimetry) can be accurately predicted for tangential treatment of the chest wall after mastectomy.

  20. Structure-based constitutive model can accurately predict planar biaxial properties of aortic wall tissue.

    PubMed

    Polzer, S; Gasser, T C; Novak, K; Man, V; Tichy, M; Skacel, P; Bursa, J

    2015-03-01

    Structure-based constitutive models might help in exploring mechanisms by which arterial wall histology is linked to wall mechanics. This study aims to validate a recently proposed structure-based constitutive model. Specifically, the model's ability to predict mechanical biaxial response of porcine aortic tissue with predefined collagen structure was tested. Histological slices from porcine thoracic aorta wall (n=9) were automatically processed to quantify the collagen fiber organization, and mechanical testing identified the non-linear properties of the wall samples (n=18) over a wide range of biaxial stretches. Histological and mechanical experimental data were used to identify the model parameters of a recently proposed multi-scale constitutive description for arterial layers. The model predictive capability was tested with respect to interpolation and extrapolation. Collagen in the media was predominantly aligned in circumferential direction (planar von Mises distribution with concentration parameter bM=1.03 ± 0.23), and its coherence decreased gradually from the luminal to the abluminal tissue layers (inner media, b=1.54 ± 0.40; outer media, b=0.72 ± 0.20). In contrast, the collagen in the adventitia was aligned almost isotropically (bA=0.27 ± 0.11), and no features, such as families of coherent fibers, were identified. The applied constitutive model captured the aorta biaxial properties accurately (coefficient of determination R(2)=0.95 ± 0.03) over the entire range of biaxial deformations and with physically meaningful model parameters. Good predictive properties, well outside the parameter identification space, were observed (R(2)=0.92 ± 0.04). Multi-scale constitutive models equipped with realistic micro-histological data can predict macroscopic non-linear aorta wall properties. Collagen largely defines already low strain properties of media, which explains the origin of wall anisotropy seen at this strain level. The structure and mechanical

  1. Using timing of ice retreat to predict timing of fall freeze-up in the Arctic

    NASA Astrophysics Data System (ADS)

    Stroeve, Julienne C.; Crawford, Alex D.; Stammerjohn, Sharon

    2016-06-01

    Reliable forecasts of the timing of sea ice advance are needed in order to reduce risks associated with operating in the Arctic as well as planning of human and environmental emergencies. This study investigates the use of a simple statistical model relating the timing of ice retreat to the timing of ice advance, taking advantage of the inherent predictive power supplied by the seasonal ice-albedo feedback and ocean heat uptake. Results show that using the last retreat date to predict the first advance date is applicable in some regions, such as Baffin Bay and the Laptev and East Siberian seas, where a predictive skill is found even after accounting for the long-term trend in both variables. Elsewhere, in the Arctic, there is some predictive skills depending on the year (e.g., Kara and Beaufort seas), but none in regions such as the Barents and Bering seas or the Sea of Okhotsk. While there is some suggestion that the relationship is strengthening over time, this may reflect that higher correlations are expected during periods when the underlying trend is strong.

  2. Full-field predictions of ice dynamic recrystallisation under simple shear conditions

    NASA Astrophysics Data System (ADS)

    Llorens, Maria-Gema; Griera, Albert; Bons, Paul D.; Lebensohn, Ricardo A.; Evans, Lynn A.; Jansen, Daniela; Weikusat, Ilka

    2016-09-01

    Understanding the flow of ice on the microstructural scale is essential for improving our knowledge of large-scale ice dynamics, and thus our ability to predict future changes of ice sheets. Polar ice behaves anisotropically during flow, which can lead to strain localisation. In order to study how dynamic recrystallisation affects to strain localisation in deep levels of polar ice sheets, we present a series of numerical simulations of ice polycrystals deformed under simple-shear conditions. The models explicitly simulate the evolution of microstructures using a full-field approach, based on the coupling of a viscoplastic deformation code (VPFFT) with dynamic recrystallisation codes. The simulations provide new insights into the distribution of stress, strain rate and lattice orientation fields with progressive strain, up to a shear strain of three. Our simulations show how the recrystallisation processes have a strong influence on the resulting microstructure (grain size and shape), while the development of lattice preferred orientations (LPO) appears to be less affected. Activation of non-basal slip systems is enhanced by recrystallisation and induces a strain hardening behaviour up to the onset of strain localisation and strain weakening behaviour. Simulations demonstrate that the strong intrinsic anisotropy of ice crystals is transferred to the polycrystalline scale and results in the development of strain localisation bands than can be masked by grain boundary migration. Therefore, the finite-strain history is non-directly reflected by the final microstructure. Masked strain localisation can be recognised in ice cores, such as the EDML, from the presence of stepped boundaries, microshear and grains with zig-zag geometries.

  3. Do physical maturity and birth date predict talent in male youth ice hockey players?

    PubMed

    Sherar, Lauren B; Baxter-Jones, Adam D G; Faulkner, Robert A; Russell, Keith W

    2007-06-01

    The aim of this study was to examine the relationships among biological maturity, physical size, relative age (i.e. birth date), and selection into a male Canadian provincial age-banded ice hockey team. In 2003, 619 male ice hockey players aged 14-15 years attended Saskatchewan provincial team selection camps, 281 of whom participated in the present study. Data from 93 age-matched controls were obtained from the Saskatchewan Pediatric Bone Mineral Accrual Study (1991-1997). During the initial selection camps, birth dates, heights, sitting heights, and body masses were recorded. Age at peak height velocity, an indicator of biological maturity, was determined in the controls and predicted in the ice hockey players. Data were analysed using one-way analysis of variance, logistic regression, and a Kolmogorov-Smirnov test. The ice hockey players selected for the final team were taller, heavier, and more mature (P < 0.05) than both the unselected players and the age-matched controls. Furthermore, age at peak height velocity predicted (P < 0.05) being selected at the first and second selection camps. The birth dates of those players selected for the team were positively skewed, with the majority of those selected being born in the months January to June. In conclusion, team selectors appear to preferentially select early maturing male ice hockey players who have birth dates early in the selection year.

  4. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  5. New consensus definition for acute kidney injury accurately predicts 30-day mortality in cirrhosis with infection

    PubMed Central

    Wong, Florence; O’Leary, Jacqueline G; Reddy, K Rajender; Patton, Heather; Kamath, Patrick S; Fallon, Michael B; Garcia-Tsao, Guadalupe; Subramanian, Ram M.; Malik, Raza; Maliakkal, Benedict; Thacker, Leroy R; Bajaj, Jasmohan S

    2015-01-01

    Background & Aims A consensus conference proposed that cirrhosis-associated acute kidney injury (AKI) be defined as an increase in serum creatinine by >50% from the stable baseline value in <6 months or by ≥0.3mg/dL in <48 hrs. We prospectively evaluated the ability of these criteria to predict mortality within 30 days among hospitalized patients with cirrhosis and infection. Methods 337 patients with cirrhosis admitted with or developed an infection in hospital (56% men; 56±10 y old; model for end-stage liver disease score, 20±8) were followed. We compared data on 30-day mortality, hospital length-of-stay, and organ failure between patients with and without AKI. Results 166 (49%) developed AKI during hospitalization, based on the consensus criteria. Patients who developed AKI had higher admission Child-Pugh (11.0±2.1 vs 9.6±2.1; P<.0001), and MELD scores (23±8 vs17±7; P<.0001), and lower mean arterial pressure (81±16mmHg vs 85±15mmHg; P<.01) than those who did not. Also higher amongst patients with AKI were mortality in ≤30 days (34% vs 7%), intensive care unit transfer (46% vs 20%), ventilation requirement (27% vs 6%), and shock (31% vs 8%); AKI patients also had longer hospital stays (17.8±19.8 days vs 13.3±31.8 days) (all P<.001). 56% of AKI episodes were transient, 28% persistent, and 16% resulted in dialysis. Mortality was 80% among those without renal recovery, higher compared to partial (40%) or complete recovery (15%), or AKI-free patients (7%; P<.0001). Conclusions 30-day mortality is 10-fold higher among infected hospitalized cirrhotic patients with irreversible AKI than those without AKI. The consensus definition of AKI accurately predicts 30-day mortality, length of hospital stay, and organ failure. PMID:23999172

  6. Accurate age scale of the Dome Fuji ice core, Antarctica from O2/N2 ratio of trapped air

    NASA Astrophysics Data System (ADS)

    Kawamura, K.; Aoki, S.; Nakazawa, T.; Suzuki, K.; Parrenin, F.

    2012-04-01

    Chronology of the first Dome Fuji deep ice core (core length: 2,500 m, ice thickness: 3,035 m) for the age range from 80 kyr to 340 kyr ago was established by orbital tuning of measured O2/N2 ratios in trapped air to local summer insolation, with precision better than about 2,000 years (Kawamura et al., 2007). The O2/N2 ratios found in polar ice cores are slightly lower than the atmospheric ratio because of size-dependent molecular fractionation during bubble close-off. The magnitude of this gas fractionation is believed to be governed by the magnitude of snow metamorphism when the layer was originally at the surface, which in turn is controlled by local summer insolation (Fujita et al., 2009). A strong advantage of the O2/N2 chronology is that there is no need to assume a lag between climatic records in the ice core and orbital forcings, becacuse O2/N2 ratios record local insolation through physical processes. Accuracy of the chronology was validated by comparing the O2/N2 chronology with U-Th radiometric chronology of speleothem records (Cheng et al., 2009) for the ends of Terminations II, III and IV, as well as several large climatic events, for which both ice-core CH4 and speleothem δ18O (a proxy for precipitation) show abrupt shifts as seen in the last glacial period. All ages from O2/N2 and U-Th chronology agreed with each other within ~2,000 yr. The O2/N2 chronology permits comparisons between Antarctic climate, greenhouse gases, astronomically calculated orbital parameters, and radiometrically-dated sea level and monsoon records. Here, we completed the measurements of O2/N2 ratios of the second Dome Fuji ice core, which reached bedrock, for the range from 2,400 to 3,028 m (320 - 700 kyr ago) at approximately 2,000-year time resolution. We made significant improvements in ice core storage practices and mass spectrometry. In particular, the ice core samples were stored at about -50 ° C until the air extraction, except during short periods of transportation

  7. An Innovative Network to Improve Sea Ice Prediction in a Changing Arctic

    DTIC Science & Technology

    2015-09-30

    Changing Arctic Cecilia M. Bitz Atmospheric Sciences MS351640 University of Washington Seattle, WA 98196-1640 phone: (206) 543-1339 fax...include modeling to place recent sea ice change into system-wide context. We will use models and observations to ask whether “2007–2012 is the New Normal... Climate Predictability Inititiative. Bitz also served on an NRC study group on Subseasonal to Seasonal Prediction, resulting in a report that is

  8. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  9. A high order accurate finite element algorithm for high Reynolds number flow prediction

    NASA Technical Reports Server (NTRS)

    Baker, A. J.

    1978-01-01

    A Galerkin-weighted residuals formulation is employed to establish an implicit finite element solution algorithm for generally nonlinear initial-boundary value problems. Solution accuracy, and convergence rate with discretization refinement, are quantized in several error norms, by a systematic study of numerical solutions to several nonlinear parabolic and a hyperbolic partial differential equation characteristic of the equations governing fluid flows. Solutions are generated using selective linear, quadratic and cubic basis functions. Richardson extrapolation is employed to generate a higher-order accurate solution to facilitate isolation of truncation error in all norms. Extension of the mathematical theory underlying accuracy and convergence concepts for linear elliptic equations is predicted for equations characteristic of laminar and turbulent fluid flows at nonmodest Reynolds number. The nondiagonal initial-value matrix structure introduced by the finite element theory is determined intrinsic to improved solution accuracy and convergence. A factored Jacobian iteration algorithm is derived and evaluated to yield a consequential reduction in both computer storage and execution CPU requirements while retaining solution accuracy.

  10. Cluster abundance in chameleon f(R) gravity I: toward an accurate halo mass function prediction

    NASA Astrophysics Data System (ADS)

    Cataneo, Matteo; Rapetti, David; Lombriser, Lucas; Li, Baojiu

    2016-12-01

    We refine the mass and environment dependent spherical collapse model of chameleon f(R) gravity by calibrating a phenomenological correction inspired by the parameterized post-Friedmann framework against high-resolution N-body simulations. We employ our method to predict the corresponding modified halo mass function, and provide fitting formulas to calculate the enhancement of the f(R) halo abundance with respect to that of General Relativity (GR) within a precision of lesssim 5% from the results obtained in the simulations. Similar accuracy can be achieved for the full f(R) mass function on the condition that the modeling of the reference GR abundance of halos is accurate at the percent level. We use our fits to forecast constraints on the additional scalar degree of freedom of the theory, finding that upper bounds competitive with current Solar System tests are within reach of cluster number count analyses from ongoing and upcoming surveys at much larger scales. Importantly, the flexibility of our method allows also for this to be applied to other scalar-tensor theories characterized by a mass and environment dependent spherical collapse.

  11. Accurate prediction of band gaps and optical properties of HfO2

    NASA Astrophysics Data System (ADS)

    Ondračka, Pavel; Holec, David; Nečas, David; Zajíčková, Lenka

    2016-10-01

    We report on optical properties of various polymorphs of hafnia predicted within the framework of density functional theory. The full potential linearised augmented plane wave method was employed together with the Tran-Blaha modified Becke-Johnson potential (TB-mBJ) for exchange and local density approximation for correlation. Unit cells of monoclinic, cubic and tetragonal crystalline, and a simulated annealing-based model of amorphous hafnia were fully relaxed with respect to internal positions and lattice parameters. Electronic structures and band gaps for monoclinic, cubic, tetragonal and amorphous hafnia were calculated using three different TB-mBJ parametrisations and the results were critically compared with the available experimental and theoretical reports. Conceptual differences between a straightforward comparison of experimental measurements to a calculated band gap on the one hand and to a whole electronic structure (density of electronic states) on the other hand, were pointed out, suggesting the latter should be used whenever possible. Finally, dielectric functions were calculated at two levels, using the random phase approximation without local field effects and with a more accurate Bethe-Salpether equation (BSE) to account for excitonic effects. We conclude that a satisfactory agreement with experimental data for HfO2 was obtained only in the latter case.

  12. Accurate prediction of V1 location from cortical folds in a surface coordinate system

    PubMed Central

    Hinds, Oliver P.; Rajendran, Niranjini; Polimeni, Jonathan R.; Augustinack, Jean C.; Wiggins, Graham; Wald, Lawrence L.; Rosas, H. Diana; Potthast, Andreas; Schwartz, Eric L.; Fischl, Bruce

    2008-01-01

    Previous studies demonstrated substantial variability of the location of primary visual cortex (V1) in stereotaxic coordinates when linear volume-based registration is used to match volumetric image intensities (Amunts et al., 2000). However, other qualitative reports of V1 location (Smith, 1904; Stensaas et al., 1974; Rademacher et al., 1993) suggested a consistent relationship between V1 and the surrounding cortical folds. Here, the relationship between folds and the location of V1 is quantified using surface-based analysis to generate a probabilistic atlas of human V1. High-resolution (about 200 μm) magnetic resonance imaging (MRI) at 7 T of ex vivo human cerebral hemispheres allowed identification of the full area via the stria of Gennari: a myeloarchitectonic feature specific to V1. Separate, whole-brain scans were acquired using MRI at 1.5 T to allow segmentation and mesh reconstruction of the cortical gray matter. For each individual, V1 was manually identified in the high-resolution volume and projected onto the cortical surface. Surface-based intersubject registration (Fischl et al., 1999b) was performed to align the primary cortical folds of individual hemispheres to those of a reference template representing the average folding pattern. An atlas of V1 location was constructed by computing the probability of V1 inclusion for each cortical location in the template space. This probabilistic atlas of V1 exhibits low prediction error compared to previous V1 probabilistic atlases built in volumetric coordinates. The increased predictability observed under surface-based registration suggests that the location of V1 is more accurately predicted by the cortical folds than by the shape of the brain embedded in the volume of the skull. In addition, the high quality of this atlas provides direct evidence that surface-based intersubject registration methods are superior to volume-based methods at superimposing functional areas of cortex, and therefore are better

  13. Predicting Trigger Level for Ice Jam Flooding of the lower Mohawk River using LiDAR and GIS

    NASA Astrophysics Data System (ADS)

    Foster, J.; Marsellos, A.; Garver, J.

    2011-12-01

    Ice jams are an annual occurrence along the Mohawk River in upstate New York. The jams commonly result in significant flooding especially when the progress of the ice is impeded by obstructions to the channel and flood plain. To minimize flooding hazards it is critical to know the trigger level of flooding so that we can better understand chronic jam points and simulate flooding events as jams occur as the lower Mohawk. A better understanding of jamming and trigger points may facilitate measures to reduce flooding and avoid the costly damage associated with these hazards. To determine the flood trigger level for one segment of the lower Mohawk we used Air-LiDAR elevation data to construct a digital elevation model to simulate a flooding event. The water flood simulation using a LiDAR elevation model allows accurate water level measurements for determining trigger levels of ice dam flooding. The study area comprises three sections of the lower Mohawk River from the (Before location) to the (After location), which are constrained by lock stations centered at the New York State Canal System Lock 9 (E9 Lock) and the B&M Rail Bridge at the Schenectady International (SI) Plant. This area is notorious for ice jams including one that resulted in a major flooding event on January 25th, 2010 which resulted in flood levels at 74.4 m in the upper portion of the second section of the study area (Lock 9) and at 73.4 m in the lower portion (SI plant). Minimum and maximum elevation levels were found to determine the values at which up stream water builds up and when flooding occurs. From these values, we are able to predict the flooding as the ice jam builds up and breaks as it progresses downstream. Similar methodology is applied to find the trigger points for flooding along other sections of the Mohawk River constrained by lock stations, and it may provide critical knowledge as to how to better manage the hazard of flooding due to ice jams.

  14. Effects of solution composition on the theoretical prediction of ice nucleation kinetics and thermodynamics.

    PubMed

    Karlsson, Jens O M

    2010-02-01

    Predictions by various mathematical models of intracellular ice formation (proposed by Mazur, Pitt, Toner, and Karlsson, respectively) were compared to the known thermodynamic and kinetic behavior of ice formation in supercooled aqueous systems. The older models (Mazur, Pitt, and Toner) significantly underestimated the magnitude of colligative nonequilibrium freezing point depression in response to increased concentration of solutes, such as salts or cryoprotectants. Furthermore, kinetics predicted using phenomenological models (by Mazur and Pitt) exhibited implausible temperature-dependence, with the probability of intracellular ice formation being allowed to increase even at temperatures below the glass transition point. The Toner model, on the other hand, produced invalid results at temperatures below -48 degrees C. The Karlsson model was the only model that consistently yielded realistic predictions over a wide range of temperatures and solute concentrations, especially in the presence of cryoprotectant additives. To facilitate adoption of the Karlsson model of intracellular ice nucleation, the complete set of model equations has been collected and described in detail.

  15. Using Reanalysis Data for the Prediction of Seasonal Wind Turbine Power Losses Due to Icing

    NASA Astrophysics Data System (ADS)

    Burtch, D.; Mullendore, G. L.; Delene, D. J.; Storm, B.

    2013-12-01

    The Northern Plains region of the United States is home to a significant amount of potential wind energy. However, in winter months capturing this potential power is severely impacted by the meteorological conditions, in the form of icing. Predicting the expected loss in power production due to icing is a valuable parameter that can be used in wind turbine operations, determination of wind turbine site locations and long-term energy estimates which are used for financing purposes. Currently, losses due to icing must be estimated when developing predictions for turbine feasibility and financing studies, while icing maps, a tool commonly used in Europe, are lacking in the United States. This study uses the Modern-Era Retrospective Analysis for Research and Applications (MERRA) dataset in conjunction with turbine production data to investigate various methods of predicting seasonal losses (October-March) due to icing at two wind turbine sites located 121 km apart in North Dakota. The prediction of icing losses is based on temperature and relative humidity thresholds and is accomplished using three methods. For each of the three methods, the required atmospheric variables are determined in one of two ways: using industry-specific software to correlate anemometer data in conjunction with the MERRA dataset and using only the MERRA dataset for all variables. For each season, a percentage of the total expected generated power lost due to icing is determined and compared to observed losses from the production data. An optimization is performed in order to determine the relative humidity threshold that minimizes the difference between the predicted and observed values. Eight seasons of data are used to determine an optimal relative humidity threshold, and a further three seasons of data are used to test this threshold. Preliminary results have shown that the optimized relative humidity threshold for the northern turbine is higher than the southern turbine for all methods

  16. Raoult’s law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments

    PubMed Central

    Bowler, Michael G.

    2017-01-01

    The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111–114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult’s law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult’s law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult’s law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample. PMID:28381983

  17. Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments.

    PubMed

    Bowler, Michael G; Bowler, David R; Bowler, Matthew W

    2017-04-01

    The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.

  18. Reward sensitivity predicts ice cream-related attentional bias assessed by inattentional blindness.

    PubMed

    Li, Xiaoming; Tao, Qian; Fang, Ya; Cheng, Chen; Hao, Yangyang; Qi, Jianjun; Li, Yu; Zhang, Wei; Wang, Ying; Zhang, Xiaochu

    2015-06-01

    The cognitive mechanism underlying the association between individual differences in reward sensitivity and food craving is unknown. The present study explored the mechanism by examining the role of reward sensitivity in attentional bias toward ice cream cues. Forty-nine college students who displayed high level of ice cream craving (HICs) and 46 who displayed low level of ice cream craving (LICs) performed an inattentional blindness (IB) task which was used to assess attentional bias for ice cream. In addition, reward sensitivity and coping style were assessed by the Behavior Inhibition System/Behavior Activation System Scales and Simplified Coping Style Questionnaire. Results showed significant higher identification rate of the critical stimulus in the HICs than LICs, suggesting greater attentional bias for ice cream in the HICs. It was indicated that attentional bias for food cues persisted even under inattentional condition. Furthermore, a significant correlation was found between the attentional bias and reward sensitivity after controlling for coping style, and reward sensitivity predicted attentional bias for food cues. The mediation analyses showed that attentional bias mediated the relationship between reward sensitivity and food craving. Those findings suggest that the association between individual differences in reward sensitivity and food craving may be attributed to attentional bias for food-related cues.

  19. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

    PubMed Central

    Garcia Lopez, Sebastian; Kim, Philip M.

    2014-01-01

    Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

  20. Development of statistical seasonal prediction models of Arctic Sea Ice concentration using CERES absorbed solar radiation

    NASA Astrophysics Data System (ADS)

    Kim, Yoojin; Kim, Ha-Rim; Choi, Yong-Sang; Kim, WonMoo; Kim, Hye-Sil

    2016-11-01

    Statistical seasonal prediction models for the Arctic sea ice concentration (SIC) were developed for the late summer (August-October) when the downward trend is dramatic. The absorbed solar radiation (ASR) at the top of the atmosphere in June has a significant seasonal leading role on the SIC. Based on the lagged ASR-SIC relationship, two simple statistical models were established: the Markovian stochastic and the linear regression models. Crossvalidated hindcasts of SIC from 1979 to 2014 by the two models were compared with each other and observation. The hindcasts showed general agreement between the models as they share a common predictor, ASR in June and the observed SIC was well reproduced, especially over the relatively thin-ice regions (of one- or multi-year sea ice). The robust predictability confirms the functional role of ASR in the prediction of SIC. In particular, the SIC prediction in October was quite promising probably due to the pronounced icealbedo feedback. The temporal correlation coefficients between the predicted SIC and the observed SIC were 0.79 and 0.82 by the Markovian and regression models, respectively. Small differences were observed between the two models; the regression model performed slightly better in August and September in terms of temporal correlation coefficients. Meanwhile, the prediction skills of the Markovian model in October were higher in the north of Chukchi, the East Siberian, and the Laptev Seas. A strong non-linear relationship between ASR in June and SIC in October in these areas would have increased the predictability of the Markovian model.

  1. Prediction of a new ice clathrate with record low density: A potential candidate as ice XIX in guest-free form

    NASA Astrophysics Data System (ADS)

    Huang, Yingying; Zhu, Chongqin; Wang, Lu; Zhao, Jijun; Zeng, Xiao Cheng

    2017-03-01

    Using extensive Monte Carlo packing algorithm and dispersion-corrected density functional theory optimization, we predict a new cubic crystalline phase of ice clathrate, named as s-IV, which is composed of eight large icosihexahedral cavities (12464418), eight intermediate dodecahedral cavities (6646), and sixteen small octahedral cavities (6246) per unit cell. Based on DFT calculations, we find that the s-IV ice clathrate with an extremely low mass density of 0.506 g/cm3. In the P-T phase diagram of water described by the TIP4P/2005 water model, the s-IV ice clathrate becomes a more stable ice polymorph in the negative-pressure region, e.g., below -3830 bar at 0 K, below -4882 bar at 115 K, and below -7292 bar at 200 K.

  2. Predictions of the onset of mini ice age in the 25th solar cycle

    NASA Astrophysics Data System (ADS)

    Kumar, Rajiv

    2016-07-01

    Predictions of the ir-regularty in the 11 year heartbeat of the sun due to asyncronous of the two layered dynamo effect would result in mini ice age as in the Maunder minimum.The onset of this event is expected in the begining of 25th solar cycle and would go to its maximum in the 26th solar cycle.The minimum temperature is expected in 2028 due to the fall of solar activity by 60 % termed as solar hibernation.The predictions are based on the observations obtained by the Royal Greenwich observatory since 1874. Keywords: Dynamo effect,munder minimum,Solar hybernation

  3. Towards more accurate wind and solar power prediction by improving NWP model physics

    NASA Astrophysics Data System (ADS)

    Steiner, Andrea; Köhler, Carmen; von Schumann, Jonas; Ritter, Bodo

    2014-05-01

    The growing importance and successive expansion of renewable energies raise new challenges for decision makers, economists, transmission system operators, scientists and many more. In this interdisciplinary field, the role of Numerical Weather Prediction (NWP) is to reduce the errors and provide an a priori estimate of remaining uncertainties associated with the large share of weather-dependent power sources. For this purpose it is essential to optimize NWP model forecasts with respect to those prognostic variables which are relevant for wind and solar power plants. An improved weather forecast serves as the basis for a sophisticated power forecasts. Consequently, a well-timed energy trading on the stock market, and electrical grid stability can be maintained. The German Weather Service (DWD) currently is involved with two projects concerning research in the field of renewable energy, namely ORKA*) and EWeLiNE**). Whereas the latter is in collaboration with the Fraunhofer Institute (IWES), the project ORKA is led by energy & meteo systems (emsys). Both cooperate with German transmission system operators. The goal of the projects is to improve wind and photovoltaic (PV) power forecasts by combining optimized NWP and enhanced power forecast models. In this context, the German Weather Service aims to improve its model system, including the ensemble forecasting system, by working on data assimilation, model physics and statistical post processing. This presentation is focused on the identification of critical weather situations and the associated errors in the German regional NWP model COSMO-DE. First steps leading to improved physical parameterization schemes within the NWP-model are presented. Wind mast measurements reaching up to 200 m height above ground are used for the estimation of the (NWP) wind forecast error at heights relevant for wind energy plants. One particular problem is the daily cycle in wind speed. The transition from stable stratification during

  4. Quantum Chemical Study of the Reaction of C+ with Interstellar Ice: Predictions of Vibrational and Electronic Spectra of Reaction Products

    NASA Astrophysics Data System (ADS)

    Woon, David E.

    2015-06-01

    The C+ cation (CII) is the dominant form of carbon in diffuse clouds and an important tracer for star formation in molecular clouds. We studied the low energy deposition of C+ on ice using density functional theory calculations on water clusters as large as 18 H2O. Barrierless reactions occur with water to form two dominant sets of products: HOC + H3O+ and CO- + 2H3O+. In order to provide testable predictions, we have computed both vibrational and electronic spectra for pure ice and processed ice clusters. While vibrational spectroscopy is expected to be able to discern that C+ has reacted with ice by the addition of H3O+ features not present in pure ice, it does not provided characteristic bands that would discern between HOC and CO-. On the other hand, predictions of electronic spectra suggest that low energy absorptions may occur for CO- and not HOC, making it possible to distinguish one product from the other.

  5. A machine learning approach to the accurate prediction of multi-leaf collimator positional errors

    NASA Astrophysics Data System (ADS)

    Carlson, Joel N. K.; Park, Jong Min; Park, So-Yeon; In Park, Jong; Choi, Yunseok; Ye, Sung-Joon

    2016-03-01

    Discrepancies between planned and delivered movements of multi-leaf collimators (MLCs) are an important source of errors in dose distributions during radiotherapy. In this work we used machine learning techniques to train models to predict these discrepancies, assessed the accuracy of the model predictions, and examined the impact these errors have on quality assurance (QA) procedures and dosimetry. Predictive leaf motion parameters for the models were calculated from the plan files, such as leaf position and velocity, whether the leaf was moving towards or away from the isocenter of the MLC, and many others. Differences in positions between synchronized DICOM-RT planning files and DynaLog files reported during QA delivery were used as a target response for training of the models. The final model is capable of predicting MLC positions during delivery to a high degree of accuracy. For moving MLC leaves, predicted positions were shown to be significantly closer to delivered positions than were planned positions. By incorporating predicted positions into dose calculations in the TPS, increases were shown in gamma passing rates against measured dose distributions recorded during QA delivery. For instance, head and neck plans with 1%/2 mm gamma criteria had an average increase in passing rate of 4.17% (SD  =  1.54%). This indicates that the inclusion of predictions during dose calculation leads to a more realistic representation of plan delivery. To assess impact on the patient, dose volumetric histograms (DVH) using delivered positions were calculated for comparison with planned and predicted DVHs. In all cases, predicted dose volumetric parameters were in closer agreement to the delivered parameters than were the planned parameters, particularly for organs at risk on the periphery of the treatment area. By incorporating the predicted positions into the TPS, the treatment planner is given a more realistic view of the dose distribution as it will truly be

  6. An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes.

    PubMed

    Wang, Jia-Nan; Jin, Jun-Ling; Geng, Yun; Sun, Shi-Ling; Xu, Hong-Liang; Lu, Ying-Hua; Su, Zhong-Min

    2013-03-15

    Recently, the extreme learning machine neural network (ELMNN) as a valid computing method has been proposed to predict the nonlinear optical property successfully (Wang et al., J. Comput. Chem. 2012, 33, 231). In this work, first, we follow this line of work to predict the electronic excitation energies using the ELMNN method. Significantly, the root mean square deviation of the predicted electronic excitation energies of 90 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivatives between the predicted and experimental values has been reduced to 0.13 eV. Second, four groups of molecule descriptors are considered when building the computing models. The results show that the quantum chemical descriptions have the closest intrinsic relation with the electronic excitation energy values. Finally, a user-friendly web server (EEEBPre: Prediction of electronic excitation energies for BODIPY dyes), which is freely accessible to public at the web site: http://202.198.129.218, has been built for prediction. This web server can return the predicted electronic excitation energy values of BODIPY dyes that are high consistent with the experimental values. We hope that this web server would be helpful to theoretical and experimental chemists in related research.

  7. A model predicting the evolution of ice particle size spectra and radiative properties of cirrus clouds. Part 2: Dependence of absorption and extinction on ice crystal morphology

    NASA Technical Reports Server (NTRS)

    Mitchell, David L.; Arnott, W. Patrick

    1994-01-01

    This study builds upon the microphysical modeling described in Part 1 by deriving formulations for the extinction and absorption coefficients in terms of the size distribution parameters predicted from the micro-physical model. The optical depth and single scatter albedo of a cirrus cloud can then be determined, which, along with the asymmetry parameter, are the input parameters needed by cloud radiation models. Through the use of anomalous diffraction theory, analytical expressions were developed describing the absorption and extinction coefficients and the single scatter albedo as functions of size distribution parameters, ice crystal shapes (or habits), wavelength, and refractive index. The extinction coefficient was formulated in terms of the projected area of the size distribution, while the absorption coefficient was formulated in terms of both the projected area and mass of the size distribution. These properties were formulated as explicit functions of ice crystal geometry and were not based on an 'effective radius.' Based on simulations of the second cirrus case study described in Part 1, absorption coefficients predicted in the near infrared for hexagonal columns and rosettes were up to 47% and 71% lower, respectively, than absorption coefficients predicted by using equivalent area spheres. This resulted in single scatter albedos in the near-infrared that were considerably greater than those predicted by the equivalent area sphere method. Reflectances in this region should therefore be underestimated using the equivalent area sphere approach. Cloud optical depth was found to depend on ice crystal habit. When the simulated cirrus cloud contained only bullet rosettes, the optical depth was 142% greater than when the cloud contained only hexagonal columns. This increase produced a doubling in cloud albedo. In the near-infrared (IR), the single scatter albedo also exhibited a significant dependence on ice crystal habit. More research is needed on the

  8. Sensor data fusion for accurate cloud presence prediction using Dempster-Shafer evidence theory.

    PubMed

    Li, Jiaming; Luo, Suhuai; Jin, Jesse S

    2010-01-01

    Sensor data fusion technology can be used to best extract useful information from multiple sensor observations. It has been widely applied in various applications such as target tracking, surveillance, robot navigation, signal and image processing. This paper introduces a novel data fusion approach in a multiple radiation sensor environment using Dempster-Shafer evidence theory. The methodology is used to predict cloud presence based on the inputs of radiation sensors. Different radiation data have been used for the cloud prediction. The potential application areas of the algorithm include renewable power for virtual power station where the prediction of cloud presence is the most challenging issue for its photovoltaic output. The algorithm is validated by comparing the predicted cloud presence with the corresponding sunshine occurrence data that were recorded as the benchmark. Our experiments have indicated that comparing to the approaches using individual sensors, the proposed data fusion approach can increase correct rate of cloud prediction by ten percent, and decrease unknown rate of cloud prediction by twenty three percent.

  9. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

    PubMed

    Wallace, Jason A; Wang, Yuhang; Shi, Chuanyin; Pastoor, Kevin J; Nguyen, Bao-Linh; Xia, Kai; Shen, Jana K

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy.

  10. NESmapper: accurate prediction of leucine-rich nuclear export signals using activity-based profiles.

    PubMed

    Kosugi, Shunichi; Yanagawa, Hiroshi; Terauchi, Ryohei; Tabata, Satoshi

    2014-09-01

    The nuclear export of proteins is regulated largely through the exportin/CRM1 pathway, which involves the specific recognition of leucine-rich nuclear export signals (NESs) in the cargo proteins, and modulates nuclear-cytoplasmic protein shuttling by antagonizing the nuclear import activity mediated by importins and the nuclear import signal (NLS). Although the prediction of NESs can help to define proteins that undergo regulated nuclear export, current methods of predicting NESs, including computational tools and consensus-sequence-based searches, have limited accuracy, especially in terms of their specificity. We found that each residue within an NES largely contributes independently and additively to the entire nuclear export activity. We created activity-based profiles of all classes of NESs with a comprehensive mutational analysis in mammalian cells. The profiles highlight a number of specific activity-affecting residues not only at the conserved hydrophobic positions but also in the linker and flanking regions. We then developed a computational tool, NESmapper, to predict NESs by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. This tool successfully reduced the considerable number of false positives, and the overall prediction accuracy was higher than that of other methods, including NESsential and Wregex. This profile-based prediction strategy is a reliable way to identify functional protein motifs. NESmapper is available at http://sourceforge.net/projects/nesmapper.

  11. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

    PubMed Central

    Kim, Minseung; Rai, Navneet; Zorraquino, Violeta; Tagkopoulos, Ilias

    2016-01-01

    A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information. We then use this resource to train a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics. The genetic and environmental ontology reconstructed from the omics data is substantially different and complementary to the genetic and chemical ontologies. The integration of different layers confers an incremental increase in the prediction performance, as does the information about the known gene regulatory and protein-protein interactions. The predictive performance of the model ranges from 0.54 to 0.87 for the various omics layers, which far exceeds various baselines. This work provides an integrative framework of omics-driven predictive modelling that is broadly applicable to guide biological discovery. PMID:27713404

  12. ICE-COLA: towards fast and accurate synthetic galaxy catalogues optimizing a quasi-N-body method

    NASA Astrophysics Data System (ADS)

    Izard, Albert; Crocce, Martin; Fosalba, Pablo

    2016-07-01

    Next generation galaxy surveys demand the development of massive ensembles of galaxy mocks to model the observables and their covariances, what is computationally prohibitive using N-body simulations. COmoving Lagrangian Acceleration (COLA) is a novel method designed to make this feasible by following an approximate dynamics but with up to three orders of magnitude speed-ups when compared to an exact N-body. In this paper, we investigate the optimization of the code parameters in the compromise between computational cost and recovered accuracy in observables such as two-point clustering and halo abundance. We benchmark those observables with a state-of-the-art N-body run, the MICE Grand Challenge simulation. We find that using 40 time-steps linearly spaced since zi ˜ 20, and a force mesh resolution three times finer than that of the number of particles, yields a matter power spectrum within 1 per cent for k ≲ 1 h Mpc-1 and a halo mass function within 5 per cent of those in the N-body. In turn, the halo bias is accurate within 2 per cent for k ≲ 0.7 h Mpc-1 whereas, in redshift space, the halo monopole and quadrupole are within 4 per cent for k ≲ 0.4 h Mpc-1. These results hold for a broad range in redshift (0 < z < 1) and for all halo mass bins investigated (M > 1012.5 h-1 M⊙). To bring accuracy in clustering to one per cent level we study various methods that re-calibrate halo masses and/or velocities. We thus propose an optimized choice of COLA code parameters as a powerful tool to optimally exploit future galaxy surveys.

  13. Empirical approaches to more accurately predict benthic-pelagic coupling in biogeochemical ocean models

    NASA Astrophysics Data System (ADS)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

    The recycling and burial of biogenic material in the sea floor plays a key role in the regulation of ocean chemistry. Proper consideration of these processes in ocean biogeochemical models is becoming increasingly recognized as an important step in model validation and prediction. However, the rate of organic matter remineralization in sediments and the benthic flux of redox-sensitive elements are difficult to predict a priori. In this communication, examples of empirical benthic flux models that can be coupled to earth system models to predict sediment-water exchange in the open ocean are presented. Large uncertainties hindering further progress in this field include knowledge of the reactivity of organic carbon reaching the sediment, the importance of episodic variability in bottom water chemistry and particle rain rates (for both the deep-sea and margins) and the role of benthic fauna. How do we meet the challenge?

  14. An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF

    PubMed Central

    Koot, Yvonne E. M.; van Hooff, Sander R.; Boomsma, Carolien M.; van Leenen, Dik; Groot Koerkamp, Marian J. A.; Goddijn, Mariëtte; Eijkemans, Marinus J. C.; Fauser, Bart C. J. M.; Holstege, Frank C. P.; Macklon, Nick S.

    2016-01-01

    The primary limiting factor for effective IVF treatment is successful embryo implantation. Recurrent implantation failure (RIF) is a condition whereby couples fail to achieve pregnancy despite consecutive embryo transfers. Here we describe the collection of gene expression profiles from mid-luteal phase endometrial biopsies (n = 115) from women experiencing RIF and healthy controls. Using a signature discovery set (n = 81) we identify a signature containing 303 genes predictive of RIF. Independent validation in 34 samples shows that the gene signature predicts RIF with 100% positive predictive value (PPV). The strength of the RIF associated expression signature also stratifies RIF patients into distinct groups with different subsequent implantation success rates. Exploration of the expression changes suggests that RIF is primarily associated with reduced cellular proliferation. The gene signature will be of value in counselling and guiding further treatment of women who fail to conceive upon IVF and suggests new avenues for developing intervention. PMID:26797113

  15. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  16. Dynamics of Flexible MLI-type Debris for Accurate Orbit Prediction

    DTIC Science & Technology

    2014-09-01

    SUBJECT TERMS EOARD, orbital debris , HAMR objects, multi-layered insulation, orbital dynamics, orbit predictions, orbital propagation 16. SECURITY...illustration are orbital debris [Souce: NASA...piece of space junk (a paint fleck) during the STS-7 mission (Photo: NASA Orbital Debris Program Office

  17. Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately predicting Alzheimer's disease progression.

    PubMed

    Stempler, Shiri; Waldman, Yedael Y; Wolf, Lior; Ruppin, Eytan

    2012-09-01

    Numerous metabolic alterations are associated with the impairment of brain cells in Alzheimer's disease (AD). Here we use gene expression microarrays of both whole hippocampus tissue and hippocampal neurons of AD patients to investigate the ability of metabolic gene expression to predict AD progression and its cognitive decline. We find that the prediction accuracy of different AD stages is markedly higher when using neuronal expression data (0.9) than when using whole tissue expression (0.76). Furthermore, the metabolic genes' expression is shown to be as effective in predicting AD severity as the entire gene list. Remarkably, a regression model from hippocampal metabolic gene expression leads to a marked correlation of 0.57 with the Mini-Mental State Examination cognitive score. Notably, the expression of top predictive neuronal genes in AD is significantly higher than that of other metabolic genes in the brains of healthy subjects. All together, the analyses point to a subset of metabolic genes that is strongly associated with normal brain functioning and whose disruption plays a major role in AD.

  18. Predicting repeat self-harm in children--how accurate can we expect to be?

    PubMed

    Chitsabesan, Prathiba; Harrington, Richard; Harrington, Valerie; Tomenson, Barbara

    2003-01-01

    The main objective of the study was to find which variables predict repetition of deliberate self-harm in children. The study is based on a group of children who took part in a randomized control trial investigating the effects of a home-based family intervention for children who had deliberately poisoned themselves. These children had a range of baseline and outcome measures collected on two occasions (two and six months follow-up). Outcome data were collected from 149 (92 %) of the initial 162 children over the six months. Twenty-three children made a further deliberate self-harm attempt within the follow-up period. A number of variables at baseline were found to be significantly associated with repeat self-harm. Parental mental health and a history of previous attempts were the strongest predictors. A model of prediction of further deliberate self-harm combining these significant individual variables produced a high positive predictive value (86 %) but had low sensitivity (28 %). Predicting repeat self-harm in children is difficult, even with a comprehensive series of assessments over multiple time points, and we need to adapt services with this in mind. We propose a model of service provision which takes these findings into account.

  19. A Regional Model for Seasonal Sea Ice Prediction in the Pacific Sector of the Arctic

    NASA Astrophysics Data System (ADS)

    Yuan, X.; Li, Y.; Chen, D.; Zhang, Q.; Li, C.; Niu, F.; Sun, Y.

    2015-12-01

    The recent results from a linear Markov model for seasonal prediction of pan-Arctic sea ice concentration (SIC) show that sea ice in the Pacific sector has the lowest predictability compared to other regions. One reason could be that the climate variability in the Atlantic sector is so dominant that other signals in the Arctic climate system do not appear in the leading modes used for model construction. This study develops a regional Markov model to improve seasonal forecasting of SIC in the Pacific sector. The model climate system consists of various combinations of the monthly mean series of SIC, sea surface temperature (SST), surface air temperature (SAT), pressure/geopotential height fields and winds at pressure levels. Multivariate empirical orthogonal functions (MEOF) and rotated MEOF are applied to each set of data to reduce the model dimensions. After a series of experiments, the final model configuration selects 23 rotated MEOF modes from a data matrix of three variables (SIC, SST and SAT). This regional model shows considerable improvement in the prediction skill in the Pacific sector in all seasons. The anomaly correlation skill increases by 0.2 at 1- to 4-month leads in the Bering Sea, and by 0.1 at 1- to 10-month leads in the Sea of Okhotsk. In general, the model performs better in summer and fall than in winter and spring. On average, the correlation skill can reach 0.6 at a 2-month (4-month) lead in the Bering Sea (the Sea of Okhotsk).

  20. Accurate prediction of the optical rotation and NMR properties for highly flexible chiral natural products.

    PubMed

    Hashmi, Muhammad Ali; Andreassend, Sarah K; Keyzers, Robert A; Lein, Matthias

    2016-09-21

    Despite advances in electronic structure theory the theoretical prediction of spectroscopic properties remains a computational challenge. This is especially true for natural products that exhibit very large conformational freedom and hence need to be sampled over many different accessible conformations. We report a strategy, which is able to predict NMR chemical shifts and more elusive properties like the optical rotation with great precision, through step-wise incremental increases of the conformational degrees of freedom. The application of this method is demonstrated for 3-epi-xestoaminol C, a chiral natural compound with a long, linear alkyl chain of 14 carbon atoms. Experimental NMR and [α]D values are reported to validate the results of the density functional theory calculations.

  1. FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues.

    PubMed

    El-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant

    2016-01-01

    A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein

  2. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data.

    PubMed

    Pagán, Josué; De Orbe, M Irene; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L; Mora, J Vivancos; Moya, José M; Ayala, José L

    2015-06-30

    Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives.

  3. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  4. Fast and accurate numerical method for predicting gas chromatography retention time.

    PubMed

    Claumann, Carlos Alberto; Wüst Zibetti, André; Bolzan, Ariovaldo; Machado, Ricardo A F; Pinto, Leonel Teixeira

    2015-08-07

    Predictive modeling for gas chromatography compound retention depends on the retention factor (ki) and on the flow of the mobile phase. Thus, different approaches for determining an analyte ki in column chromatography have been developed. The main one is based on the thermodynamic properties of the component and on the characteristics of the stationary phase. These models can be used to estimate the parameters and to optimize the programming of temperatures, in gas chromatography, for the separation of compounds. Different authors have proposed the use of numerical methods for solving these models, but these methods demand greater computational time. Hence, a new method for solving the predictive modeling of analyte retention time is presented. This algorithm is an alternative to traditional methods because it transforms its attainments into root determination problems within defined intervals. The proposed approach allows for tr calculation, with accuracy determined by the user of the methods, and significant reductions in computational time; it can also be used to evaluate the performance of other prediction methods.

  5. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  6. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data

    PubMed Central

    Pagán, Josué; Irene De Orbe, M.; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L.; Vivancos Mora, J.; Moya, José M.; Ayala, José L.

    2015-01-01

    Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives. PMID:26134103

  7. Accurate prediction of drug-induced liver injury using stem cell-derived populations.

    PubMed

    Szkolnicka, Dagmara; Farnworth, Sarah L; Lucendo-Villarin, Baltasar; Storck, Christopher; Zhou, Wenli; Iredale, John P; Flint, Oliver; Hay, David C

    2014-02-01

    Despite major progress in the knowledge and management of human liver injury, there are millions of people suffering from chronic liver disease. Currently, the only cure for end-stage liver disease is orthotopic liver transplantation; however, this approach is severely limited by organ donation. Alternative approaches to restoring liver function have therefore been pursued, including the use of somatic and stem cell populations. Although such approaches are essential in developing scalable treatments, there is also an imperative to develop predictive human systems that more effectively study and/or prevent the onset of liver disease and decompensated organ function. We used a renewable human stem cell resource, from defined genetic backgrounds, and drove them through developmental intermediates to yield highly active, drug-inducible, and predictive human hepatocyte populations. Most importantly, stem cell-derived hepatocytes displayed equivalence to primary adult hepatocytes, following incubation with known hepatotoxins. In summary, we have developed a serum-free, scalable, and shippable cell-based model that faithfully predicts the potential for human liver injury. Such a resource has direct application in human modeling and, in the future, could play an important role in developing renewable cell-based therapies.

  8. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    NASA Astrophysics Data System (ADS)

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-02-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally--a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process.

  9. Can tritiated water-dilution space accurately predict total body water in chukar partridges

    SciTech Connect

    Crum, B.G.; Williams, J.B.; Nagy, K.A.

    1985-11-01

    Total body water (TBW) volumes determined from the dilution space of injected tritiated water have consistently overestimated actual water volumes (determined by desiccation to constant mass) in reptiles and mammals, but results for birds are controversial. We investigated potential errors in both the dilution method and the desiccation method in an attempt to resolve this controversy. Tritiated water dilution yielded an accurate measurement of water mass in vitro. However, in vivo, this method yielded a 4.6% overestimate of the amount of water (3.1% of live body mass) in chukar partridges, apparently largely because of loss of tritium from body water to sites of dissociable hydrogens on body solids. An additional source of overestimation (approximately 2% of body mass) was loss of tritium to the solids in blood samples during distillation of blood to obtain pure water for tritium analysis. Measuring tritium activity in plasma samples avoided this problem but required measurement of, and correction for, the dry matter content in plasma. Desiccation to constant mass by lyophilization or oven-drying also overestimated the amount of water actually in the bodies of chukar partridges by 1.4% of body mass, because these values included water adsorbed onto the outside of feathers. When desiccating defeathered carcasses, oven-drying at 70 degrees C yielded TBW values identical to those obtained from lyophilization, but TBW was overestimated (0.5% of body mass) by drying at 100 degrees C due to loss of organic substances as well as water.

  10. Does preoperative cross-sectional imaging accurately predict main duct involvement in intraductal papillary mucinous neoplasm?

    PubMed

    Barron, M R; Roch, A M; Waters, J A; Parikh, J A; DeWitt, J M; Al-Haddad, M A; Ceppa, E P; House, M G; Zyromski, N J; Nakeeb, A; Pitt, H A; Schmidt, C Max

    2014-03-01

    Main pancreatic duct (MPD) involvement is a well-demonstrated risk factor for malignancy in intraductal papillary mucinous neoplasm (IPMN). Preoperative radiographic determination of IPMN type is heavily relied upon in oncologic risk stratification. We hypothesized that radiographic assessment of MPD involvement in IPMN is an accurate predictor of pathological MPD involvement. Data regarding all patients undergoing resection for IPMN at a single academic institution between 1992 and 2012 were gathered prospectively. Retrospective analysis of imaging and pathologic data was undertaken. Preoperative classification of IPMN type was based on cross-sectional imaging (MRI/magnetic resonance cholangiopancreatography (MRCP) and/or CT). Three hundred sixty-two patients underwent resection for IPMN. Of these, 334 had complete data for analysis. Of 164 suspected branch duct (BD) IPMN, 34 (20.7%) demonstrated MPD involvement on final pathology. Of 170 patients with suspicion of MPD involvement, 50 (29.4%) demonstrated no MPD involvement. Of 34 patients with suspected BD-IPMN who were found to have MPD involvement on pathology, 10 (29.4%) had invasive carcinoma. Alternatively, 2/50 (4%) of the patients with suspected MPD involvement who ultimately had isolated BD-IPMN demonstrated invasive carcinoma. Preoperative radiographic IPMN type did not correlate with final pathology in 25% of the patients. In addition, risk of invasive carcinoma correlates with pathologic presence of MPD involvement.

  11. DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach

    PubMed Central

    Wang, Zhiheng; Yang, Qianqian; Li, Tonghua; Cong, Peisheng

    2015-01-01

    The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. Availability The DisoMCS is available at http://cal.tongji.edu.cn/disorder/. PMID:26090958

  12. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    SciTech Connect

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-28

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  13. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    NASA Astrophysics Data System (ADS)

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-01

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  14. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    PubMed

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

  15. Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

    PubMed

    Bakhtiarizadeh, Mohammad Reza; Moradi-Shahrbabak, Mohammad; Ebrahimi, Mansour; Ebrahimie, Esmaeil

    2014-09-07

    Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity. To identify LBPs from non-LBPs, the performances of support vector machine (SVM) and neural network were compared in this study. Comprehensive protein features and various techniques were employed to create datasets. Five-fold cross-validation (CV) and independent evaluation (IE) tests were used to assess the validity of the two methods. The results indicated that SVM outperforms neural network. SVM achieved 89.28% (CV) and 89.55% (IE) overall accuracy in identification of LBPs from non-LBPs and 92.06% (CV) and 92.90% (IE) (in average) for classification of different LBPs classes. Increasing the number and the range of extracted protein features as well as optimization of the SVM parameters significantly increased the efficiency of LBPs class prediction in comparison to the only previous report in this field. Altogether, the results showed that the SVM algorithm can be run on broad, computationally calculated protein features and offers a promising tool in detection of LBPs classes. The proposed approach has the potential to integrate and improve the common sequence alignment based methods.

  16. Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e

    PubMed Central

    Cilia, Elisa; Vuister, Geerten W.; Lenaerts, Tom

    2012-01-01

    Experimental NMR relaxation studies have shown that peptide binding induces dynamical changes at the side-chain level throughout the second PDZ domain of PTP1e, identifying as such the collection of residues involved in long-range communication. Even though different computational approaches have identified subsets of residues that were qualitatively comparable, no quantitative analysis of the accuracy of these predictions was thus far determined. Here, we show that our information theoretical method produces quantitatively better results with respect to the experimental data than some of these earlier methods. Moreover, it provides a global network perspective on the effect experienced by the different residues involved in the process. We also show that these predictions are consistent within both the human and mouse variants of this domain. Together, these results improve the understanding of intra-protein communication and allostery in PDZ domains, underlining at the same time the necessity of producing similar data sets for further validation of thses kinds of methods. PMID:23209399

  17. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    SciTech Connect

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

  18. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  19. How Accurate Is the Prediction of Maximal Oxygen Uptake with Treadmill Testing?

    PubMed Central

    Wicks, John R.; Oldridge, Neil B.

    2016-01-01

    Background Cardiorespiratory fitness measured by treadmill testing has prognostic significance in determining mortality with cardiovascular and other chronic disease states. The accuracy of a recently developed method for estimating maximal oxygen uptake (VO2peak), the heart rate index (HRI), is dependent only on heart rate (HR) and was tested against oxygen uptake (VO2), either measured or predicted from conventional treadmill parameters (speed, incline, protocol time). Methods The HRI equation, METs = 6 x HRI– 5, where HRI = maximal HR/resting HR, provides a surrogate measure of VO2peak. Forty large scale treadmill studies were identified through a systematic search using MEDLINE, Google Scholar and Web of Science in which VO2peak was either measured (TM-VO2meas; n = 20) or predicted (TM-VO2pred; n = 20) based on treadmill parameters. All studies were required to have reported group mean data of both resting and maximal HRs for determination of HR index-derived oxygen uptake (HRI-VO2). Results The 20 studies with measured VO2 (TM-VO2meas), involved 11,477 participants (median 337) with a total of 105,044 participants (median 3,736) in the 20 studies with predicted VO2 (TM-VO2pred). A difference of only 0.4% was seen between mean (±SD) VO2peak for TM- VO2meas and HRI-VO2 (6.51±2.25 METs and 6.54±2.28, respectively; p = 0.84). In contrast, there was a highly significant 21.1% difference between mean (±SD) TM-VO2pred and HRI-VO2 (8.12±1.85 METs and 6.71±1.92, respectively; p<0.001). Conclusion Although mean TM-VO2meas and HRI-VO2 were almost identical, mean TM-VO2pred was more than 20% greater than mean HRI-VO2. PMID:27875547

  20. A Foundation for the Accurate Prediction of the Soft Error Vulnerability of Scientific Applications

    SciTech Connect

    Bronevetsky, G; de Supinski, B; Schulz, M

    2009-02-13

    Understanding the soft error vulnerability of supercomputer applications is critical as these systems are using ever larger numbers of devices that have decreasing feature sizes and, thus, increasing frequency of soft errors. As many large scale parallel scientific applications use BLAS and LAPACK linear algebra routines, the soft error vulnerability of these methods constitutes a large fraction of the applications overall vulnerability. This paper analyzes the vulnerability of these routines to soft errors by characterizing how their outputs are affected by injected errors and by evaluating several techniques for predicting how errors propagate from the input to the output of each routine. The resulting error profiles can be used to understand the fault vulnerability of full applications that use these routines.

  1. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.

    PubMed

    Faraggi, Eshel; Kouza, Maksim; Zhou, Yaoqi; Kloczkowski, Andrzej

    2017-01-01

    A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for ASAquick are available from Research and Information Systems at http://mamiris.com and from the Battelle Center for Mathematical Medicine at http://mathmed.org .

  2. Sequence features accurately predict genome-wide MeCP2 binding in vivo

    PubMed Central

    Rube, H. Tomas; Lee, Wooje; Hejna, Miroslav; Chen, Huaiyang; Yasui, Dag H.; Hess, John F.; LaSalle, Janine M.; Song, Jun S.; Gong, Qizhi

    2016-01-01

    Methyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2-binding data, we show that DNA sequence features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported genome-wide association with methylation is in part due to MeCP2's affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2 binding downstream of promoters correlates with increased expression in Mecp2-deficient neurons. PMID:27008915

  3. Simplified versus geometrically accurate models of forefoot anatomy to predict plantar pressures: A finite element study.

    PubMed

    Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

    2016-01-25

    Integration of patient-specific biomechanical measurements into the design of therapeutic footwear has been shown to improve clinical outcomes in patients with diabetic foot disease. The addition of numerical simulations intended to optimise intervention design may help to build on these advances, however at present the time and labour required to generate and run personalised models of foot anatomy restrict their routine clinical utility. In this study we developed second-generation personalised simple finite element (FE) models of the forefoot with varying geometric fidelities. Plantar pressure predictions from barefoot, shod, and shod with insole simulations using simplified models were compared to those obtained from CT-based FE models incorporating more detailed representations of bone and tissue geometry. A simplified model including representations of metatarsals based on simple geometric shapes, embedded within a contoured soft tissue block with outer geometry acquired from a 3D surface scan was found to provide pressure predictions closest to the more complex model, with mean differences of 13.3kPa (SD 13.4), 12.52kPa (SD 11.9) and 9.6kPa (SD 9.3) for barefoot, shod, and insole conditions respectively. The simplified model design could be produced in <1h compared to >3h in the case of the more detailed model, and solved on average 24% faster. FE models of the forefoot based on simplified geometric representations of the metatarsal bones and soft tissue surface geometry from 3D surface scans may potentially provide a simulation approach with improved clinical utility, however further validity testing around a range of therapeutic footwear types is required.

  4. Development of a method to accurately calculate the Dpb and quickly predict the strength of a chemical bond

    NASA Astrophysics Data System (ADS)

    Du, Xia; Zhao, Dong-Xia; Yang, Zhong-Zhi

    2013-02-01

    A new approach to characterize and measure bond strength has been developed. First, we propose a method to accurately calculate the potential acting on an electron in a molecule (PAEM) at the saddle point along a chemical bond in situ, denoted by Dpb. Then, a direct method to quickly evaluate bond strength is established. We choose some familiar molecules as models for benchmarking this method. As a practical application, the Dpb of base pairs in DNA along C-H and N-H bonds are obtained for the first time. All results show that C7-H of A-T and C8-H of G-C are the relatively weak bonds that are the injured positions in DNA damage. The significance of this work is twofold: (i) A method is developed to calculate Dpb of various sizable molecules in situ quickly and accurately; (ii) This work demonstrates the feasibility to quickly predict the bond strength in macromolecules.

  5. Fast and accurate prediction for aerodynamic forces and moments acting on satellites flying in Low-Earth Orbit

    NASA Astrophysics Data System (ADS)

    Jin, Xuhon; Huang, Fei; Hu, Pengju; Cheng, Xiaoli

    2016-11-01

    A fundamental prerequisite for satellites operating in a Low Earth Orbit (LEO) is the availability of fast and accurate prediction of non-gravitational aerodynamic forces, which is characterised by the free molecular flow regime. However, conventional computational methods like the analytical integral method and direct simulation Monte Carlo (DSMC) technique are found failing to deal with flow shadowing and multiple reflections or computationally expensive. This work develops a general computer program for the accurate calculation of aerodynamic forces in the free molecular flow regime using the test particle Monte Carlo (TPMC) method, and non-gravitational aerodynamic forces actiong on the Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellite is calculated for different freestream conditions and gas-surface interaction models by the computer program.

  6. Time-dependent neutrino emission from Mrk 421 during flares and predictions for IceCube

    NASA Astrophysics Data System (ADS)

    Petropoulou, Maria; Coenders, Stefan; Dimitrakoudis, Stavros

    2016-07-01

    Blazars, a subclass of active galactic nuclei, are prime candidate sources for the high energy neutrinos recently detected by IceCube. Being one of the brightest sources in the extragalactic X-ray and γ-ray sky as well as one of the nearest blazars to Earth, Mrk 421 is an excellent source for testing the scenario of the blazar-neutrino connection, especially during flares where time-dependent neutrino searches may have a higher detection probability. Here, we model the spectral energy distribution of Mrk 421 during a 13-day flare in 2010 with unprecedented multi-wavelength coverage, and calculate the respective neutrino flux. We find a correlation between the >1 PeV neutrino and photon fluxes, in all energy bands. Using typical IceCube through-going muon event samples with good angular resolution and high statistics, wederive the mean event rate above 100 TeV (˜0.57 evt/yr) and show that it is comparable to that expected from a four-month quiescent period in 2009. Due to the short duration of the flare, an accumulation of similar flares over several years would be necessary to produce a meaningful signal for IceCube. To better assess this, we apply the correlation between the neutrino and γ-ray fluxes to the 6.9 yr Fermi-LAT light curve of Mrk 421. We find that the mean event count above 1 PeV for the full IceCube detector livetime is 3.59 ± 0.60 (2.73 ± 0.38) νμ +νbarμ with (without) major flares included in our analysis. This estimate exceeds, within the uncertainties, the 95% (90%) threshold value for the detection of one or more muon (anti-)neutrinos. Meanwhile, the most conservative scenario, where no correlation of γ-rays and neutrinos is assumed, predicts 1.60 ± 0.16νμ +νbarμ events. We conclude that a non-detection of high-energy neutrinos by IceCube would probe the neutrino/γ-ray flux correlation during major flares or/and the hadronic contribution to the blazar emission.

  7. Simplified risk score models accurately predict the risk of major in-hospital complications following percutaneous coronary intervention.

    PubMed

    Resnic, F S; Ohno-Machado, L; Selwyn, A; Simon, D I; Popma, J J

    2001-07-01

    The objectives of this analysis were to develop and validate simplified risk score models for predicting the risk of major in-hospital complications after percutaneous coronary intervention (PCI) in the era of widespread stenting and use of glycoprotein IIb/IIIa antagonists. We then sought to compare the performance of these simplified models with those of full logistic regression and neural network models. From January 1, 1997 to December 31, 1999, data were collected on 4,264 consecutive interventional procedures at a single center. Risk score models were derived from multiple logistic regression models using the first 2,804 cases and then validated on the final 1,460 cases. The area under the receiver operating characteristic (ROC) curve for the risk score model that predicted death was 0.86 compared with 0.85 for the multiple logistic model and 0.83 for the neural network model (validation set). For the combined end points of death, myocardial infarction, or bypass surgery, the corresponding areas under the ROC curves were 0.74, 0.78, and 0.81, respectively. Previously identified risk factors were confirmed in this analysis. The use of stents was associated with a decreased risk of in-hospital complications. Thus, risk score models can accurately predict the risk of major in-hospital complications after PCI. Their discriminatory power is comparable to those of logistic models and neural network models. Accurate bedside risk stratification may be achieved with these simple models.

  8. A snow and ice melt seasonal prediction modelling system for Alpine reservoirs

    NASA Astrophysics Data System (ADS)

    Förster, Kristian; Oesterle, Felix; Hanzer, Florian; Schöber, Johannes; Huttenlau, Matthias; Strasser, Ulrich

    2016-10-01

    The timing and the volume of snow and ice melt in Alpine catchments are crucial for management operations of reservoirs and hydropower generation. Moreover, a sustainable reservoir operation through reservoir storage and flow control as part of flood risk management is important for downstream communities. Forecast systems typically provide predictions for a few days in advance. Reservoir operators would benefit if lead times could be extended in order to optimise the reservoir management. Current seasonal prediction products such as the NCEP (National Centers for Environmental Prediction) Climate Forecast System version 2 (CFSv2) enable seasonal forecasts up to nine months in advance, with of course decreasing accuracy as lead-time increases. We present a coupled seasonal prediction modelling system that runs at monthly time steps for a small catchment in the Austrian Alps (Gepatschalm). Meteorological forecasts are obtained from the CFSv2 model. Subsequently, these data are downscaled to the Alpine Water balance And Runoff Estimation model AWARE running at monthly time step. Initial conditions are obtained using the physically based, hydro-climatological snow model AMUNDSEN that predicts hourly fields of snow water equivalent and snowmelt at a regular grid with 50 m spacing. Reservoir inflow is calculated taking into account various runs of the CFSv2 model. These simulations are compared with observed inflow volumes for the melting and accumulation period 2015.

  9. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes

    PubMed Central

    Zhao, Li; Chen, Yiyun; Bajaj, Amol Onkar; Eblimit, Aiden; Xu, Mingchu; Soens, Zachry T.; Wang, Feng; Ge, Zhongqi; Jung, Sung Yun; He, Feng; Li, Yumei; Wensel, Theodore G.; Qin, Jun; Chen, Rui

    2016-01-01

    Proteomic profiling on subcellular fractions provides invaluable information regarding both protein abundance and subcellular localization. When integrated with other data sets, it can greatly enhance our ability to predict gene function genome-wide. In this study, we performed a comprehensive proteomic analysis on the light-sensing compartment of photoreceptors called the outer segment (OS). By comparing with the protein profile obtained from the retina tissue depleted of OS, an enrichment score for each protein is calculated to quantify protein subcellular localization, and 84% accuracy is achieved compared with experimental data. By integrating the protein OS enrichment score, the protein abundance, and the retina transcriptome, the probability of a gene playing an essential function in photoreceptor cells is derived with high specificity and sensitivity. As a result, a list of genes that will likely result in human retinal disease when mutated was identified and validated by previous literature and/or animal model studies. Therefore, this new methodology demonstrates the synergy of combining subcellular fractionation proteomics with other omics data sets and is generally applicable to other tissues and diseases. PMID:26912414

  10. Accurate prediction of the refractive index of polymers using first principles and data modeling

    NASA Astrophysics Data System (ADS)

    Afzal, Mohammad Atif Faiz; Cheng, Chong; Hachmann, Johannes

    Organic polymers with a high refractive index (RI) have recently attracted considerable interest due to their potential application in optical and optoelectronic devices. The ability to tailor the molecular structure of polymers is the key to increasing the accessible RI values. Our work concerns the creation of predictive in silico models for the optical properties of organic polymers, the screening of large-scale candidate libraries, and the mining of the resulting data to extract the underlying design principles that govern their performance. This work was set up to guide our experimentalist partners and allow them to target the most promising candidates. Our model is based on the Lorentz-Lorenz equation and thus includes the polarizability and number density values for each candidate. For the former, we performed a detailed benchmark study of different density functionals, basis sets, and the extrapolation scheme towards the polymer limit. For the number density we devised an exceedingly efficient machine learning approach to correlate the polymer structure and the packing fraction in the bulk material. We validated the proposed RI model against the experimentally known RI values of 112 polymers. We could show that the proposed combination of physical and data modeling is both successful and highly economical to characterize a wide range of organic polymers, which is a prerequisite for virtual high-throughput screening.

  11. The human skin/chick chorioallantoic membrane model accurately predicts the potency of cosmetic allergens.

    PubMed

    Slodownik, Dan; Grinberg, Igor; Spira, Ram M; Skornik, Yehuda; Goldstein, Ronald S

    2009-04-01

    The current standard method for predicting contact allergenicity is the murine local lymph node assay (LLNA). Public objection to the use of animals in testing of cosmetics makes the development of a system that does not use sentient animals highly desirable. The chorioallantoic membrane (CAM) of the chick egg has been extensively used for the growth of normal and transformed mammalian tissues. The CAM is not innervated, and embryos are sacrificed before the development of pain perception. The aim of this study was to determine whether the sensitization phase of contact dermatitis to known cosmetic allergens can be quantified using CAM-engrafted human skin and how these results compare with published EC3 data obtained with the LLNA. We studied six common molecules used in allergen testing and quantified migration of epidermal Langerhans cells (LC) as a measure of their allergic potency. All agents with known allergic potential induced statistically significant migration of LC. The data obtained correlated well with published data for these allergens generated using the LLNA test. The human-skin CAM model therefore has great potential as an inexpensive, non-radioactive, in vivo alternative to the LLNA, which does not require the use of sentient animals. In addition, this system has the advantage of testing the allergic response of human, rather than animal skin.

  12. Searching for Computational Strategies to Accurately Predict pKas of Large Phenolic Derivatives.

    PubMed

    Rebollar-Zepeda, Aida Mariana; Campos-Hernández, Tania; Ramírez-Silva, María Teresa; Rojas-Hernández, Alberto; Galano, Annia

    2011-08-09

    Twenty-two reaction schemes have been tested, within the cluster-continuum model including up to seven explicit water molecules. They have been used in conjunction with nine different methods, within the density functional theory and with second-order Møller-Plesset. The quality of the pKa predictions was found to be strongly dependent on the chosen scheme, while only moderately influenced by the method of calculation. We recommend the E1 reaction scheme [HA + OH(-) (3H2O) ↔ A(-) (H2O) + 3H2O], since it yields mean unsigned errors (MUE) lower than 1 unit of pKa for most of the tested functionals. The best pKa values obtained from this reaction scheme are those involving calculations with PBE0 (MUE = 0.77), TPSS (MUE = 0.82), BHandHLYP (MUE = 0.82), and B3LYP (MUE = 0.86) functionals. This scheme has the additional advantage, compared to the proton exchange method, which also gives very small values of MUE, of being experiment independent. It should be kept in mind, however, that these recommendations are valid within the cluster-continuum model, using the polarizable continuum model in conjunction with the united atom Hartree-Fock cavity and the strategy based on thermodynamic cycles. Changes in any of these aspects of the used methodology may lead to different outcomes.

  13. Towards Relaxing the Spherical Solar Radiation Pressure Model for Accurate Orbit Predictions

    NASA Astrophysics Data System (ADS)

    Lachut, M.; Bennett, J.

    2016-09-01

    The well-known cannonball model has been used ubiquitously to capture the effects of atmospheric drag and solar radiation pressure on satellites and/or space debris for decades. While it lends itself naturally to spherical objects, its validity in the case of non-spherical objects has been debated heavily for years throughout the space situational awareness community. One of the leading motivations to improve orbit predictions by relaxing the spherical assumption, is the ongoing demand for more robust and reliable conjunction assessments. In this study, we explore the orbit propagation of a flat plate in a near-GEO orbit under the influence of solar radiation pressure, using a Lambertian BRDF model. Consequently, this approach will account for the spin rate and orientation of the object, which is typically determined in practice using a light curve analysis. Here, simulations will be performed which systematically reduces the spin rate to demonstrate the point at which the spherical model no longer describes the orbital elements of the spinning plate. Further understanding of this threshold would provide insight into when a higher fidelity model should be used, thus resulting in improved orbit propagations. Therefore, the work presented here is of particular interest to organizations and researchers that maintain their own catalog, and/or perform conjunction analyses.

  14. Towards Accurate Prediction of Turbulent, Three-Dimensional, Recirculating Flows with the NCC

    NASA Technical Reports Server (NTRS)

    Iannetti, A.; Tacina, R.; Jeng, S.-M.; Cai, J.

    2001-01-01

    The National Combustion Code (NCC) was used to calculate the steady state, nonreacting flow field of a prototype Lean Direct Injection (LDI) swirler. This configuration used nine groups of eight holes drilled at a thirty-five degree angle to induce swirl. These nine groups created swirl in the same direction, or a corotating pattern. The static pressure drop across the holes was fixed at approximately four percent. Computations were performed on one quarter of the geometry, because the geometry is considered rotationally periodic every ninety degrees. The final computational grid used was approximately 2.26 million tetrahedral cells, and a cubic nonlinear k - epsilon model was used to model turbulence. The NCC results were then compared to time averaged Laser Doppler Velocimetry (LDV) data. The LDV measurements were performed on the full geometry, but four ninths of the geometry was measured. One-, two-, and three-dimensional representations of both flow fields are presented. The NCC computations compare both qualitatively and quantitatively well to the LDV data, but differences exist downstream. The comparison is encouraging, and shows that NCC can be used for future injector design studies. To improve the flow prediction accuracy of turbulent, three-dimensional, recirculating flow fields with the NCC, recommendations are given.

  15. Software Design Description for the Polar Ice Prediction System (PIPS) Version 3.0

    DTIC Science & Technology

    2008-11-05

    THICKNESS AND TEMPERATURE FOR THE TWO EXTREMA IN SNOW DEPTH. MAXIMUM SNOW DEPTH IS CALCULATED BASED ON ARCHIMEDES ’ PRINCIPLE FOR THE GIVEN ICE...have the ice concentration as a multiplicative factor to be consistent with the formal theory of free drift in low ice concentration areas. A...ice thickness and temperature for the two extrema in snow depth. Maximum snow depth is calculated based on Archimedes ’ Principle for the given ice

  16. The development of a coupled ice-ocean model for forecasting ice conditions in the Arctic

    NASA Astrophysics Data System (ADS)

    Riedlinger, Shelley H.; Preller, Ruth H.

    1991-09-01

    A coupled ice-ocean model has been developed to investigate how a better simulation of ice-ocean interaction can improve sea ice forecasting capabilities. The coupling of the ice and ocean results in improved temporal variability of ocean circulation and heat and salt exchange between ice and ocean. The U.S. Navy's Polar Ice Prediction System is coupled to a diagnostic version of the Bryan-Cox three-dimensional ocean circulation model. A horizontal grid spacing of 127 km was used in the coupled model with 17 vertical levels from the surface to the ocean bottom. Atmospheric data from the Naval Operational Global Atmospheric Prediction System (NOGAPS) for 1986 were used to force the model. The ice-ocean model simulation yielded realistic ice thickness distributions, ice drifts, and ocean currents. The model predicted accurate seasonal trends in ice growth and decay. Excess ice is often grown in the Greenland and Barents seas in fall and winter. This is due, in part, to the model's grid resolution which does not accurately resolve narrow currents, such as the West Spitsbergen Current. A sensitivity study of the heat transfer coefficients used in the ice model showed that the ice edge could be improved by using different coefficient values for thick ice, thin ice, and open water. Other sensitivity studies examined the effect of removing the "distorted" physics frequently used in the Bryan-Cox ocean circulation model and the effect of the vertical eddy momentum coefficient on the surface ocean circulation. An additional simulation was made using 1989 NOGAPS forcing to examine what type of variability could occur when using different years of NOGAPS forcing in the diagnostic ocean model. Significant differences occurred between the 1989 and 1986 ice thickness distributions as well as the oceanic heat fluxes. These differences show that the forecast system, which presently uses an ocean "climatology," can benefit from the variability allowed by the diagnostic ocean model.

  17. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    SciTech Connect

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-11-15

    attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries.

  18. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    PubMed Central

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-01-01

    attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries. PMID:26520735

  19. How Accurate Are the Anthropometry Equations in in Iranian Military Men in Predicting Body Composition?

    PubMed Central

    Shakibaee, Abolfazl; Faghihzadeh, Soghrat; Alishiri, Gholam Hossein; Ebrahimpour, Zeynab; Faradjzadeh, Shahram; Sobhani, Vahid; Asgari, Alireza

    2015-01-01

    Background: The body composition varies according to different life styles (i.e. intake calories and caloric expenditure). Therefore, it is wise to record military personnel’s body composition periodically and encourage those who abide to the regulations. Different methods have been introduced for body composition assessment: invasive and non-invasive. Amongst them, the Jackson and Pollock equation is most popular. Objectives: The recommended anthropometric prediction equations for assessing men’s body composition were compared with dual-energy X-ray absorptiometry (DEXA) gold standard to develop a modified equation to assess body composition and obesity quantitatively among Iranian military men. Patients and Methods: A total of 101 military men aged 23 - 52 years old with a mean age of 35.5 years were recruited and evaluated in the present study (average height, 173.9 cm and weight, 81.5 kg). The body-fat percentages of subjects were assessed both with anthropometric assessment and DEXA scan. The data obtained from these two methods were then compared using multiple regression analysis. Results: The mean and standard deviation of body fat percentage of the DEXA assessment was 21.2 ± 4.3 and body fat percentage obtained from three Jackson and Pollock 3-, 4- and 7-site equations were 21.1 ± 5.8, 22.2 ± 6.0 and 20.9 ± 5.7, respectively. There was a strong correlation between these three equations and DEXA (R² = 0.98). Conclusions: The mean percentage of body fat obtained from the three equations of Jackson and Pollock was very close to that of body fat obtained from DEXA; however, we suggest using a modified Jackson-Pollock 3-site equation for volunteer military men because the 3-site equation analysis method is simpler and faster than other methods. PMID:26715964

  20. Deformation, Failure, and Fatigue Life of SiC/Ti-15-3 Laminates Accurately Predicted by MAC/GMC

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2002-01-01

    NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) (ref.1) has been extended to enable fully coupled macro-micro deformation, failure, and fatigue life predictions for advanced metal matrix, ceramic matrix, and polymer matrix composites. Because of the multiaxial nature of the code's underlying micromechanics model, GMC--which allows the incorporation of complex local inelastic constitutive models--MAC/GMC finds its most important application in metal matrix composites, like the SiC/Ti-15-3 composite examined here. Furthermore, since GMC predicts the microscale fields within each constituent of the composite material, submodels for local effects such as fiber breakage, interfacial debonding, and matrix fatigue damage can and have been built into MAC/GMC. The present application of MAC/GMC highlights the combination of these features, which has enabled the accurate modeling of the deformation, failure, and life of titanium matrix composites.

  1. Industrial Compositional Streamline Simulation for Efficient and Accurate Prediction of Gas Injection and WAG Processes

    SciTech Connect

    Margot Gerritsen

    2008-10-31

    Gas-injection processes are widely and increasingly used for enhanced oil recovery (EOR). In the United States, for example, EOR production by gas injection accounts for approximately 45% of total EOR production and has tripled since 1986. The understanding of the multiphase, multicomponent flow taking place in any displacement process is essential for successful design of gas-injection projects. Due to complex reservoir geometry, reservoir fluid properties and phase behavior, the design of accurate and efficient numerical simulations for the multiphase, multicomponent flow governing these processes is nontrivial. In this work, we developed, implemented and tested a streamline based solver for gas injection processes that is computationally very attractive: as compared to traditional Eulerian solvers in use by industry it computes solutions with a computational speed orders of magnitude higher and a comparable accuracy provided that cross-flow effects do not dominate. We contributed to the development of compositional streamline solvers in three significant ways: improvement of the overall framework allowing improved streamline coverage and partial streamline tracing, amongst others; parallelization of the streamline code, which significantly improves wall clock time; and development of new compositional solvers that can be implemented along streamlines as well as in existing Eulerian codes used by industry. We designed several novel ideas in the streamline framework. First, we developed an adaptive streamline coverage algorithm. Adding streamlines locally can reduce computational costs by concentrating computational efforts where needed, and reduce mapping errors. Adapting streamline coverage effectively controls mass balance errors that mostly result from the mapping from streamlines to pressure grid. We also introduced the concept of partial streamlines: streamlines that do not necessarily start and/or end at wells. This allows more efficient coverage and avoids

  2. Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?

    PubMed

    Ballester, Pedro J; Schreyer, Adrian; Blundell, Tom L

    2014-03-24

    Predicting the binding affinities of large sets of diverse molecules against a range of macromolecular targets is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for exploiting and analyzing the outputs of docking, which is in turn an important tool in problems such as structure-based drug design. Classical scoring functions assume a predetermined theory-inspired functional form for the relationship between the variables that describe an experimentally determined or modeled structure of a protein-ligand complex and its binding affinity. The inherent problem of this approach is in the difficulty of explicitly modeling the various contributions of intermolecular interactions to binding affinity. New scoring functions based on machine-learning regression models, which are able to exploit effectively much larger amounts of experimental data and circumvent the need for a predetermined functional form, have already been shown to outperform a broad range of state-of-the-art scoring functions in a widely used benchmark. Here, we investigate the impact of the chemical description of the complex on the predictive power of the resulting scoring function using a systematic battery of numerical experiments. The latter resulted in the most accurate scoring function to date on the benchmark. Strikingly, we also found that a more precise chemical description of the protein-ligand complex does not generally lead to a more accurate prediction of binding affinity. We discuss four factors that may contribute to this result: modeling assumptions, codependence of representation and regression, data restricted to the bound state, and conformational heterogeneity in data.

  3. Easy-to-use, general, and accurate multi-Kinect calibration and its application to gait monitoring for fall prediction.

    PubMed

    Staranowicz, Aaron N; Ray, Christopher; Mariottini, Gian-Luca

    2015-01-01

    Falls are the most-common causes of unintentional injury and death in older adults. Many clinics, hospitals, and health-care providers are urgently seeking accurate, low-cost, and easy-to-use technology to predict falls before they happen, e.g., by monitoring the human walking pattern (or "gait"). Despite the wide popularity of Microsoft's Kinect and the plethora of solutions for gait monitoring, no strategy has been proposed to date to allow non-expert users to calibrate the cameras, which is essential to accurately fuse the body motion observed by each camera in a single frame of reference. In this paper, we present a novel multi-Kinect calibration algorithm that has advanced features when compared to existing methods: 1) is easy to use, 2) it can be used in any generic Kinect arrangement, and 3) it provides accurate calibration. Extensive real-world experiments have been conducted to validate our algorithm and to compare its performance against other multi-Kinect calibration approaches, especially to show the improved estimate of gait parameters. Finally, a MATLAB Toolbox has been made publicly available for the entire research community.

  4. How the Assumed Size Distribution of Dust Minerals Affects the Predicted Ice Forming Nuclei

    NASA Technical Reports Server (NTRS)

    Perlwitz, Jan P.; Fridlind, Ann M.; Garcia-Pando, Carlos Perez; Miller, Ron L.; Knopf, Daniel A.

    2015-01-01

    The formation of ice in clouds depends on the availability of ice forming nuclei (IFN). Dust aerosol particles are considered the most important source of IFN at a global scale. Recent laboratory studies have demonstrated that the mineral feldspar provides the most efficient dust IFN for immersion freezing and together with kaolinite for deposition ice nucleation, and that the phyllosilicates illite and montmorillonite (a member of the smectite group) are of secondary importance.A few studies have applied global models that simulate mineral specific dust to predict the number and geographical distribution of IFN. These studies have been based on the simple assumption that the mineral composition of soil as provided in data sets from the literature translates directly into the mineral composition of the dust aerosols. However, these tables are based on measurements of wet-sieved soil where dust aggregates are destroyed to a large degree. In consequence, the size distribution of dust is shifted to smaller sizes, and phyllosilicates like illite, kaolinite, and smectite are only found in the size range 2 m. In contrast, in measurements of the mineral composition of dust aerosols, the largest mass fraction of these phyllosilicates is found in the size range 2 m as part of dust aggregates. Conversely, the mass fraction of feldspar is smaller in this size range, varying with the geographical location. This may have a significant effect on the predicted IFN number and its geographical distribution.An improved mineral specific dust aerosol module has been recently implemented in the NASA GISS Earth System ModelE2. The dust module takes into consideration the disaggregated state of wet-sieved soil, on which the tables of soil mineral fractions are based. To simulate the atmospheric cycle of the minerals, the mass size distribution of each mineral in aggregates that are emitted from undispersed parent soil is reconstructed. In the current study, we test the null

  5. How the Assumed Size Distribution of Dust Minerals Affects the Predicted Ice Forming Nuclei

    NASA Astrophysics Data System (ADS)

    Perlwitz, J. P.; Fridlind, A. M.; Pérez García-Pando, C.; Miller, R. L.; Knopf, D. A.

    2015-12-01

    The formation of ice in clouds depends on the availability of ice forming nuclei (IFN). Dust aerosol particles are considered the most important source of IFN at a global scale. Recent laboratory studies have demonstrated that the mineral feldspar provides the most efficient dust IFN for immersion freezing and together with kaolinite for deposition ice nucleation, and that the phyllosilicates illite and montmorillonite (a member of the smectite group) are of secondary importance.A few studies have applied global models that simulate mineral specific dust to predict the number and geographical distribution of IFN. These studies have been based on the simple assumption that the mineral composition of soil as provided in data sets from the literature translates directly into the mineral composition of the dust aerosols. However, these tables are based on measurements of wet-sieved soil where dust aggregates are destroyed to a large degree. In consequence, the size distribution of dust is shifted to smaller sizes, and phyllosilicates like illite, kaolinite, and smectite are only found in the size range <2 μm. In contrast, in measurements of the mineral composition of dust aerosols, the largest mass fraction of these phyllosilicates is found in the size range >2 μm as part of dust aggregates. Conversely, the mass fraction of feldspar is smaller in this size range, varying with the geographical location. This may have a significant effect on the predicted IFN number and its geographical distribution.An improved mineral specific dust aerosol module has been recently implemented in the NASA GISS Earth System ModelE2. The dust module takes into consideration the disaggregated state of wet-sieved soil, on which the tables of soil mineral fractions are based. To simulate the atmospheric cycle of the minerals, the mass size distribution of each mineral in aggregates that are emitted from undispersed parent soil is reconstructed. In the current study, we test the null

  6. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race

    PubMed Central

    Hourihan, Kathleen L.; Benjamin, Aaron S.; Liu, Xiping

    2012-01-01

    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness’s claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness. PMID:23162788

  7. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed.

  8. Shrinking the Psoriasis Assessment Gap: Early Gene-Expression Profiling Accurately Predicts Response to Long-Term Treatment.

    PubMed

    Correa da Rosa, Joel; Kim, Jaehwan; Tian, Suyan; Tomalin, Lewis E; Krueger, James G; Suárez-Fariñas, Mayte

    2017-02-01

    There is an "assessment gap" between the moment a patient's response to treatment is biologically determined and when a response can actually be determined clinically. Patients' biochemical profiles are a major determinant of clinical outcome for a given treatment. It is therefore feasible that molecular-level patient information could be used to decrease the assessment gap. Thanks to clinically accessible biopsy samples, high-quality molecular data for psoriasis patients are widely available. Psoriasis is therefore an excellent disease for testing the prospect of predicting treatment outcome from molecular data. Our study shows that gene-expression profiles of psoriasis skin lesions, taken in the first 4 weeks of treatment, can be used to accurately predict (>80% area under the receiver operating characteristic curve) the clinical endpoint at 12 weeks. This could decrease the psoriasis assessment gap by 2 months. We present two distinct prediction modes: a universal predictor, aimed at forecasting the efficacy of untested drugs, and specific predictors aimed at forecasting clinical response to treatment with four specific drugs: etanercept, ustekinumab, adalimumab, and methotrexate. We also develop two forms of prediction: one from detailed, platform-specific data and one from platform-independent, pathway-based data. We show that key biomarkers are associated with responses to drugs and doses and thus provide insight into the biology of pathogenesis reversion.

  9. Prediction of ice content in biological model solutions when frozen under high pressure.

    PubMed

    Guignon, B; Aparicio, C; Otero, L; Sanz, P D

    2009-01-01

    High pressure is, at least, as effective as cryoprotective agents (CPAs) and are used for decreasing both homogenous nucleation and freezing temperatures. This fact gives rise to a great variety of possible cryopreservation processes under high pressure. They have not been optimized yet, since they are relatively recent and are mainly based on the pressure-temperature phase diagram of pure water. Very few phase diagrams of biological material are available under pressure. This is owing to the lack of suitable equipment and to the difficulties encountered in carrying out the measurements. Different aqueous solutions of salt and CPAs as biological models are studied in the range of 0 degrees C down to -35 degrees C, 0.1 up to 250 MPa, and 0-20% w/w total solute concentration. The phase transition curves of glycerol and of sodium chloride with either glycerol or sucrose in aqueous solutions are determined in a high hydrostatic pressure vessel. The experimental phase diagrams of binary solutions were well described by a third-degree polynomial equation. It was also shown that Robinson and Stokes' equation at high pressure succeeds in predicting the phase diagrams of both binary and ternary solutions. The solute cryoconcentration and the ice content were calculated as a function of temperature and pressure conditions during the freezing of a binary solution. This information should provide a basis upon which high-pressure cryopreservation processes may be performed and the damages derived from ice formation evaluated.

  10. The Regional Polar Ice Prediction System - Barents Sea (RPIPS-B): A technical Description

    DTIC Science & Technology

    1989-05-01

    two-level approach (Hibler, and ice thickness changes . The term Sh is the net 1979). This approach breaks ice into two categories, growth or melt of ice...S.. is the change in thick and thin, %\\ith the division between the two being compactness due to the growth or decay of ihc. 0.5 in. The compactness...hc’icrc arid the small increase in ice thickness at transect J - 5, the ocean. This problem could h td ,’iih these figures show little change in ice

  11. Accurate prediction of unsteady and time-averaged pressure loads using a hybrid Reynolds-Averaged/large-eddy simulation technique

    NASA Astrophysics Data System (ADS)

    Bozinoski, Radoslav

    Significant research has been performed over the last several years on understanding the unsteady aerodynamics of various fluid flows. Much of this work has focused on quantifying the unsteady, three-dimensional flow field effects which have proven vital to the accurate prediction of many fluid and aerodynamic problems. Up until recently, engineers have predominantly relied on steady-state simulations to analyze the inherently three-dimensional ow structures that are prevalent in many of today's "real-world" problems. Increases in computational capacity and the development of efficient numerical methods can change this and allow for the solution of the unsteady Reynolds-Averaged Navier-Stokes (RANS) equations for practical three-dimensional aerodynamic applications. An integral part of this capability has been the performance and accuracy of the turbulence models coupled with advanced parallel computing techniques. This report begins with a brief literature survey of the role fully three-dimensional, unsteady, Navier-Stokes solvers have on the current state of numerical analysis. Next, the process of creating a baseline three-dimensional Multi-Block FLOw procedure called MBFLO3 is presented. Solutions for an inviscid circular arc bump, laminar at plate, laminar cylinder, and turbulent at plate are then presented. Results show good agreement with available experimental, numerical, and theoretical data. Scalability data for the parallel version of MBFLO3 is presented and shows efficiencies of 90% and higher for processes of no less than 100,000 computational grid points. Next, the description and implementation techniques used for several turbulence models are presented. Following the successful implementation of the URANS and DES procedures, the validation data for separated, non-reattaching flows over a NACA 0012 airfoil, wall-mounted hump, and a wing-body junction geometry are presented. Results for the NACA 0012 showed significant improvement in flow predictions

  12. Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging

    NASA Astrophysics Data System (ADS)

    Hughes, Timothy J.; Kandathil, Shaun M.; Popelier, Paul L. A.

    2015-02-01

    As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G**, B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol-1, decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol-1.

  13. Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging.

    PubMed

    Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A

    2015-02-05

    As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1).

  14. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    PubMed Central

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-01-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally—a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process. PMID:26887592

  15. Lava heating and loading of ice sheets on early Mars: Predictions for meltwater generation, groundwater recharge, and resulting landforms

    NASA Astrophysics Data System (ADS)

    Cassanelli, James P.; Head, James W.

    2016-06-01

    Recent modeling studies of the early Mars climate predict a predominantly cold climate, characterized by the formation of regional ice sheets across the highland areas of Mars. Formation of the predicted "icy highlands" ice sheets is coincident with a peak in the volcanic flux of Mars involving the emplacement of the Late Noachian - Early Hesperian ridged plains unit. We explore the relationship between the predicted early Mars "icy highlands" ice sheets, and the extensive early flood volcanism to gain insight into the surface conditions prevalent during the Late Noachian to Early Hesperian transition period. Using Hesperia Planum as a type area, we develop an ice sheet lava heating and loading model. We quantitatively assess the thermal and melting processes involved in the lava heating and loading process following the chronological sequence of lava emplacement. We test a broad range of parameters to thoroughly constrain the lava heating and loading process and outline predictions for the formation of resulting geological features. We apply the theoretical model to a study area within the Hesperia Planum region and assess the observed geology against predictions derived from the ice sheet lava heating and loading model. Due to the highly cratered nature of the Noachian highlands terrain onto which the volcanic plains were emplaced, we predict highly asymmetrical lava loading conditions. Crater interiors are predicted to accumulate greater thicknesses of lava over more rapid timescales, while in the intercrater plains, lava accumulation occurs over longer timescales and does not reach great thicknesses. We find that top-down melting due to conductive heat transfer from supraglacial lava flows is generally limited when the emplaced lava flows are less than ∼10 m thick, but is very significant at lava flow thicknesses of ∼100 m or greater. We find that bottom-up cryosphere and ice sheet melting is most likely to occur within crater interiors where lavas

  16. Using Web-based Interspecies Correlation Estimation (Web-ICE) models as a tool for acute toxicity prediction

    EPA Science Inventory

    In order to assess risk of contaminants to taxa with limited or no toxicity data available, Interspecies Correlation Estimation (ICE) models have been developed by the U.S. Environmental Protection Agency to extrapolate contaminant sensitivity predictions based on data from commo...

  17. User's manual for the NASA Lewis ice accretion/heat transfer prediction code with electrothermal deicer input

    NASA Technical Reports Server (NTRS)

    Masiulaniec, Konstanty C.; Wright, William B.

    1994-01-01

    A version of LEWICE has been developed that incorporates a recently developed electrothermal deicer code, developed at the University of Toledo by William B. Wright. This was accomplished, in essence, by replacing a subroutine in LEWICE, called EBAL, which balanced the energies at the ice surface, with a subroutine called UTICE. UTICE performs this same energy balance, as well as handles all the time-timperature transients below the ice surface, for all of the layers of a composite blade as well as the ice layer itself. This new addition is set up in such a fashion that a user may specify any number of heaters, any heater chordwise length, and any heater gap desired. The heaters may be fired in unison, or they may be cycled with periods independent of each other. The heater intensity may also be varied. In addition, the user may specify any number of layers and thicknesses depthwise into the blade. Thus, the new addition has maximum flexibility in modeling virtually any electrothermal deicer installed into any airfoil. It should be noted that the model simulates both shedding and runback. With the runback capability, it can simulate the anti-icing mode of heater performance, as well as detect icing downstream of the heaters due to runback in unprotected portions of the airfoil. This version of LEWICE can be run in three modes. In mode 1, no conduction heat transfer is modeled (which would be equivalent to the original version of LEWICE). In mode 2, all heat transfer is considered due to conduction but no heaters are firing. In mode 3, conduction heat transfer where the heaters are engaged is modeled, with subsequent ice shedding. When run in the first mode, there is virtually identical agreement with the original version of LEWICE in the prediction of accreted ice shapes. The code may be run in the second mode to determine the effects of conduction on the ice accretion process.

  18. TIMP2•IGFBP7 biomarker panel accurately predicts acute kidney injury in high-risk surgical patients

    PubMed Central

    Gunnerson, Kyle J.; Shaw, Andrew D.; Chawla, Lakhmir S.; Bihorac, Azra; Al-Khafaji, Ali; Kashani, Kianoush; Lissauer, Matthew; Shi, Jing; Walker, Michael G.; Kellum, John A.

    2016-01-01

    BACKGROUND Acute kidney injury (AKI) is an important complication in surgical patients. Existing biomarkers and clinical prediction models underestimate the risk for developing AKI. We recently reported data from two trials of 728 and 408 critically ill adult patients in whom urinary TIMP2•IGFBP7 (NephroCheck, Astute Medical) was used to identify patients at risk of developing AKI. Here we report a preplanned analysis of surgical patients from both trials to assess whether urinary tissue inhibitor of metalloproteinase 2 (TIMP-2) and insulin-like growth factor–binding protein 7 (IGFBP7) accurately identify surgical patients at risk of developing AKI. STUDY DESIGN We enrolled adult surgical patients at risk for AKI who were admitted to one of 39 intensive care units across Europe and North America. The primary end point was moderate-severe AKI (equivalent to KDIGO [Kidney Disease Improving Global Outcomes] stages 2–3) within 12 hours of enrollment. Biomarker performance was assessed using the area under the receiver operating characteristic curve, integrated discrimination improvement, and category-free net reclassification improvement. RESULTS A total of 375 patients were included in the final analysis of whom 35 (9%) developed moderate-severe AKI within 12 hours. The area under the receiver operating characteristic curve for [TIMP-2]•[IGFBP7] alone was 0.84 (95% confidence interval, 0.76–0.90; p < 0.0001). Biomarker performance was robust in sensitivity analysis across predefined subgroups (urgency and type of surgery). CONCLUSION For postoperative surgical intensive care unit patients, a single urinary TIMP2•IGFBP7 test accurately identified patients at risk for developing AKI within the ensuing 12 hours and its inclusion in clinical risk prediction models significantly enhances their performance. LEVEL OF EVIDENCE Prognostic study, level I. PMID:26816218

  19. A novel fibrosis index comprising a non-cholesterol sterol accurately predicts HCV-related liver cirrhosis.

    PubMed

    Ydreborg, Magdalena; Lisovskaja, Vera; Lagging, Martin; Brehm Christensen, Peer; Langeland, Nina; Buhl, Mads Rauning; Pedersen, Court; Mørch, Kristine; Wejstål, Rune; Norkrans, Gunnar; Lindh, Magnus; Färkkilä, Martti; Westin, Johan

    2014-01-01

    Diagnosis of liver cirrhosis is essential in the management of chronic hepatitis C virus (HCV) infection. Liver biopsy is invasive and thus entails a risk of complications as well as a potential risk of sampling error. Therefore, non-invasive diagnostic tools are preferential. The aim of the present study was to create a model for accurate prediction of liver cirrhosis based on patient characteristics and biomarkers of liver fibrosis, including a panel of non-cholesterol sterols reflecting cholesterol synthesis and absorption and secretion. We evaluated variables with potential predictive significance for liver fibrosis in 278 patients originally included in a multicenter phase III treatment trial for chronic HCV infection. A stepwise multivariate logistic model selection was performed with liver cirrhosis, defined as Ishak fibrosis stage 5-6, as the outcome variable. A new index, referred to as Nordic Liver Index (NoLI) in the paper, was based on the model: Log-odds (predicting cirrhosis) = -12.17+ (age × 0.11) + (BMI (kg/m(2)) × 0.23) + (D7-lathosterol (μg/100 mg cholesterol)×(-0.013)) + (Platelet count (x10(9)/L) × (-0.018)) + (Prothrombin-INR × 3.69). The area under the ROC curve (AUROC) for prediction of cirrhosis was 0.91 (95% CI 0.86-0.96). The index was validated in a separate cohort of 83 patients and the AUROC for this cohort was similar (0.90; 95% CI: 0.82-0.98). In conclusion, the new index may complement other methods in diagnosing cirrhosis in patients with chronic HCV infection.

  20. Estimating the state of a geophysical system with sparse observations: time delay methods to achieve accurate initial states for prediction

    NASA Astrophysics Data System (ADS)

    An, Zhe; Rey, Daniel; Ye, Jingxin; Abarbanel, Henry D. I.

    2017-01-01

    The problem of forecasting the behavior of a complex dynamical system through analysis of observational time-series data becomes difficult when the system expresses chaotic behavior and the measurements are sparse, in both space and/or time. Despite the fact that this situation is quite typical across many fields, including numerical weather prediction, the issue of whether the available observations are "sufficient" for generating successful forecasts is still not well understood. An analysis by Whartenby et al. (2013) found that in the context of the nonlinear shallow water equations on a β plane, standard nudging techniques require observing approximately 70 % of the full set of state variables. Here we examine the same system using a method introduced by Rey et al. (2014a), which generalizes standard nudging methods to utilize time delayed measurements. We show that in certain circumstances, it provides a sizable reduction in the number of observations required to construct accurate estimates and high-quality predictions. In particular, we find that this estimate of 70 % can be reduced to about 33 % using time delays, and even further if Lagrangian drifter locations are also used as measurements.

  1. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    NASA Astrophysics Data System (ADS)

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S.; Shirley, Eric L.; Prendergast, David

    2017-03-01

    Constrained-occupancy delta-self-consistent-field (Δ SCF ) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1 s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The Δ SCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle Δ SCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.

  2. The Importance of History for Predicting the Future of the West Antarctic Ice Sheet

    NASA Astrophysics Data System (ADS)

    Bindschadler, R.

    2008-12-01

    The West Antarctic Ice Sheet (WAIS) initiative began in 1990, following on earlier studies of the 'Siple Coast' ice streams and the Ross Ice Shelf. The past nearly two decades of field and satellite research of the West Antarctic ice sheet have produced an astounding number of discoveries, not the least of which is the variability of the West Antarctic ice sheet on time scales from seconds (yes, seconds!) to many millennia. The shorter-time-scale variations, such as the recent acceleration and thinning of glaciers draining into the Amundsen Sea, have illustrated serious weaknesses in what were once regarded as excellent models of ice sheet dynamics. Repairing this modeling capability requires understanding and incorporating external and internal processes previously regarded as less important. Ice-sheet history remains the best means to test, tune and validate numerical models of ice sheets. Cenozoic-age behavior may seem too ancient to matter to a centennial-time-scale focus on the future, but it is precisely through a long history, that the variety of more extreme ice sheet configurations can be extracted. Such upper or lower bound estimates have served the WAIS community well over the years to help justify research needed to assess the probability of dramatic behavior. Now, with the necessity of model revisions central to the WAIS effort, time histories of ice sheet behavior over both short and long time scales will return to a position of extreme importance.

  3. The Predictive Skill of Tropical Sea Surface Temperatures, Eurasian Snow Cover and Arctic Sea Ice on Mid-High Latitude Winter Weather

    NASA Astrophysics Data System (ADS)

    Cohen, J. L.; Furtado, J. C.; Tziperman, E.

    2015-12-01

    The Northern Hemisphere (NH) polar jet stream, or eddy-driven jet, represents both the boundary between colder polar air and warmer lower-latitude air and the primary storm track for extratropical cyclones. Therefore, any vacillations in the jet stream can alter weather regimes regionally and hemispherically. The most active period for the NH polar jet stream is during boreal winter, when the jet is at its seasonal maximum because of the steepened meridional temperature gradient. Forecasting the position and strength of the jet stream is critical for accurate temperature and precipitation forecasts for the high to middle latitudes. One major mode that describes the movements of the jet stream is the North Atlantic Oscillation or Arctic Oscillation (N/AO). Short-term and seasonal weather forecasters alike seek methods and mechanisms to extend predictability of an otherwise internal mode of variability in order to better prepare society for significant changes in precipitation and temperature during the winter. These changes may include short-lived but high-impact extreme weather events (e.g., cold air outbreaks, snowstorms) or season-long anomalies that can affect society for subsequent seasons (e.g., floods and droughts). Both snow cover and sea ice have been proposed as potentially modifying the N/AO model of variability. I will present some recent observational and modeling results on the hemispheric atmospheric response to snow cover and sea ice variability and the potential predictive skill of these high latitude boundary forcings. The expectation is that by the end of 2015 one of the strongest El Niño's in the observational record will be in full swing. Therefore I will also present some observational and modeling results on the possible influence of ENSO on extratropical climate variability for comparison with results from snow cover and sea ice.

  4. Probing Pluto's Underworld : Predicted Ice Temperatures from Microwave Radiometry Decoupled from Surface Conditions

    NASA Astrophysics Data System (ADS)

    Le Gall, Alice; Lorenz, Ralph; Leyrat, Cedric

    2015-11-01

    The Pluto dwarf planet has been successfully observed in July 2015 by the New Horizons spacecraft (NASA) during a close-targeted flyby which reavealed surprising and fascinating landscapes. While data are still being downlinked on the ground, we propose to present a prediction of the observation of the Radio Science Experiment experiment (REX) that occured on July 14, 2015 and aimed at measuring the microwave brightness temperature of Pluto’s night side.Present models admit a wide range of 2015 surface conditions at Pluto and Charon, where the atmospheric pressure may undergo dramatic seasonal variation and for which measurements have been performed by the New Horizons mission. One anticipated observation is the microwave brightness temperature, heretofore anticipated as indicating surface conditions relevant to surface-atmosphere equilibrium. However, drawing on recent experience with Cassini observations at Iapetus and Titan, we call attention to the large electrical skin depth of outer solar system materials such as methane, nitrogen or water ice, such that this observation may indicate temperatures averaged over depths of several or tens of meters beneath the surface.Using a seasonally-forced thermal model to determine microwave emission we predict that the southern hemisphere observations (in the polar night in July 2015) of New Horizons should display relatively warm effective temperatures of about 40 K. This would reflect the deep heat buried over the last century of summer, even if the atmospheric pressure suggests that the surface nitrogen frost point may be much lower. We will present our predictions and discuss their impact for the interpretation of the REX measurements.

  5. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance

    PubMed Central

    Hong, Ha; Solomon, Ethan A.; DiCarlo, James J.

    2015-01-01

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior. PMID:26424887

  6. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance.

    PubMed

    Majaj, Najib J; Hong, Ha; Solomon, Ethan A; DiCarlo, James J

    2015-09-30

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior.

  7. An ultra-clean technique for accurately analysing Pb isotopes and heavy metals at high spatial resolution in ice cores with sub-pg g(-1) Pb concentrations.

    PubMed

    Burn, Laurie J; Rosman, Kevin J R; Candelone, Jean-Pierre; Vallelonga, Paul; Burton, Graeme R; Smith, Andrew M; Morgan, Vin I; Barbante, Carlo; Hong, Sungmin; Boutron, Claude F

    2009-02-23

    Measurements of Pb isotope ratios in ice containing sub-pg g(-1) concentrations are easily compromised by contamination, particularly where limited sample is available. Improved techniques are essential if Antarctic ice cores are to be analysed with sufficient spatial resolution to reveal seasonal variations due to climate. This was achieved here by using stainless steel chisels and saws and strict protocols in an ultra-clean cold room to decontaminate and section ice cores. Artificial ice cores, prepared from high purity water were used to develop and refine the procedures and quantify blanks. Ba and In, two other important elements present at pg g(-1) and fg g(-1) concentrations in Polar ice, were also measured. The final blank amounted to 0.2+/-0.2 pg of Pb with (206)Pb/(207)Pb and (208)Pb/(207)Pb ratios of 1.16+/-0.12 and 2.35+/-0.16, respectively, 1.5+/-0.4 pg of Ba and 0.6+/-2.0 fg of In, most of which probably originates from abrasion of the steel saws by the ice. The procedure was demonstrated on a Holocene Antarctic ice core section and was shown to contribute blanks of only approximately 5%, approximately 14% and approximately 0.8% to monthly resolved samples with respective Pb, Ba and In concentrations of 0.12 pg g(-1), 0.3 pg g(-1) and 2.3 fg g(-1). Uncertainties in the Pb isotopic ratio measurements were degraded by only approximately 0.2%.

  8. Predicting the abundance of ice nucleating particles of biological origin in precipitation

    NASA Astrophysics Data System (ADS)

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy; Alewell, Christine

    2016-04-01

    Ice nucleation is a key step for the formation of precipitation on Earth. Ice nucleating particles (INPs) of biological origin catalyse the freezing of supercooled cloud droplets at temperatures warmer than -12 ° C. In order to understand the effective role of these INPs in conditioning precipitation, it is of primary importance to describe and predict their variability in the atmosphere. Over the course of two years, 14 sampling campaigns in precipitating clouds were conducted at the High Altitude Research Station Jungfraujoch, in the Swiss Alps, at 3580 m a.s.l. A total of 106 freshly fallen snow samples were analysed immediately on site for the concentration of INPs active at -8 ° C (INPs-8) by immersion freezing. Values of INPs-8 ranged from 0.21 to 434ṡml-1. Environmental parameters (like temperature of the air, wind speed, the stable oxygen ratio δ18O of snow, the number of particles larger than 0.5 μm) were used as independent variables to build a set of multiple linear regression models to describe and predict the observed variations of INPs-8 over time. The model providing the best results was based on fV (the fraction of remaining vapour in precipitating clouds, derived from δ18O) and on wind speed. It indicates that a coincidence of strong atmospheric turbulence and little prior precipitation from a cloud coincides with large concentrations of INPs-8. These conditions can be frequently encountered when air masses are suddenly forced to rise, for instance by the passage of a cold front, where also meteorological conditions are favourable to the onset of precipitation. To obtain more information on the presence of INPs-8 of biological origin and their relative composition, a set of precipitation samples were progressively filtered through different meshes (5 μm, 1.2 μm, 0.22 μm) followed by heating (40 ° C and 80 ° C). Almost all ice nucleating activity is lost after heating at 80 ° C, and a significant part of INPs-8 is sensitive to warming

  9. Accurate ab initio predictions of ionization energies and heats of formation for the 2-propyl, phenyl, and benzyl radicals

    NASA Astrophysics Data System (ADS)

    Lau, K.-C.; Ng, C. Y.

    2006-01-01

    The ionization energies (IEs) for the 2-propyl (2-C3H7), phenyl (C6H5), and benzyl (C6H5CH2) radicals have been calculated by the wave-function-based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled cluster level with single and double excitations plus quasiperturbative triple excitation [CCSD(T)]. The zero-point vibrational energy correction, the core-valence electronic correction, and the scalar relativistic effect correction have been also made in these calculations. Although a precise IE value for the 2-C3H7 radical has not been directly determined before due to the poor Franck-Condon factor for the photoionization transition at the ionization threshold, the experimental value deduced indirectly using other known energetic data is found to be in good accord with the present CCSD(T)/CBS prediction. The comparison between the predicted value through the focal-point analysis and the highly precise experimental value for the IE(C6H5CH2) determined in the previous pulsed field ionization photoelectron (PFI-PE) study shows that the CCSD(T)/CBS method is capable of providing an accurate IE prediction for C6H5CH2, achieving an error limit of 35 meV. The benchmarking of the CCSD(T)/CBS IE(C6H5CH2) prediction suggests that the CCSD(T)/CBS IE(C6H5) prediction obtained here has a similar accuracy of 35 meV. Taking into account this error limit for the CCSD(T)/CBS prediction and the experimental uncertainty, the CCSD(T)/CBS IE(C6H5) value is also consistent with the IE(C6H5) reported in the previous HeI photoelectron measurement. Furthermore, the present study provides support for the conclusion that the CCSD(T)/CBS approach with high-level energy corrections can be used to provide reliable IE predictions for C3-C7 hydrocarbon radicals with an uncertainty of +/-35 meV. Employing the atomization scheme, we have also computed the 0 K (298 K) heats of formation in kJ/mol at the CCSD(T)/CBS level for 2-C3H7

  10. Application of a High-Fidelity Icing Analysis Method to a Model-Scale Rotor in Forward Flight

    NASA Technical Reports Server (NTRS)

    Narducci, Robert; Orr, Stanley; Kreeger, Richard E.

    2012-01-01

    An icing analysis process involving the loose coupling of OVERFLOW-RCAS for rotor performance prediction and with LEWICE3D for thermal analysis and ice accretion is applied to a model-scale rotor for validation. The process offers high-fidelity rotor analysis for the noniced and iced rotor performance evaluation that accounts for the interaction of nonlinear aerodynamics with blade elastic deformations. Ice accumulation prediction also involves loosely coupled data exchanges between OVERFLOW and LEWICE3D to produce accurate ice shapes. Validation of the process uses data collected in the 1993 icing test involving Sikorsky's Powered Force Model. Non-iced and iced rotor performance predictions are compared to experimental measurements as are predicted ice shapes.

  11. Development, sensitivity analysis, and uncertainty quantification of high-fidelity arctic sea ice models.

    SciTech Connect

    Peterson, Kara J.; Bochev, Pavel Blagoveston; Paskaleva, Biliana S.

    2010-09-01

    Arctic sea ice is an important component of the global climate system and due to feedback effects the Arctic ice cover is changing rapidly. Predictive mathematical models are of paramount importance for accurate estimates of the future ice trajectory. However, the sea ice components of Global Climate Models (GCMs) vary significantly in their prediction of the future state of Arctic sea ice and have generally underestimated the rate of decline in minimum sea ice extent seen over the past thirty years. One of the contributing factors to this variability is the sensitivity of the sea ice to model physical parameters. A new sea ice model that has the potential to improve sea ice predictions incorporates an anisotropic elastic-decohesive rheology and dynamics solved using the material-point method (MPM), which combines Lagrangian particles for advection with a background grid for gradient computations. We evaluate the variability of the Los Alamos National Laboratory CICE code and the MPM sea ice code for a single year simulation of the Arctic basin using consistent ocean and atmospheric forcing. Sensitivities of ice volume, ice area, ice extent, root mean square (RMS) ice speed, central Arctic ice thickness, and central Arctic ice speed with respect to ten different dynamic and thermodynamic parameters are evaluated both individually and in combination using the Design Analysis Kit for Optimization and Terascale Applications (DAKOTA). We find similar responses for the two codes and some interesting seasonal variability in the strength of the parameters on the solution.

  12. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

    PubMed

    Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

    2017-03-31

    One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

  13. More accurate determination of the quantity of ice crystallized at low cooling rates in the glycerol and 1,2-propanediol aqueous solutions: comparison with equilibrium.

    PubMed

    Boutron, P

    1984-04-01

    It is generally assumed that when cells are cooled at rates close to those corresponding to the maximum of survival, once supercooling has ceased, above the eutectic melting temperature the extracellular ice is in equilibrium with the residual solution. This did not seem evident to us due to the difficulty of ice crystallization in cryoprotective solutions. The maximum quantities of ice crystallized in glycerol and 1,2-propanediol solutions have been calculated from the area of the solidification and fusion peaks obtained with a Perkin-Elmer DSC-2 differential scanning calorimeter. The accuracy has been improved by several corrections: better defined baseline, thermal variation of the heat of fusion of the ice, heat of solution of the water from its melting with the residual solution. More ice crystallizes in the glycerol than in the 1,2-propanediol solutions, of which the amorphous residue contains about 40 to 55% 1,2-propanediol. The equilibrium values are unknown in the presence of 1,2-propanediol. With glycerol, in our experiments, the maximum is first lower than the equilibrium but approaches it as the concentration increases. It is not completely determined by the colligative properties of the solutes.

  14. A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Cannon, William R.; Oehmen, Christopher S.; Shah, Anuj R.; Gurumoorthi, Vidhya; Lipton, Mary S.; Waters, Katrina M.

    2008-07-01

    Motivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares these profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (MS/MS) studies. It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic). Results: We present a Support Vector Machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity, and polarity for the quantitative prediction of proteotypic peptides. Using three independently derived AMT databases (Shewanella oneidensis, Salmonella typhimurium, Yersinia pestis) for training and validation within and across species, the SVM resulted in an average accuracy measure of ~0.8 with a standard deviation of less than 0.025. Furthermore, we demonstrate that these results are achievable with a small set of 12 variables and can achieve high proteome coverage. Availability: http://omics.pnl.gov/software/STEPP.php

  15. High IFIT1 expression predicts improved clinical outcome, and IFIT1 along with MGMT more accurately predicts prognosis in newly diagnosed glioblastoma.

    PubMed

    Zhang, Jin-Feng; Chen, Yao; Lin, Guo-Shi; Zhang, Jian-Dong; Tang, Wen-Long; Huang, Jian-Huang; Chen, Jin-Shou; Wang, Xing-Fu; Lin, Zhi-Xiong

    2016-06-01

    Interferon-induced protein with tetratricopeptide repeat 1 (IFIT1) plays a key role in growth suppression and apoptosis promotion in cancer cells. Interferon was reported to induce the expression of IFIT1 and inhibit the expression of O-6-methylguanine-DNA methyltransferase (MGMT).This study aimed to investigate the expression of IFIT1, the correlation between IFIT1 and MGMT, and their impact on the clinical outcome in newly diagnosed glioblastoma. The expression of IFIT1 and MGMT and their correlation were investigated in the tumor tissues from 70 patients with newly diagnosed glioblastoma. The effects on progression-free survival and overall survival were evaluated. Of 70 cases, 57 (81.4%) tissue samples showed high expression of IFIT1 by immunostaining. The χ(2) test indicated that the expression of IFIT1 and MGMT was negatively correlated (r = -0.288, P = .016). Univariate and multivariate analyses confirmed high IFIT1 expression as a favorable prognostic indicator for progression-free survival (P = .005 and .017) and overall survival (P = .001 and .001), respectively. Patients with 2 favorable factors (high IFIT1 and low MGMT) had an improved prognosis as compared with others. The results demonstrated significantly increased expression of IFIT1 in newly diagnosed glioblastoma tissue. The negative correlation between IFIT1 and MGMT expression may be triggered by interferon. High IFIT1 can be a predictive biomarker of favorable clinical outcome, and IFIT1 along with MGMT more accurately predicts prognosis in newly diagnosed glioblastoma.

  16. A time accurate prediction of the viscous flow in a turbine stage including a rotor in motion

    NASA Astrophysics Data System (ADS)

    Shavalikul, Akamol

    accurate flow characteristics in the NGV domain and the rotor domain with less computational time and computer memory requirements. In contrast, the time accurate flow simulation can predict all unsteady flow characteristics occurring in the turbine stage, but with high computational resource requirements. (Abstract shortened by UMI.)

  17. Predicting global atmospheric ice nuclei distributions and their impacts on climate.

    PubMed

    DeMott, P J; Prenni, A J; Liu, X; Kreidenweis, S M; Petters, M D; Twohy, C H; Richardson, M S; Eidhammer, T; Rogers, D C

    2010-06-22

    Knowledge of cloud and precipitation formation processes remains incomplete, yet global precipitation is predominantly produced by clouds containing the ice phase. Ice first forms in clouds warmer than -36 degrees C on particles termed ice nuclei. We combine observations from field studies over a 14-year period, from a variety of locations around the globe, to show that the concentrations of ice nuclei active in mixed-phase cloud conditions can be related to temperature and the number concentrations of particles larger than 0.5 microm in diameter. This new relationship reduces unexplained variability in ice nuclei concentrations at a given temperature from approximately 10(3) to less than a factor of 10, with the remaining variability apparently due to variations in aerosol chemical composition or other factors. When implemented in a global climate model, the new parameterization strongly alters cloud liquid and ice water distributions compared to the simple, temperature-only parameterizations currently widely used. The revised treatment indicates a global net cloud radiative forcing increase of approximately 1 W m(-2) for each order of magnitude increase in ice nuclei concentrations, demonstrating the strong sensitivity of climate simulations to assumptions regarding the initiation of cloud glaciation.

  18. Predicting global atmospheric ice nuclei distributions and their impacts on climate

    PubMed Central

    DeMott, P. J.; Prenni, A. J.; Liu, X.; Kreidenweis, S. M.; Petters, M. D.; Twohy, C. H.; Richardson, M. S.; Eidhammer, T.; Rogers, D. C.

    2010-01-01

    Knowledge of cloud and precipitation formation processes remains incomplete, yet global precipitation is predominantly produced by clouds containing the ice phase. Ice first forms in clouds warmer than -36 °C on particles termed ice nuclei. We combine observations from field studies over a 14-year period, from a variety of locations around the globe, to show that the concentrations of ice nuclei active in mixed-phase cloud conditions can be related to temperature and the number concentrations of particles larger than 0.5 μm in diameter. This new relationship reduces unexplained variability in ice nuclei concentrations at a given temperature from ∼103 to less than a factor of 10, with the remaining variability apparently due to variations in aerosol chemical composition or other factors. When implemented in a global climate model, the new parameterization strongly alters cloud liquid and ice water distributions compared to the simple, temperature-only parameterizations currently widely used. The revised treatment indicates a global net cloud radiative forcing increase of ∼1 W m-2 for each order of magnitude increase in ice nuclei concentrations, demonstrating the strong sensitivity of climate simulations to assumptions regarding the initiation of cloud glaciation. PMID:20534566

  19. Predicting Next Year's Resources--Short-Term Enrollment Forecasting for Accurate Budget Planning. AIR Forum Paper 1978.

    ERIC Educational Resources Information Center

    Salley, Charles D.

    Accurate enrollment forecasts are a prerequisite for reliable budget projections. This is because tuition payments make up a significant portion of a university's revenue, and anticipated revenue is the immediate constraint on current operating expenditures. Accurate forecasts are even more critical to revenue projections when a university's…

  20. Polar predictability: exploring the influence of GCM and regional model uncertainty on future ice sheet climates

    NASA Astrophysics Data System (ADS)

    Reusch, D. B.

    2015-12-01

    Evaluating uncertainty in GCMs and regional-scale forecast models is an essential step in the development of climate change predictions. Polar-region skill is particularly important due to the potential for changes affecting both local (ice sheet) and global (sea level) environments through more frequent/intense surface melting and changes in precipitation type/amount. High-resolution, regional-scale models also use GCMs as a source of boundary/initial conditions in future scenarios, thus inheriting a measure of GCM-derived externally-driven uncertainty. We examine inter- and intramodel uncertainty through statistics from decadal climatologies and analyses of variability based on self-organizing maps (SOMs), a nonlinear data analysis tool. We evaluate a 19-member CMIP5 subset and the 30-member CESM1.0-CAM5-BGC Large Ensemble (CESMLE) during polar melt seasons (boreal/austral summer) for recent (1981-2000) and future (2081-2100, RCP 8.5) decades. Regional-model uncertainty is examined with a subset of these GCMs driving Polar WRF simulations. Decadal climatologies relative to a reference (recent: the ERA-Interim reanalysis; future: a skillful modern GCM) identify model uncertainty in bulk, e.g., BNU-ESM is too warm, CMCC-CM too cold. While quite useful for model screening, diagnostic benefit is often indirect. SOMs extend our diagnostics by providing a concise, objective summary of model variability as a set of generalized patterns. Joint analysis of reference and test models summarizes the variability of multiple realizations of climate (all the models), benchmarks each model versus the reference (frequency analysis helps identify the patterns behind GCM bias), and places each GCM in a common context. Joint SOM analysis of CESMLE members shows how initial conditions contribute to differences in modeled climates, providing useful information about internal variability, such as contributions from each member to overall uncertainty using pattern frequencies. In the

  1. From Ponds to Predictions: What Do We Need to Know About Small-Scale Sea Ice Processes in a Rapidly Changing Arctic?

    NASA Astrophysics Data System (ADS)

    Eicken, H.; Petrich, C.

    2014-12-01

    Areal coverage and spatial distribution of sea-ice melt ponds are key factors in determining the response of the Arctic Ocean's ice cover to changes in atmospheric forcing, its importance in enhancing high-latitude warming and its function in polar marine ecosystems. A review of remote-sensing and field observations, in conjunction with process studies in coastal Alaska, highlights the importance of sub-floe scale ice properties and processes in controlling ponding, thereby constraining seasonal evolution and decay of the ice cover. Field observations and model simulations have shown how pond areal extent and hence ice albedo depend on the combination of snow or ice ablation rates, ice permeability and surface topography. Seasonal and short-term variations of these three factors explain much of the observed spatial and temporal variability in the large-scale pond areal fraction. Recent work on Alaska shorefast ice suggests that the snow-cover depth distribution may predetermine ponding patterns months ahead of spring melt. Specifically, through the formation of wind crusts, snow depth variations are locked in place. After onset of melt, formation and deepening of ponds is enhanced in thin-snow areas, with pond spatial patterns replicating snow dune topography. Both deepening of ponds and preferential pond drainage through small-scale flaws and cracks then constrain the eventual break-up of the ice cover. Field observations and aerial photography indicate that with increasing wave action in an ice-diminished Arctic Ocean, ponds and drainage features precondition ice for break-up and fragmentation. Model simulations by Schröder et al. (doi:10.1038/nclimate2203) hint at other, as of yet poorly understood mechanisms that link pond coverage to the degree of seasonal ice retreat. Key measurements and potential datasets that can help improve understanding and prediction of a changing ice cover on seasonal scales will be discussed.

  2. Comparison of Aircraft Icing Growth Assessment Software

    NASA Technical Reports Server (NTRS)

    Wright, William; Potapczuk, Mark G.; Levinson, Laurie H.

    2011-01-01

    A research project is underway to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. An extensive comparison of the results in a quantifiable manner against the database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has been performed, including additional data taken to extend the database in the Super-cooled Large Drop (SLD) regime. The project shows the differences in ice shape between LEWICE 3.2.2, GlennICE, and experimental data. The project addresses the validation of the software against a recent set of ice-shape data in the SLD regime. This validation effort mirrors a similar effort undertaken for previous validations of LEWICE. Those reports quantified the ice accretion prediction capabilities of the LEWICE software. Several ice geometry features were proposed for comparing ice shapes in a quantitative manner. The resulting analysis showed that LEWICE compared well to the available experimental data.

  3. Population Synthesis in the Blue. IV. Accurate Model Predictions for Lick Indices and UBV Colors in Single Stellar Populations

    NASA Astrophysics Data System (ADS)

    Schiavon, Ricardo P.

    2007-07-01

    We present a new set of model predictions for 16 Lick absorption line indices from Hδ through Fe5335 and UBV colors for single stellar populations with ages ranging between 1 and 15 Gyr, [Fe/H] ranging from -1.3 to +0.3, and variable abundance ratios. The models are based on accurate stellar parameters for the Jones library stars and a new set of fitting functions describing the behavior of line indices as a function of effective temperature, surface gravity, and iron abundance. The abundances of several key elements in the library stars have been obtained from the literature in order to characterize the abundance pattern of the stellar library, thus allowing us to produce model predictions for any set of abundance ratios desired. We develop a method to estimate mean ages and abundances of iron, carbon, nitrogen, magnesium, and calcium that explores the sensitivity of the various indices modeled to those parameters. The models are compared to high-S/N data for Galactic clusters spanning the range of ages, metallicities, and abundance patterns of interest. Essentially all line indices are matched when the known cluster parameters are adopted as input. Comparing the models to high-quality data for galaxies in the nearby universe, we reproduce previous results regarding the enhancement of light elements and the spread in the mean luminosity-weighted ages of early-type galaxies. When the results from the analysis of blue and red indices are contrasted, we find good consistency in the [Fe/H] that is inferred from different Fe indices. Applying our method to estimate mean ages and abundances from stacked SDSS spectra of early-type galaxies brighter than L*, we find mean luminosity-weighed ages of the order of ~8 Gyr and iron abundances slightly below solar. Abundance ratios, [X/Fe], tend to be higher than solar and are positively correlated with galaxy luminosity. Of all elements, nitrogen is the more strongly correlated with galaxy luminosity, which seems to indicate

  4. Do Skilled Elementary Teachers Hold Scientific Conceptions and Can They Accurately Predict the Type and Source of Students' Preconceptions of Electric Circuits?

    ERIC Educational Resources Information Center

    Lin, Jing-Wen

    2016-01-01

    Holding scientific conceptions and having the ability to accurately predict students' preconceptions are a prerequisite for science teachers to design appropriate constructivist-oriented learning experiences. This study explored the types and sources of students' preconceptions of electric circuits. First, 438 grade 3 (9 years old) students were…

  5. Ceres: predictions for near-surface water ice stability and implications for plume generating processes

    USGS Publications Warehouse

    Titus, Timothy N.

    2015-01-01

    This paper will constrain the possible sources and processes for the formation of recently observed H2O vapor plumes above the surface of the dwarf planet Ceres. Two hypotheses have been proposed: (1) cryovolcanism where the water source is the mantle and the heating source is still unknown or (2) comet-like sublimation where near-surface water ice is vaporized by seasonally increasing solar insolation. We test hypothesis #2, comet-like near-surface sublimation, by using a thermal model to examine the stability of water-ice in the near surface. For a reasonable range of physical parameters (thermal inertia, surface roughness, slopes), we find that water ice is only stable at latitudes higher than ~40-60 degrees. These results indicate that either (a) the physical properties of Ceres are unlike our expectations or (b) an alternative to comet-like sublimation, such as the cryovolcanism hypothesis, must be invoked.

  6. Predictions of vertical uplift caused by changing polar ice volumes on a viscoelastic earth

    NASA Technical Reports Server (NTRS)

    Wahr, John; Dazhong, Han; Trupin, Andrew

    1995-01-01

    Measurements of crustal uplift from bedrock around the edges of Antarctica or Greenland could help constrain the mass balance of those ice caps. Present-day changes in ice could cause vertical displacement rates of several mm/yr around Antarctica and up to 10-15 mm/yr around Greenland. Horizontal displacement rates are likely to be about 1/3 the vertical rates. The viscoelastic response of the earth to past changes in ice could cause uplift rates that are several times larger. By measuring both gravity and vertical displacements, it is possible to remove the viscoelastic effects, so that the observations can be used to constrain present-day thickness changes.

  7. Collaborative Project. Understanding the effects of tides and eddies on the ocean dynamics, sea ice cover and decadal/centennial climate prediction using the Regional Arctic Climate Model (RACM)

    SciTech Connect

    Hutchings, Jennifer; Joseph, Renu

    2013-09-14

    The goal of this project is to develop an eddy resolving ocean model (POP) with tides coupled to a sea ice model (CICE) within the Regional Arctic System Model (RASM) to investigate the importance of ocean tides and mesoscale eddies in arctic climate simulations and quantify biases associated with these processes and how their relative contribution may improve decadal to centennial arctic climate predictions. Ocean, sea ice and coupled arctic climate response to these small scale processes will be evaluated with regard to their influence on mass, momentum and property exchange between oceans, shelf-basin, ice-ocean, and ocean-atmosphere. The project will facilitate the future routine inclusion of polar tides and eddies in Earth System Models when computing power allows. As such, the proposed research addresses the science in support of the BER’s Climate and Environmental Sciences Division Long Term Measure as it will improve the ocean and sea ice model components as well as the fully coupled RASM and Community Earth System Model (CESM) and it will make them more accurate and computationally efficient.

  8. Towards Improving Sea Ice Predictabiity: Evaluating Climate Models Against Satellite Sea Ice Observations

    NASA Astrophysics Data System (ADS)

    Stroeve, J. C.

    2014-12-01

    September sea ice extent is near the long-term trend, contributions tend to be accurate. Years when the observed extent departs from the trend have proven harder to predict. Predictability skill does not appear to be more accurate for dynamical models over statistical ones, nor is there a measurable improvement in skill as the summer progresses.

  9. Radar Differential Phase Signatures of Ice Orientation for the Prediction of Lightning Initiation and Cessation

    NASA Technical Reports Server (NTRS)

    Carey, L.D.; Petersen, W.A.; Deierling, W.

    2009-01-01

    The majority of lightning-related casualties typically occur during thunderstorm initiation (e.g., first flash) or dissipation (e.g., last flash). The physics of electrification and lightning production during thunderstorm initiation is fairly well understood. As such, the literature includes a number of studies presenting various radar techniques (using reflectivity and, if available, other dual-polarimetric parameters) for the anticipation of initial electrification and first lightning flash. These radar techniques have shown considerable skill at forecasting first flash. On the other hand, electrical processes and lightning production during thunderstorm dissipation are not nearly as well understood and few, if any, successful techniques have been developed to anticipate the last flash and subsequent cessation of lightning. One promising approach involves the use of dual-polarimetric radar variables to infer the presence of oriented ice crystals in lightning producing storms. In the absence of strong vertical electric fields, ice crystals fall with their largest (semi-major) axis in the horizontal associated with gravitational and aerodynamic forces. In thunderstorms, strong vertical electric fields (100-200 kV m(sup -1)) have been shown to orient small (less than 2 mm) ice crystals such that their semi-major axis is vertical (or nearly vertical). After a lightning flash, the electric field is typically relaxed and prior radar research suggests that ice crystals rapidly resume their preferred horizontal orientation. In active thunderstorms, the vertical electric field quickly recovers and the ice crystals repeat this cycle of orientation for each nearby flash. This change in ice crystal orientation from primarily horizontal to vertical during the development of strong vertical electric fields prior to a lightning flash forms the physical basis for anticipating lightning initiation and, potentially, cessation. Research has shown that radar reflectivity (Z) and

  10. Acute toxicity prediction to threatened and endangered species using Interspecies Correlation Estimation (ICE) models

    EPA Science Inventory

    Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA’s Internet application Web-ICE is a suite of Interspecies Correlati...

  11. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

  12. Accurate and computationally efficient prediction of thermochemical properties of biomolecules using the generalized connectivity-based hierarchy.

    PubMed

    Sengupta, Arkajyoti; Ramabhadran, Raghunath O; Raghavachari, Krishnan

    2014-08-14

    In this study we have used the connectivity-based hierarchy (CBH) method to derive accurate heats of formation of a range of biomolecules, 18 amino acids and 10 barbituric acid/uracil derivatives. The hierarchy is based on the connectivity of the different atoms in a large molecule. It results in error-cancellation reaction schemes that are automated, general, and can be readily used for a broad range of organic molecules and biomolecules. Herein, we first locate stable conformational and tautomeric forms of these biomolecules using an accurate level of theory (viz. CCSD(T)/6-311++G(3df,2p)). Subsequently, the heats of formation of the amino acids are evaluated using the CBH-1 and CBH-2 schemes and routinely employed density functionals or wave function-based methods. The calculated heats of formation obtained herein using modest levels of theory and are in very good agreement with those obtained using more expensive W1-F12 and W2-F12 methods on amino acids and G3 results on barbituric acid derivatives. Overall, the present study (a) highlights the small effect of including multiple conformers in determining the heats of formation of biomolecules and (b) in concurrence with previous CBH studies, proves that use of the more effective error-cancelling isoatomic scheme (CBH-2) results in more accurate heats of formation with modestly sized basis sets along with common density functionals or wave function-based methods.

  13. Predicting abundance and variability of ice nucleating particles in precipitation at the high-altitude observatory Jungfraujoch

    NASA Astrophysics Data System (ADS)

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E.; Herrmann, Erik; Henne, Stephan; Steinbacher, Martin; Alewell, Christine

    2016-07-01

    Nucleation of ice affects the properties of clouds and the formation of precipitation. Quantitative data on how ice nucleating particles (INPs) determine the distribution, occurrence and intensity of precipitation are still scarce. INPs active at -8 °C (INPs-8) were observed for 2 years in precipitation samples at the High-Altitude Research Station Jungfraujoch (Switzerland) at 3580 m a.s.l. Several environmental parameters were scanned for their capability to predict the observed abundance and variability of INPs-8. Those singularly presenting the best correlations with observed number of INPs-8 (residual fraction of water vapour, wind speed, air temperature, number of particles with diameter larger than 0.5 µm, season, and source region of particles) were implemented as potential predictor variables in statistical multiple linear regression models. These models were calibrated with 84 precipitation samples collected during the first year of observations; their predictive power was successively validated on the set of 15 precipitation samples collected during the second year. The model performing best in calibration and validation explains more than 75 % of the whole variability of INPs-8 in precipitation and indicates that a high abundance of INPs-8 is to be expected whenever high wind speed coincides with air masses having experienced little or no precipitation prior to sampling. Such conditions occur during frontal passages, often accompanied by precipitation. Therefore, the circumstances when INPs-8 could be sufficiently abundant to initiate the ice phase in clouds may frequently coincide with meteorological conditions favourable to the onset of precipitation events.

  14. False alarms: How early warning signals falsely predict abrupt sea ice loss

    NASA Astrophysics Data System (ADS)

    Wagner, Till J. W.; Eisenman, Ian

    2015-12-01

    Uncovering universal early warning signals for critical transitions has become a coveted goal in diverse scientific disciplines, ranging from climate science to financial mathematics. There has been a flurry of recent research proposing such signals, with increasing autocorrelation and increasing variance being among the most widely discussed candidates. A number of studies have suggested that increasing autocorrelation alone may suffice to signal an impending transition, although some others have questioned this. Here we consider variance and autocorrelation in the context of sea ice loss in an idealized model of the global climate system. The model features no bifurcation, nor increased rate of retreat, as the ice disappears. Nonetheless, the autocorrelation of summer sea ice area is found to increase in a global warming scenario. The variance, by contrast, decreases. A simple physical mechanism is proposed to explain the occurrence of increasing autocorrelation but not variance when there is no approaching bifurcation. Additionally, a similar mechanism is shown to allow an increase in both indicators with no physically attainable bifurcation. This implies that relying on autocorrelation and variance as early warning signals can raise false alarms in the climate system, warning of "tipping points" that are not actually there.

  15. Can the conventional sextant prostate biopsy accurately predict unilateral prostate cancer in low-risk, localized, prostate cancer?

    PubMed

    Mayes, Janice M; Mouraviev, Vladimir; Sun, Leon; Tsivian, Matvey; Madden, John F; Polascik, Thomas J

    2011-01-01

    We evaluate the reliability of routine sextant prostate biopsy to detect unilateral lesions. A total of 365 men with complete records including all clinical and pathologic variables who underwent a preoperative sextant biopsy and subsequent radical prostatectomy (RP) for clinically localized prostate cancer at our medical center between January 1996 and December 2006 were identified. When the sextant biopsy detects unilateral disease, according to RP results, the NPV is high (91%) with a low false negative rate (9%). However, the sextant biopsy has a PPV of 28% with a high false positive rate (72%). Therefore, a routine sextant prostate biopsy cannot provide reliable, accurate information about the unilaterality of tumor lesion(s).

  16. Modern Airfoil Ice Accretions

    NASA Technical Reports Server (NTRS)

    Addy, Harold E., Jr.; Potapczuk, Mark G.; Sheldon, David W.

    1997-01-01

    This report presents results from the first icing tests performed in the Modem Airfoils program. Two airfoils have been subjected to icing tests in the NASA Lewis Icing Research Tunnel (IRT). Both airfoils were two dimensional airfoils; one was representative of a commercial transport airfoil while the other was representative of a business jet airfoil. The icing test conditions were selected from the FAR Appendix C envelopes. Effects on aerodynamic performance are presented including the effects of varying amounts of glaze ice as well as the effects of approximately the same amounts of glaze, mixed, and rime ice. Actual ice shapes obtained in these tests are also presented for these cases. In addition, comparisons are shown between ice shapes from the tests and ice shapes predicted by the computer code, LEWICE for similar conditions. Significant results from the tests are that relatively small amounts of ice can have nearly as much effect on airfoil lift coefficient as much greater amounts of ice and that glaze ice usually has a more detrimental effect than either rime or mixed ice. LEWICE predictions of ice shapes, in general, compared reasonably well with ice shapes obtained in the IRT, although differences in details of the ice shapes were observed.

  17. Is Demography Destiny? Application of Machine Learning Techniques to Accurately Predict Population Health Outcomes from a Minimal Demographic Dataset

    PubMed Central

    Luo, Wei; Nguyen, Thin; Nichols, Melanie; Tran, Truyen; Rana, Santu; Gupta, Sunil; Phung, Dinh; Venkatesh, Svetha; Allender, Steve

    2015-01-01

    For years, we have relied on population surveys to keep track of regional public health statistics, including the prevalence of non-communicable diseases. Because of the cost and limitations of such surveys, we often do not have the up-to-date data on health outcomes of a region. In this paper, we examined the feasibility of inferring regional health outcomes from socio-demographic data that are widely available and timely updated through national censuses and community surveys. Using data for 50 American states (excluding Washington DC) from 2007 to 2012, we constructed a machine-learning model to predict the prevalence of six non-communicable disease (NCD) outcomes (four NCDs and two major clinical risk factors), based on population socio-demographic characteristics from the American Community Survey. We found that regional prevalence estimates for non-communicable diseases can be reasonably predicted. The predictions were highly correlated with the observed data, in both the states included in the derivation model (median correlation 0.88) and those excluded from the development for use as a completely separated validation sample (median correlation 0.85), demonstrating that the model had sufficient external validity to make good predictions, based on demographics alone, for areas not included in the model development. This highlights both the utility of this sophisticated approach to model development, and the vital importance of simple socio-demographic characteristics as both indicators and determinants of chronic disease. PMID:25938675

  18. Is demography destiny? Application of machine learning techniques to accurately predict population health outcomes from a minimal demographic dataset.

    PubMed

    Luo, Wei; Nguyen, Thin; Nichols, Melanie; Tran, Truyen; Rana, Santu; Gupta, Sunil; Phung, Dinh; Venkatesh, Svetha; Allender, Steve

    2015-01-01

    For years, we have relied on population surveys to keep track of regional public health statistics, including the prevalence of non-communicable diseases. Because of the cost and limitations of such surveys, we often do not have the up-to-date data on health outcomes of a region. In this paper, we examined the feasibility of inferring regional health outcomes from socio-demographic data that are widely available and timely updated through national censuses and community surveys. Using data for 50 American states (excluding Washington DC) from 2007 to 2012, we constructed a machine-learning model to predict the prevalence of six non-communicable disease (NCD) outcomes (four NCDs and two major clinical risk factors), based on population socio-demographic characteristics from the American Community Survey. We found that regional prevalence estimates for non-communicable diseases can be reasonably predicted. The predictions were highly correlated with the observed data, in both the states included in the derivation model (median correlation 0.88) and those excluded from the development for use as a completely separated validation sample (median correlation 0.85), demonstrating that the model had sufficient external validity to make good predictions, based on demographics alone, for areas not included in the model development. This highlights both the utility of this sophisticated approach to model development, and the vital importance of simple socio-demographic characteristics as both indicators and determinants of chronic disease.

  19. A Maximal Graded Exercise Test to Accurately Predict VO2max in 18-65-Year-Old Adults

    ERIC Educational Resources Information Center

    George, James D.; Bradshaw, Danielle I.; Hyde, Annette; Vehrs, Pat R.; Hager, Ronald L.; Yanowitz, Frank G.

    2007-01-01

    The purpose of this study was to develop an age-generalized regression model to predict maximal oxygen uptake (VO sub 2 max) based on a maximal treadmill graded exercise test (GXT; George, 1996). Participants (N = 100), ages 18-65 years, reached a maximal level of exertion (mean plus or minus standard deviation [SD]; maximal heart rate [HR sub…

  20. Accurate Prediction of Protein Functional Class From Sequence in the Mycobacterium Tuberculosis and Escherichia Coli Genomes Using Data Mining

    PubMed Central

    Karwath, Andreas; Clare, Amanda; Dehaspe, Luc

    2000-01-01

    The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli. PMID:11119305

  1. Herbivore-induced plant volatiles accurately predict history of coexistence, diet breadth, and feeding mode of herbivores.

    PubMed

    Danner, Holger; Desurmont, Gaylord A; Cristescu, Simona M; van Dam, Nicole M

    2017-01-30

    Herbivore-induced plant volatiles (HIPVs) serve as specific cues to higher trophic levels. Novel, exotic herbivores entering native foodwebs may disrupt the infochemical network as a result of changes in HIPV profiles. Here, we analysed HIPV blends of native Brassica rapa plants infested with one of 10 herbivore species with different coexistence histories, diet breadths and feeding modes. Partial least squares (PLS) models were fitted to assess whether HIPV blends emitted by Dutch B. rapa differ between native and exotic herbivores, between specialists and generalists, and between piercing-sucking and chewing herbivores. These models were used to predict the status of two additional herbivores. We found that HIPV blends predicted the evolutionary history, diet breadth and feeding mode of the herbivore with an accuracy of 80% or higher. Based on the HIPVs, the PLS models reliably predicted that Trichoplusia ni and Spodoptera exigua are perceived as exotic, leaf-chewing generalists by Dutch B. rapa plants. These results indicate that there are consistent and predictable differences in HIPV blends depending on global herbivore characteristics, including coexistence history. Consequently, native organisms may be able to rapidly adapt to potentially disruptive effects of exotic herbivores on the infochemical network.

  2. Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

    PubMed Central

    Gusenleitner, Daniel; Auerbach, Scott S.; Melia, Tisha; Gómez, Harold F.; Sherr, David H.; Monti, Stefano

    2014-01-01

    Background Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. Results In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. Conclusion Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure. PMID:25058030

  3. A predictive model for routing of supraglacial meltwater to the bed of glaciers: application to Leverett Glacier, western Greenland Ice Sheet

    NASA Astrophysics Data System (ADS)

    Clason, Caroline; Mair, Douglas; Nienow, Peter

    2010-05-01

    Recent studies have shown that Greenland outlet glacier velocities may be responding to increased meltwater generation (Shepherd et al, 2009; Zwally et al, 2002). Where sufficient supraglacial meltwater is routed into crevasses and moulins it could act to lubricate the bed, resulting in dynamic thinning and accelerated transfer of ice mass to glacier termini. The extent to which this mechanism contributes to mass loss is largely unknown, but may be increasingly important if current trends of warming are to continue, particularly in high northerly latitudes. This study introduces a modelling routine for prediction of moulin formation and quantification of meltwater delivery to the bed from digital elevation models, ice surface velocity data and meteorological input data. Supraglacial meltwater pathways are predicted from ice surface topography using a single flow direction hydrological flow routing algorithm. A temperature-index model driven by measured air temperature is used to produce values of distributed ice surface melt, integrated within stream accumulation to produce estimates of supraglacial stream discharge throughout the predicted network. Ice surface strain rates are calculated from satellite-derived surface velocities acquired using feature tracking. Strain rates are converted to stresses through the constitutive relation for glacier ice, after Nye (1957). Surface tensile stresses are calculated from the resultant principal stresses using the Von Mises criteria for failure of ductile materials, with areas of crevassing predicted where tensile stresses exceed a prescribed value of fracture toughness. Where supraglacial streams and areas of crevassing intersect, surficial moulin locations are predicted. A simple model for propagation of water-filled crevasses is applied to determine where moulins will penetrate through the full ice thickness, delivering meltwater to the bed. Derived from linear elastic fracture mechanics, the model calculates crevasse

  4. Accurate and efficient prediction of fine-resolution hydrologic and carbon dynamic simulations from coarse-resolution models

    NASA Astrophysics Data System (ADS)

    Pau, George Shu Heng; Shen, Chaopeng; Riley, William J.; Liu, Yaning

    2016-02-01

    The topography, and the biotic and abiotic parameters are typically upscaled to make watershed-scale hydrologic-biogeochemical models computationally tractable. However, upscaling procedure can produce biases when nonlinear interactions between different processes are not fully captured at coarse resolutions. Here we applied the Proper Orthogonal Decomposition Mapping Method (PODMM) to downscale the field solutions from a coarse (7 km) resolution grid to a fine (220 m) resolution grid. PODMM trains a reduced-order model (ROM) with coarse-resolution and fine-resolution solutions, here obtained using PAWS+CLM, a quasi-3-D watershed processes model that has been validated for many temperate watersheds. Subsequent fine-resolution solutions were approximated based only on coarse-resolution solutions and the ROM. The approximation errors were efficiently quantified using an error estimator. By jointly estimating correlated variables and temporally varying the ROM parameters, we further reduced the approximation errors by up to 20%. We also improved the method's robustness by constructing multiple ROMs using different set of variables, and selecting the best approximation based on the error estimator. The ROMs produced accurate downscaling of soil moisture, latent heat flux, and net primary production with O(1000) reduction in computational cost. The subgrid distributions were also nearly indistinguishable from the ones obtained using the fine-resolution model. Compared to coarse-resolution solutions, biases in upscaled ROM solutions were reduced by up to 80%. This method has the potential to help address the long-standing spatial scaling problem in hydrology and enable long-time integration, parameter estimation, and stochastic uncertainty analysis while accurately representing the heterogeneities.

  5. How accurately can subject-specific finite element models predict strains and strength of human femora? Investigation using full-field measurements.

    PubMed

    Grassi, Lorenzo; Väänänen, Sami P; Ristinmaa, Matti; Jurvelin, Jukka S; Isaksson, Hanna

    2016-03-21

    Subject-specific finite element models have been proposed as a tool to improve fracture risk assessment in individuals. A thorough laboratory validation against experimental data is required before introducing such models in clinical practice. Results from digital image correlation can provide full-field strain distribution over the specimen surface during in vitro test, instead of at a few pre-defined locations as with strain gauges. The aim of this study was to validate finite element models of human femora against experimental data from three cadaver femora, both in terms of femoral strength and of the full-field strain distribution collected with digital image correlation. The results showed a high accuracy between predicted and measured principal strains (R(2)=0.93, RMSE=10%, 1600 validated data points per specimen). Femoral strength was predicted using a rate dependent material model with specific strain limit values for yield and failure. This provided an accurate prediction (<2% error) for two out of three specimens. In the third specimen, an accidental change in the boundary conditions occurred during the experiment, which compromised the femoral strength validation. The achieved strain accuracy was comparable to that obtained in state-of-the-art studies which validated their prediction accuracy against 10-16 strain gauge measurements. Fracture force was accurately predicted, with the predicted failure location being very close to the experimental fracture rim. Despite the low sample size and the single loading condition tested, the present combined numerical-experimental method showed that finite element models can predict femoral strength by providing a thorough description of the local bone mechanical response.

  6. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

    PubMed Central

    2014-01-01

    Background Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. Results SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. Conclusions SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/. PMID:24980894

  7. Accurate prediction of the electronic properties of low-dimensional graphene derivatives using a screened hybrid density functional.

    PubMed

    Barone, Veronica; Hod, Oded; Peralta, Juan E; Scuseria, Gustavo E

    2011-04-19

    Over the last several years, low-dimensional graphene derivatives, such as carbon nanotubes and graphene nanoribbons, have played a central role in the pursuit of a plausible carbon-based nanotechnology. Their electronic properties can be either metallic or semiconducting depending purely on morphology, but predicting their electronic behavior has proven challenging. The combination of experimental efforts with modeling of these nanometer-scale structures has been instrumental in gaining insight into their physical and chemical properties and the processes involved at these scales. Particularly, approximations based on density functional theory have emerged as a successful computational tool for predicting the electronic structure of these materials. In this Account, we review our efforts in modeling graphitic nanostructures from first principles with hybrid density functionals, namely the Heyd-Scuseria-Ernzerhof (HSE) screened exchange hybrid and the hybrid meta-generalized functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh). These functionals provide a powerful tool for quantitatively studying structure-property relations and the effects of external perturbations such as chemical substitutions, electric and magnetic fields, and mechanical deformations on the electronic and magnetic properties of these low-dimensional carbon materials. We show how HSE and TPSSh successfully predict the electronic properties of these materials, providing a good description of their band structure and density of states, their work function, and their magnetic ordering in the cases in which magnetism arises. Moreover, these approximations are capable of successfully predicting optical transitions (first and higher order) in both metallic and semiconducting single-walled carbon nanotubes of various chiralities and diameters with impressive accuracy. This versatility includes the correct prediction of the trigonal warping splitting in metallic nanotubes. The results predicted

  8. An Electroacoustic Hearing Protector Simulator That Accurately Predicts Pressure Levels in the Ear Based on Standard Performance Metrics

    DTIC Science & Technology

    2013-08-01

    24 Figure 20. ABQ experiment showing five volunteers located 1.0 m from source in upper-left panel wearing...study (Royster et al.,1996) in which users self-fit hearing protectors (ANSI S12.6- 2008 method B: user fit) with no experimenter instruction gives an...values provided by the experimenters and simulator fits for the intact and modified muffs. Figure 22 (upper panel) shows the simulator prediction

  9. Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock

    NASA Astrophysics Data System (ADS)

    Cleves, Ann E.; Jain, Ajay N.

    2015-06-01

    Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided docking protocol was tested on a set of ten protein targets using a total of 949 ligands. The benchmark data set, called PINC ("PINC Is Not Cognate"), is publicly available. Protein pocket similarity was used to choose representative structures for ensemble-docking. The docking protocol made use of known ligand poses prior to the cutoff-date, both to help guide the configurational search and to adjust the rank of predicted poses. Overall, the top-scoring pose family was correct over 60 % of the time, with the top-two pose families approaching a 75 % success rate. Correct poses among all those predicted were identified nearly 90 % of the time. The largest improvements came from the use of molecular similarity to improve ligand pose rankings and the strategy for identifying representative protein structures. With the exception of a single outlier target, the knowledge-guided docking protocol produced results matching the quality of cognate-ligand re-docking, but it did so on a very challenging temporally-segregated cross-docking benchmark.

  10. Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.

    PubMed

    Cleves, Ann E; Jain, Ajay N

    2015-06-01

    Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided docking protocol was tested on a set of ten protein targets using a total of 949 ligands. The benchmark data set, called PINC ("PINC Is Not Cognate"), is publicly available. Protein pocket similarity was used to choose representative structures for ensemble-docking. The docking protocol made use of known ligand poses prior to the cutoff-date, both to help guide the configurational search and to adjust the rank of predicted poses. Overall, the top-scoring pose family was correct over 60 % of the time, with the top-two pose families approaching a 75 % success rate. Correct poses among all those predicted were identified nearly 90 % of the time. The largest improvements came from the use of molecular similarity to improve ligand pose rankings and the strategy for identifying representative protein structures. With the exception of a single outlier target, the knowledge-guided docking protocol produced results matching the quality of cognate-ligand re-docking, but it did so on a very challenging temporally-segregated cross-docking benchmark.

  11. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing

    PubMed Central

    Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing. PMID:27441628

  12. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

    PubMed

    Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea

    2014-01-01

    In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.

  13. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  14. How many clinic BP readings are needed to predict cardiovascular events as accurately as ambulatory BP monitoring?

    PubMed

    Eguchi, K; Hoshide, S; Shimada, K; Kario, K

    2014-12-01

    We tested the hypothesis that multiple clinic blood pressure (BP) readings over an extended baseline period would be as predictive as ambulatory BP (ABP) for cardiovascular disease (CVD). Clinic and ABP monitoring were performed in 457 hypertensive patients at baseline. Clinic BP was measured monthly and the means of the first 3, 5 and 10 clinic BP readings were taken as the multiple clinic BP readings. The subjects were followed up, and stroke, HARD CVD, and ALL CVD events were determined as outcomes. In multivariate Cox regression analyses, ambulatory systolic BP (SBP) best predicted three outcomes independently of baseline and multiple clinic SBP readings. The mean of 10 clinic SBP readings predicted stroke (hazards ratio (HR)=1.39, 95% confidence interval (CI)=1.02-1.90, P=0.04) and ALL CVD (HR=1.41, 95% CI=1.13-1.74, P=0.002) independently of baseline clinic SBP. Clinic SBPs by three and five readings were not associated with any CVD events, except that clinic SBP by three readings was associated with ALL CVD (P=0.015). Besides ABP values, the mean of the first 10 clinic SBP values was a significant predictor of stroke and ALL CVD events. It is important to take more than several clinic BP readings early after the baseline period for the risk stratification of future CVD events.

  15. Dual X-ray absorptiometry accurately predicts carcass composition from live sheep and chemical composition of live and dead sheep.

    PubMed

    Pearce, K L; Ferguson, M; Gardner, G; Smith, N; Greef, J; Pethick, D W

    2009-01-01

    Fifty merino wethers (liveweight range from 44 to 81kg, average of 58.6kg) were lot fed for 42d and scanned through a dual X-ray absorptiometry (DXA) as both a live animal and whole carcass (carcass weight range from 15 to 32kg, average of 22.9kg) producing measures of total tissue, lean, fat and bone content. The carcasses were subsequently boned out into saleable cuts and the weights and yield of boned out muscle, fat and bone recorded. The relationship between chemical lean (protein+water) was highly correlated with DXA carcass lean (r(2)=0.90, RSD=0.674kg) and moderately with DXA live lean (r(2)=0.72, RSD=1.05kg). The relationship between the chemical fat was moderately correlated with DXA carcass fat (r(2)=0.86, RSD=0.42kg) and DXA live fat (r(2)=0.70, RSD=0.71kg). DXA carcass and live animal bone was not well correlated with chemical ash (both r(2)=0.38, RSD=0.3). DXA carcass lean was moderately well predicted from DXA live lean with the inclusion of bodyweight in the regression (r(2)=0.82, RSD=0.87kg). DXA carcass fat was well predicted from DXA live fat (r(2)=0.86, RSD=0.54kg). DXA carcass lean and DXA carcass fat with the inclusion of carcass weight in the regression significantly predicted boned out muscle (r(2)=0.97, RSD=0.32kg) and fat weight, respectively (r(2)=0.92, RSD=0.34kg). The use of DXA live lean and DXA live fat with the inclusion of bodyweight to predict boned out muscle (r(2)=0.83, RSD=0.75kg) and fat (r(2)=0.86, RSD=0.46kg) weight, respectively, was moderate. The use of DXA carcass and live lean and fat to predict boned out muscle and fat yield was not correlated as weight. The future for the DXA will exist in the determination of body composition in live animals and carcasses in research experiments but there is potential for the DXA to be used as an online carcass grading system.

  16. Ice core and climate reanalysis analogs to predict Antarctic and Southern Hemisphere climate changes

    NASA Astrophysics Data System (ADS)

    Mayewski, P. A.; Carleton, A. M.; Birkel, S. D.; Dixon, D.; Kurbatov, A. V.; Korotkikh, E.; McConnell, J.; Curran, M.; Cole-Dai, J.; Jiang, S.; Plummer, C.; Vance, T.; Maasch, K. A.; Sneed, S. B.; Handley, M.

    2017-01-01

    A primary goal of the SCAR (Scientific Committee for Antarctic Research) initiated AntClim21 (Antarctic Climate in the 21st Century) Scientific Research Programme is to develop analogs for understanding past, present and future climates for the Antarctic and Southern Hemisphere. In this contribution to AntClim21 we provide a framework for achieving this goal that includes: a description of basic climate parameters; comparison of existing climate reanalyses; and ice core sodium records as proxies for the frequencies of marine air mass intrusion spanning the past ∼2000 years. The resulting analog examples include: natural variability, a continuation of the current trend in Antarctic and Southern Ocean climate characterized by some regions of warming and some cooling at the surface of the Southern Ocean, Antarctic ozone healing, a generally warming climate and separate increases in the meridional and zonal winds. We emphasize changes in atmospheric circulation because the atmosphere rapidly transports heat, moisture, momentum, and pollutants, throughout the middle to high latitudes. In addition, atmospheric circulation interacts with temporal variations (synoptic to monthly scales, inter-annual, decadal, etc.) of sea ice extent and concentration. We also investigate associations between Antarctic atmospheric circulation features, notably the Amundsen Sea Low (ASL), and primary climate teleconnections including the SAM (Southern Annular Mode), ENSO (El Nîno Southern Oscillation), the Pacific Decadal Oscillation (PDO), the AMO (Atlantic Multidecadal Oscillation), and solar irradiance variations.

  17. Shallow ice approximation, second order shallow ice approximation, and full Stokes models: A discussion of their roles in palaeo-ice sheet modelling and development

    NASA Astrophysics Data System (ADS)

    Kirchner, N.; Ahlkrona, J.; Gowan, E. J.; Lötstedt, P.; Lea, J. M.; Noormets, R.; von Sydow, L.; Dowdeswell, J. A.; Benham, T.

    2016-09-01

    Full Stokes ice sheet models provide the most accurate description of ice sheet flow, and can therefore be used to reduce existing uncertainties in predicting the contribution of ice sheets to future sea level rise on centennial time-scales. The level of accuracy at which millennial time-scale palaeo-ice sheet simulations resolve ice sheet flow lags the standards set by Full Stokes models, especially, when Shallow Ice Approximation (SIA) models are used. Most models used in paleo-ice sheet modeling were developed at a time when computer power was very limited, and rely on several assumptions. At the time there was no means of verifying the assumptions by other than mathematical arguments. However, with the computer power and refined Full Stokes models available today, it is possible to test these assumptions numerically. In this paper, we review (Ahlkrona et al., 2013a) where such tests were performed and inaccuracies in commonly used arguments were found. We also summarize (Ahlkrona et al., 2013b) where the implications of the inaccurate assumptions are analyzed for two paleo-models - the SIA and the SOSIA. We review these works without resorting to mathematical detail, in order to make them accessible to a wider audience with a general interest in palaeo-ice sheet modelling. Specifically, we discuss two implications of relevance for palaeo-ice sheet modelling. First, classical SIA models are less accurate than assumed in their original derivation. Secondly, and contrary to previous recommendations, the SOSIA model is ruled out as a practicable tool for palaeo-ice sheet simulations. We conclude with an outlook concerning the new Ice Sheet Coupled Approximation Level (ISCAL) method presented in Ahlkrona et al. (2016), that has the potential to match the accuracy standards of full Stokes model on palaeo-timescales of tens of thousands of years, and to become an alternative to hybrid models currently used in palaeo-ice sheet modelling. The method is applied to an ice

  18. Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia

    PubMed Central

    Yuan, Xuye; Chen, Jiajia; Lin, Yuxin; Li, Yin; Xu, Lihua; Chen, Luonan; Hua, Haiying; Shen, Bairong

    2017-01-01

    Leukemia is a leading cause of cancer deaths in the developed countries. Great efforts have been undertaken in search of diagnostic biomarkers of leukemia. However, leukemia is highly complex and heterogeneous, involving interaction among multiple molecular components. Individual molecules are not necessarily sensitive diagnostic indicators. Network biomarkers are considered to outperform individual molecules in disease characterization. We applied an integrative approach that identifies active network modules as putative biomarkers for leukemia diagnosis. We first reconstructed the leukemia-specific PPI network using protein-protein interactions from the Protein Interaction Network Analysis (PINA) and protein annotations from GeneGo. The network was further integrated with gene expression profiles to identify active modules with leukemia relevance. Finally, the candidate network-based biomarker was evaluated for the diagnosing performance. A network of 97 genes and 400 interactions was identified for accurate diagnosis of leukemia. Functional enrichment analysis revealed that the network biomarkers were enriched in pathways in cancer. The network biomarkers could discriminate leukemia samples from the normal controls more effectively than the known biomarkers. The network biomarkers provide a useful tool to diagnose leukemia and also aids in further understanding the molecular basis of leukemia. PMID:28243332

  19. A 3D-CFD code for accurate prediction of fluid flows and fluid forces in seals

    NASA Technical Reports Server (NTRS)

    Athavale, M. M.; Przekwas, A. J.; Hendricks, R. C.

    1994-01-01

    Current and future turbomachinery requires advanced seal configurations to control leakage, inhibit mixing of incompatible fluids and to control the rotodynamic response. In recognition of a deficiency in the existing predictive methodology for seals, a seven year effort was established in 1990 by NASA's Office of Aeronautics Exploration and Technology, under the Earth-to-Orbit Propulsion program, to develop validated Computational Fluid Dynamics (CFD) concepts, codes and analyses for seals. The effort will provide NASA and the U.S. Aerospace Industry with advanced CFD scientific codes and industrial codes for analyzing and designing turbomachinery seals. An advanced 3D CFD cylindrical seal code has been developed, incorporating state-of-the-art computational methodology for flow analysis in straight, tapered and stepped seals. Relevant computational features of the code include: stationary/rotating coordinates, cylindrical and general Body Fitted Coordinates (BFC) systems, high order differencing schemes, colocated variable arrangement, advanced turbulence models, incompressible/compressible flows, and moving grids. This paper presents the current status of code development, code demonstration for predicting rotordynamic coefficients, numerical parametric study of entrance loss coefficients for generic annular seals, and plans for code extensions to labyrinth, damping, and other seal configurations.

  20. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information.

    PubMed

    Walsh, Susan; Liu, Fan; Ballantyne, Kaye N; van Oven, Mannis; Lao, Oscar; Kayser, Manfred

    2011-06-01

    A new era of 'DNA intelligence' is arriving in forensic biology, due to the impending ability to predict externally visible characteristics (EVCs) from biological material such as those found at crime scenes. EVC prediction from forensic samples, or from body parts, is expected to help concentrate police investigations towards finding unknown individuals, at times when conventional DNA profiling fails to provide informative leads. Here we present a robust and sensitive tool, termed IrisPlex, for the accurate prediction of blue and brown eye colour from DNA in future forensic applications. We used the six currently most eye colour-informative single nucleotide polymorphisms (SNPs) that previously revealed prevalence-adjusted prediction accuracies of over 90% for blue and brown eye colour in 6168 Dutch Europeans. The single multiplex assay, based on SNaPshot chemistry and capillary electrophoresis, both widely used in forensic laboratories, displays high levels of genotyping sensitivity with complete profiles generated from as little as 31pg of DNA, approximately six human diploid cell equivalents. We also present a prediction model to correctly classify an individual's eye colour, via probability estimation solely based on DNA data, and illustrate the accuracy of the developed prediction test on 40 individuals from various geographic origins. Moreover, we obtained insights into the worldwide allele distribution of these six SNPs using the HGDP-CEPH samples of 51 populations. Eye colour prediction analyses from HGDP-CEPH samples provide evidence that the test and model presented here perform reliably without prior ancestry information, although future worldwide genotype and phenotype data shall confirm this notion. As our IrisPlex eye colour prediction test is capable of immediate implementation in forensic casework, it represents one of the first steps forward in the creation of a fully individualised EVC prediction system for future use in forensic DNA intelligence.

  1. Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population

    PubMed Central

    McCoy, Rajiv C.; Garud, Nandita R.; Kelley, Joanna L.; Boggs, Carol L.; Petrov, Dmitri A.

    2015-01-01

    The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interested in the demographic history of populations, information that is rarely available from historical records. Methods have been developed to infer demographic parameters from genomic data, but it is not well understood how inferred parameters compare to true population history or depend on aspects of experimental design. Here we present and evaluate a method of SNP discovery using RNA-sequencing and demographic inference using the program δaδi, which uses a diffusion approximation to the allele frequency spectrum to fit demographic models. We test these methods in a population of the checkerspot butterfly Euphydryas gillettii. This population was intentionally introduced to Gothic, Colorado in 1977 and has since experienced extreme fluctuations including bottlenecks of fewer than 25 adults, as documented by nearly annual field surveys. Using RNA-sequencing of eight individuals from Colorado and eight individuals from a native population in Wyoming, we generate the first genomic resources for this system. While demographic inference is commonly used to examine ancient demography, our study demonstrates that our inexpensive, all-in-one approach to marker discovery and genotyping provides sufficient data to accurately infer the timing of a recent bottleneck. This demographic scenario is relevant for many species of conservation concern, few of which have sequenced genomes. Our results are remarkably insensitive to sample size or number of genomic markers, which has important implications for applying this method to other non-model systems. PMID:24237665

  2. Predictions and Studies with a One-Dimensional Ice/Ocean Model.

    DTIC Science & Technology

    1987-04-01

    d. Sound speed 10 4. Effect of changing o and qb 10 5. Deep ocean heat flux (Hd,. P ) 11 6. Case 2-solar radiation stored in brine pockets II a. Setup...F F )/q - T 4+ k i(T - Tp)/ (hiA P Bwhen Ts is above freezing. + (hSk i /k s ))] The growth or decay of ice at the bottom is deter- mined from [4Tp...freezing, is computed fromATS = IF1 + Ft + FL + (1-=i)F R 4 +i FL +10i R Ah iPt (FS- F / .(7) hi (F s FA)/ q -Orp4 .ki(T- Tp)/hi] iB T P The

  3. An accurate method to predict the stress concentration in composite laminates with a circular hole under tensile loading

    NASA Astrophysics Data System (ADS)

    Russo, A.; Zuccarello, B.

    2007-07-01

    The paper presents a theoretical-numerical hybrid method for determining the stresses distribution in composite laminates containing a circular hole and subjected to uniaxial tensile loading. The method is based upon an appropriate corrective function allowing a simple and rapid evaluation of stress distributions in a generic plate of finite width with a hole based on the theoretical stresses distribution in an infinite plate with the same hole geometry and material. In order to verify the accuracy of the method proposed, various numerical and experimental tests have been performed by considering different laminate lay-ups; in particular, the experimental results have shown that a combined use of the method proposed and the well-know point-stress criterion leads to reliable strength predictions for GFRP or CFRP laminates with a circular hole.

  4. Cloud ice caused by atmospheric mineral dust - Part 1: Parameterization of ice nuclei concentration in the NMME-DREAM model

    NASA Astrophysics Data System (ADS)

    Nickovic, Slobodan; Cvetkovic, Bojan; Madonna, Fabio; Rosoldi, Marco; Pejanovic, Goran; Petkovic, Slavko; Nikolic, Jugoslav

    2016-09-01

    Dust aerosols are very efficient ice nuclei, important for heterogeneous cloud glaciation even in regions distant from desert sources. A new generation of ice nucleation parameterizations, including dust as an ice nucleation agent, opens the way towards a more accurate treatment of cold cloud formation in atmospheric models. Using such parameterizations, we have developed a regional dust-atmospheric modelling system capable of predicting, in real time, dust-induced ice nucleation. We executed the model with the added ice nucleation component over the Mediterranean region, exposed to moderate Saharan dust transport, over two periods lasting 15 and 9 days, respectively. The model results were compared against satellite and ground-based cloud-ice-related measurements, provided by SEVIRI (Spinning Enhanced Visible and InfraRed Imager) and the CNR-IMAA Atmospheric Observatory (CIAO) in Potenza, southern Italy. The predicted ice nuclei concentration showed a reasonable level of agreement when compared against the observed spatial and temporal patterns of cloud ice water. The developed methodology permits the use of ice nuclei as input into the cloud microphysics schemes of atmospheric models, assuming that this approach could improve the predictions of cloud formation and associated precipitation.

  5. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems

    SciTech Connect

    Samudrala, Ram; Heffron, Fred; McDermott, Jason E.

    2009-04-24

    The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates, effector proteins, are not. We have used a machine learning approach to identify new secreted effectors. The method integrates evolutionary measures, such as the pattern of homologs in a range of other organisms, and sequence-based features, such as G+C content, amino acid composition and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from Salmonella typhimurium and validated on a corresponding set of effectors from Pseudomonas syringae, after eliminating effectors with detectable sequence similarity. The method was able to identify all of the known effectors in P. syringae with a specificity of 84% and sensitivity of 82%. The reciprocal validation, training on P. syringae and validating on S. typhimurium, gave similar results with a specificity of 86% when the sensitivity level was 87%. These results show that type III effectors in disparate organisms share common features. We found that maximal performance is attained by including an N-terminal sequence of only 30 residues, which agrees with previous studies indicating that this region contains the secretion signal. We then used the method to define the most important residues in this putative secretion signal. Finally, we present novel predictions of secreted effectors in S. typhimurium, some of which have been experimentally validated, and apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis. This approach is a novel and effective way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.

  6. A single bioavailability model can accurately predict Ni toxicity to green microalgae in soft and hard surface waters.

    PubMed

    Deleebeeck, Nele M E; De Laender, Frederik; Chepurnov, Victor A; Vyverman, Wim; Janssen, Colin R; De Schamphelaere, Karel A C

    2009-04-01

    The major research questions addressed in this study were (i) whether green microalgae living in soft water (operationally defined water hardness<10mg CaCO(3)/L) are intrinsically more sensitive to Ni than green microalgae living in hard water (operationally defined water hardness >25mg CaCO(3)/L), and (ii) whether a single bioavailability model can be used to predict the effect of water hardness on the toxicity of Ni to green microalgae in both soft and hard water. Algal growth inhibition tests were conducted with clones of 10 different species collected in soft and hard water lakes in Sweden. Soft water algae were tested in a 'soft' and a 'moderately hard' test medium (nominal water hardness=6.25 and 16.3mg CaCO(3)/L, respectively), whereas hard water algae were tested in a 'moderately hard' and a 'hard' test medium (nominal water hardness=16.3 and 43.4 mg CaCO(3)/L, respectively). The results from the growth inhibition tests in the 'moderately hard' test medium revealed no significant sensitivity differences between the soft and the hard water algae used in this study. Increasing water hardness significantly reduced Ni toxicity to both soft and hard water algae. Because it has previously been demonstrated that Ca does not significantly protect the unicellular green alga Pseudokirchneriella subcapitata against Ni toxicity, it was assumed that the protective effect of water hardness can be ascribed to Mg alone. The logK(MgBL) (=5.5) was calculated to be identical for the soft and the hard water algae used in this study. A single bioavailability model can therefore be used to predict Ni toxicity to green microalgae in soft and hard surface waters as a function of water hardness.

  7. Mapping Ice with Airborne Lasers

    NASA Video Gallery

    Determining whether polar ice quantities are growing or shrinking requires accurate and detailed measurements, year over year. To help make those measurements, IceBridge mission aircraft fire 3,000...

  8. Generalized spin-ratio scaled MP2 method for accurate prediction of intermolecular interactions for neutral and ionic species

    NASA Astrophysics Data System (ADS)

    Tan, Samuel; Barrera Acevedo, Santiago; Izgorodina, Ekaterina I.

    2017-02-01

    The accurate calculation of intermolecular interactions is important to our understanding of properties in large molecular systems. The high computational cost of the current "gold standard" method, coupled cluster with singles and doubles and perturbative triples (CCSD(T), limits its application to small- to medium-sized systems. Second-order Møller-Plesset perturbation (MP2) theory is a cheaper alternative for larger systems, although at the expense of its decreased accuracy, especially when treating van der Waals complexes. In this study, a new modification of the spin-component scaled MP2 method was proposed for a wide range of intermolecular complexes including two well-known datasets, S22 and S66, and a large dataset of ionic liquids consisting of 174 single ion pairs, IL174. It was found that the spin ratio, ɛΔ s=E/INT O SEIN T S S , calculated as the ratio of the opposite-spin component to the same-spin component of the interaction correlation energy fell in the range of 0.1 and 1.6, in contrast to the range of 3-4 usually observed for the ratio of absolute correlation energy, ɛs=E/OSES S , in individual molecules. Scaled coefficients were found to become negative when the spin ratio fell in close proximity to 1.0, and therefore, the studied intermolecular complexes were divided into two groups: (1) complexes with ɛΔ s< 1 and (2) complexes with ɛΔ s≥ 1 . A separate set of coefficients was obtained for both groups. Exclusion of counterpoise correction during scaling was found to produce superior results due to decreased error. Among a series of Dunning's basis sets, cc-pVTZ and cc-pVQZ were found to be the best performing ones, with a mean absolute error of 1.4 kJ mol-1 and maximum errors below 6.2 kJ mol-1. The new modification, spin-ratio scaled second-order Møller-Plesset perturbation, treats both dispersion-driven and hydrogen-bonded complexes equally well, thus validating its robustness with respect to the interaction type ranging from ionic

  9. Accurate Predictions of Mean Geomagnetic Dipole Excursion and Reversal Frequencies, Mean Paleomagnetic Field Intensity, and the Radius of Earth's Core Using McLeod's Rule

    NASA Technical Reports Server (NTRS)

    Voorhies, Coerte V.; Conrad, Joy

    1996-01-01

    The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field

  10. Integrating metabolic performance, thermal tolerance, and plasticity enables for more accurate predictions on species vulnerability to acute and chronic effects of global warming.

    PubMed

    Magozzi, Sarah; Calosi, Piero

    2015-01-01

    Predicting species vulnerability to global warming requires a comprehensive, mechanistic understanding of sublethal and lethal thermal tolerances. To date, however, most studies investigating species physiological responses to increasing temperature have focused on the underlying physiological traits of either acute or chronic tolerance in isolation. Here we propose an integrative, synthetic approach including the investigation of multiple physiological traits (metabolic performance and thermal tolerance), and their plasticity, to provide more accurate and balanced predictions on species and assemblage vulnerability to both acute and chronic effects of global warming. We applied this approach to more accurately elucidate relative species vulnerability to warming within an assemblage of six caridean prawns occurring in the same geographic, hence macroclimatic, region, but living in different thermal habitats. Prawns were exposed to four incubation temperatures (10, 15, 20 and 25 °C) for 7 days, their metabolic rates and upper thermal limits were measured, and plasticity was calculated according to the concept of Reaction Norms, as well as Q10 for metabolism. Compared to species occupying narrower/more stable thermal niches, species inhabiting broader/more variable thermal environments (including the invasive Palaemon macrodactylus) are likely to be less vulnerable to extreme acute thermal events as a result of their higher upper thermal limits. Nevertheless, they may be at greater risk from chronic exposure to warming due to the greater metabolic costs they incur. Indeed, a trade-off between acute and chronic tolerance was apparent in the assemblage investigated. However, the invasive species P. macrodactylus represents an exception to this pattern, showing elevated thermal limits and plasticity of these limits, as well as a high metabolic control. In general, integrating multiple proxies for species physiological acute and chronic responses to increasing

  11. Predicting College Students' First Year Success: Should Soft Skills Be Taken into Consideration to More Accurately Predict the Academic Achievement of College Freshmen?

    ERIC Educational Resources Information Center

    Powell, Erica Dion

    2013-01-01

    This study presents a survey developed to measure the skills of entering college freshmen in the areas of responsibility, motivation, study habits, literacy, and stress management, and explores the predictive power of this survey as a measure of academic performance during the first semester of college. The survey was completed by 334 incoming…

  12. Microdosing of a Carbon-14 Labeled Protein in Healthy Volunteers Accurately Predicts Its Pharmacokinetics at Therapeutic Dosages.

    PubMed

    Vlaming, M L H; van Duijn, E; Dillingh, M R; Brands, R; Windhorst, A D; Hendrikse, N H; Bosgra, S; Burggraaf, J; de Koning, M C; Fidder, A; Mocking, J A J; Sandman, H; de Ligt, R A F; Fabriek, B O; Pasman, W J; Seinen, W; Alves, T; Carrondo, M; Peixoto, C; Peeters, P A M; Vaes, W H J

    2015-08-01

    Preclinical development of new biological entities (NBEs), such as human protein therapeutics, requires considerable expenditure of time and costs. Poor prediction of pharmacokinetics in humans further reduces net efficiency. In this study, we show for the first time that pharmacokinetic data of NBEs in humans can be successfully obtained early in the drug development process by the use of microdosing in a small group of healthy subjects combined with ultrasensitive accelerator mass spectrometry (AMS). After only minimal preclinical testing, we performed a first-in-human phase 0/phase 1 trial with a human recombinant therapeutic protein (RESCuing Alkaline Phosphatase, human recombinant placental alkaline phosphatase [hRESCAP]) to assess its safety and kinetics. Pharmacokinetic analysis showed dose linearity from microdose (53 μg) [(14) C]-hRESCAP to therapeutic doses (up to 5.3 mg) of the protein in healthy volunteers. This study demonstrates the value of a microdosing approach in a very small cohort for accelerating the clinical development of NBEs.

  13. Women's age and embryo developmental speed accurately predict clinical pregnancy after single vitrified-warmed blastocyst transfer.

    PubMed

    Kato, Keiichi; Ueno, Satoshi; Yabuuchi, Akiko; Uchiyama, Kazuo; Okuno, Takashi; Kobayashi, Tamotsu; Segawa, Tomoya; Teramoto, Shokichi

    2014-10-01

    The aim of this study was to establish a simple, objective blastocyst grading system using women's age and embryo developmental speed to predict clinical pregnancy after single vitrified-warmed blastocyst transfer. A 6-year retrospective cohort study was conducted in a private infertility centre. A total of 7341 single vitrified-armed blastocyst transfer cycles were included, divided into those carried out between 2006 and 2011 (6046 cycles) and 2012 (1295 cycles). Clinical pregnancy rate, ongoing pregnancy rate and delivery rates were stratified by women's age (<35, 35-37, 38-39, 40-41, 42-45 years) and time to blastocyst expansion (<120, 120-129, 130-139, 140-149, >149 h) as embryo developmental speed. In all the age groups, clinical pregnancy rate, ongoing pregnancy rate and delivery rates decreased as the embryo developmental speed decreased (P < 0.0001). A simple five-grade score based on women's age and embryo developmental speed was determined by actual clinical pregnancy rates observed in the 2006-2011 cohort. Subsequently, the novel grading score was validated in the 2012 cohort (1295 cycles), finding an excellent association. In conclusion, we established a novel blastocyst grading system using women's age and embryo developmental speed as objective parameters.

  14. Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

    PubMed Central

    Essaghir, Ahmed; Toffalini, Federica; Knoops, Laurent; Kallin, Anders; van Helden, Jacques; Demoulin, Jean-Baptiste

    2010-01-01

    Deciphering transcription factor networks from microarray data remains difficult. This study presents a simple method to infer the regulation of transcription factors from microarray data based on well-characterized target genes. We generated a catalog containing transcription factors associated with 2720 target genes and 6401 experimentally validated regulations. When it was available, a distinction between transcriptional activation and inhibition was included for each regulation. Next, we built a tool (www.tfacts.org) that compares submitted gene lists with target genes in the catalog to detect regulated transcription factors. TFactS was validated with published lists of regulated genes in various models and compared to tools based on in silico promoter analysis. We next analyzed the NCI60 cancer microarray data set and showed the regulation of SOX10, MITF and JUN in melanomas. We then performed microarray experiments comparing gene expression response of human fibroblasts stimulated by different growth factors. TFactS predicted the specific activation of Signal transducer and activator of transcription factors by PDGF-BB, which was confirmed experimentally. Our results show that the expression levels of transcription factor target genes constitute a robust signature for transcription factor regulation, and can be efficiently used for microarray data mining. PMID:20215436

  15. Geometry Modeling and Grid Generation for "Icing Effects" and "Ice Accretion" Simulations on Airfoils

    NASA Technical Reports Server (NTRS)

    Choo, Yung; Vickerman, Mary; Lee, Ki D.; Thompson, David S.

    2000-01-01

    There are two distinct icing-related problems for airfoils that can be simulated. One is predicting the effects of ice on the aerodynamic performance of airfoils when ice geometry is known ("icing effects" study). The other is simulating ice accretion under specified icing conditions ("ice accretion" simulation). This paper will address development of two different software packages for two-dimensional geometry preparation and grid generation for both "icing effects" and "ice accretion" studies.

  16. Infectious titres of sheep scrapie and bovine spongiform encephalopathy agents cannot be accurately predicted from quantitative laboratory test results.

    PubMed

    González, Lorenzo; Thorne, Leigh; Jeffrey, Martin; Martin, Stuart; Spiropoulos, John; Beck, Katy E; Lockey, Richard W; Vickery, Christopher M; Holder, Thomas; Terry, Linda

    2012-11-01

    It is widely accepted that abnormal forms of the prion protein (PrP) are the best surrogate marker for the infectious agent of prion diseases and, in practice, the detection of such disease-associated (PrP(d)) and/or protease-resistant (PrP(res)) forms of PrP is the cornerstone of diagnosis and surveillance of the transmissible spongiform encephalopathies (TSEs). Nevertheless, some studies question the consistent association between infectivity and abnormal PrP detection. To address this discrepancy, 11 brain samples of sheep affected with natural scrapie or experimental bovine spongiform encephalopathy were selected on the basis of the magnitude and predominant types of PrP(d) accumulation, as shown by immunohistochemical (IHC) examination; contra-lateral hemi-brain samples were inoculated at three different dilutions into transgenic mice overexpressing ovine PrP and were also subjected to quantitative analysis by three biochemical tests (BCTs). Six samples gave 'low' infectious titres (10⁶·⁵ to 10⁶·⁷ LD₅₀ g⁻¹) and five gave 'high titres' (10⁸·¹ to ≥ 10⁸·⁷ LD₅₀ g⁻¹) and, with the exception of the Western blot analysis, those two groups tended to correspond with samples with lower PrP(d)/PrP(res) results by IHC/BCTs. However, no statistical association could be confirmed due to high individual sample variability. It is concluded that although detection of abnormal forms of PrP by laboratory methods remains useful to confirm TSE infection, infectivity titres cannot be predicted from quantitative test results, at least for the TSE sources and host PRNP genotypes used in this study. Furthermore, the near inverse correlation between infectious titres and Western blot results (high protease pre-treatment) argues for a dissociation between infectivity and PrP(res).

  17. Antarctic ice-sheet loss driven by basal melting of ice shelves.

    PubMed

    Pritchard, H D; Ligtenberg, S R M; Fricker, H A; Vaughan, D G; van den Broeke, M R; Padman, L

    2012-04-25

    Accurate prediction of global sea-level rise requires that we understand the cause of recent, widespread and intensifying glacier acceleration along Antarctic ice-sheet coastal margins. Atmospheric and oceanic forcing have the potential to reduce the thickness and extent of floating ice shelves, potentially limiting their ability to buttress the flow of grounded tributary glaciers. Indeed, recent ice-shelf collapse led to retreat and acceleration of several glaciers on the Antarctic Peninsula. But the extent and magnitude of ice-shelf thickness change, the underlying causes of such change, and its link to glacier flow rate are so poorly understood that its future impact on the ice sheets cannot yet be predicted. Here we use satellite laser altimetry and modelling of the surface firn layer to reveal the circum-Antarctic pattern of ice-shelf thinning through increased basal melt. We deduce that this increased melt is the primary control of Antarctic ice-sheet loss, through a reduction in buttressing of the adjacent ice sheet leading to accelerated glacier flow. The highest thinning rates occur where warm water at depth can access thick ice shelves via submarine troughs crossing the continental shelf. Wind forcing could explain the dominant patterns of both basal melting and the surface melting and collapse of Antarctic ice shelves, through ocean upwelling in the Amundsen and Bellingshausen seas, and atmospheric warming on the Antarctic Peninsula. This implies that climate forcing through changing winds influences Antarctic ice-sheet mass balance, and hence global sea level, on annual to decadal timescales.

  18. Ocean variability contributing to basal melt rate near the ice front of Ross Ice Shelf, Antarctica

    NASA Astrophysics Data System (ADS)

    Arzeno, Isabella B.; Beardsley, Robert C.; Limeburner, Richard; Owens, Breck; Padman, Laurie; Springer, Scott R.; Stewart, Craig L.; Williams, Michael J. M.

    2014-07-01

    Basal melting of ice shelves is an important, but poorly understood, cause of Antarctic ice sheet mass loss and freshwater production. We use data from two moorings deployed through Ross Ice Shelf, ˜6 and ˜16 km south of the ice front east of Ross Island, and numerical models to show how the basal melting rate near the ice front depends on sub-ice-shelf ocean variability. The moorings measured water velocity, conductivity, and temperature for ˜2 months starting in late November 2010. About half of the current velocity variance was due to tides, predominantly diurnal components, with the remainder due to subtidal oscillations with periods of a few days. Subtidal variability was dominated by barotropic currents that were large until mid-December and significantly reduced afterward. Subtidal currents were correlated between moorings but uncorrelated with local winds, suggesting the presence of waves or eddies that may be associated with the abrupt change in water column thickness and strong hydrographic gradients at the ice front. Estimated melt rate was ˜1.2 ± 0.5 m a-1 at each site during the deployment period, consistent with measured trends in ice surface elevation from GPS time series. The models predicted similar annual-averaged melt rates with a strong annual cycle related to seasonal provision of warm water to the ice base. These results show that accurately modeling the high spatial and temporal ocean variability close to the ice-shelf front is critical to predicting time-dependent and mean values of meltwater production and ice-shelf thinning.

  19. The Antarctic Ice.

    ERIC Educational Resources Information Center

    Radok, Uwe

    1985-01-01

    The International Antarctic Glaciological Project has collected information on the East Antarctic ice sheet since 1969. Analysis of ice cores revealed climatic history, and radar soundings helped map bedrock of the continent. Computer models of the ice sheet and its changes over time will aid in predicting the future. (DH)

  20. Noncontrast computed tomography can predict the outcome of shockwave lithotripsy via accurate stone measurement and abdominal fat distribution determination.

    PubMed

    Geng, Jiun-Hung; Tu, Hung-Pin; Shih, Paul Ming-Chen; Shen, Jung-Tsung; Jang, Mei-Yu; Wu, Wen-Jen; Li, Ching-Chia; Chou, Yii-Her; Juan, Yung-Shun

    2015-01-01

    Urolithiasis is a common disease of the urinary system. Extracorporeal shockwave lithotripsy (SWL) has become one of the standard treatments for renal and ureteral stones; however, the success rates range widely and failure of stone disintegration may cause additional outlay, alternative procedures, and even complications. We used the data available from noncontrast abdominal computed tomography (NCCT) to evaluate the impact of stone parameters and abdominal fat distribution on calculus-free rates following SWL. We retrospectively reviewed 328 patients who had urinary stones and had undergone SWL from August 2012 to August 2013. All of them received pre-SWL NCCT; 1 month after SWL, radiography was arranged to evaluate the condition of the fragments. These patients were classified into stone-free group and residual stone group. Unenhanced computed tomography variables, including stone attenuation, abdominal fat area, and skin-to-stone distance (SSD) were analyzed. In all, 197 (60%) were classified as stone-free and 132 (40%) as having residual stone. The mean ages were 49.35 ± 13.22 years and 55.32 ± 13.52 years, respectively. On univariate analysis, age, stone size, stone surface area, stone attenuation, SSD, total fat area (TFA), abdominal circumference, serum creatinine, and the severity of hydronephrosis revealed statistical significance between these two groups. From multivariate logistic regression analysis, the independent parameters impacting SWL outcomes were stone size, stone attenuation, TFA, and serum creatinine. [Adjusted odds ratios and (95% confidence intervals): 9.49 (3.72-24.20), 2.25 (1.22-4.14), 2.20 (1.10-4.40), and 2.89 (1.35-6.21) respectively, all p < 0.05]. In the present study, stone size, stone attenuation, TFA and serum creatinine were four independent predictors for stone-free rates after SWL. These findings suggest that pretreatment NCCT may predict the outcomes after SWL. Consequently, we can use these predictors for selecting

  1. Stochastic ice stream dynamics

    NASA Astrophysics Data System (ADS)

    Mantelli, Elisa; Bertagni, Matteo Bernard; Ridolfi, Luca

    2016-08-01

    Ice streams are narrow corridors of fast-flowing ice that constitute the arterial drainage network of ice sheets. Therefore, changes in ice stream flow are key to understanding paleoclimate, sea level changes, and rapid disintegration of ice sheets during deglaciation. The dynamics of ice flow are tightly coupled to the climate system through atmospheric temperature and snow recharge, which are known exhibit stochastic variability. Here we focus on the interplay between stochastic climate forcing and ice stream temporal dynamics. Our work demonstrates that realistic climate fluctuations are able to (i) induce the coexistence of dynamic behaviors that would be incompatible in a purely deterministic system and (ii) drive ice stream flow away from the regime expected in a steady climate. We conclude that environmental noise appears to be crucial to interpreting the past behavior of ice sheets, as well as to predicting their future evolution.

  2. Stochastic ice stream dynamics

    PubMed Central

    Bertagni, Matteo Bernard; Ridolfi, Luca

    2016-01-01

    Ice streams are narrow corridors of fast-flowing ice that constitute the arterial drainage network of ice sheets. Therefore, changes in ice stream flow are key to understanding paleoclimate, sea level changes, and rapid disintegration of ice sheets during deglaciation. The dynamics of ice flow are tightly coupled to the climate system through atmospheric temperature and snow recharge, which are known exhibit stochastic variability. Here we focus on the interplay between stochastic climate forcing and ice stream temporal dynamics. Our work demonstrates that realistic climate fluctuations are able to (i) induce the coexistence of dynamic behaviors that would be incompatible in a purely deterministic system and (ii) drive ice stream flow away from the regime expected in a steady climate. We conclude that environmental noise appears to be crucial to interpreting the past behavior of ice sheets, as well as to predicting their future evolution. PMID:27457960

  3. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints.

    PubMed

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-02-24

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS-inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car.

  4. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints

    PubMed Central

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-01-01

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS–inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car. PMID:26927108

  5. Profile-QSAR: a novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity.

    PubMed

    Martin, Eric; Mukherjee, Prasenjit; Sullivan, David; Jansen, Johanna

    2011-08-22

    Profile-QSAR is a novel 2D predictive model building method for kinases. This "meta-QSAR" method models the activity of each compound against a new kinase target as a linear combination of its predicted activities against a large panel of 92 previously studied kinases comprised from 115 assays. Profile-QSAR starts with a sparse incomplete kinase by compound (KxC) activity matrix, used to generate Bayesian QSAR models for the 92 "basis-set" kinases. These Bayesian QSARs generate a complete "synthetic" KxC activity matrix of predictions. These synthetic activities are used as "chemical descriptors" to train partial-least squares (PLS) models, from modest amounts of medium-throughput screening data, for predicting activity against new kinases. The Profile-QSAR predictions for the 92 kinases (115 assays) gave a median external R²(ext) = 0.59 on 25% held-out test sets. The method has proven accurate enough to predict pairwise kinase selectivities with a median correlation of R²(ext) = 0.61 for 958 kinase pairs with at least 600 common compounds. It has been further expanded by adding a "C(k)XC" cellular activity matrix to the KxC matrix to predict cellular activity for 42 kinase driven cellular assays with median R²(ext) = 0.58 for 24 target modulation assays and R²(ext) = 0.41 for 18 cell proliferation assays. The 2D Profile-QSAR, along with the 3D Surrogate AutoShim, are the foundations of an internally developed iterative medium-throughput screening (IMTS) methodology for virtual screening (VS) of compound archives as an alternative to experimental high-throughput screening (HTS). The method has been applied to 20 actual prospective kinase projects. Biological results have so far been obtained in eight of them. Q² values ranged from 0.3 to 0.7. Hit-rates at 10 uM for experimentally tested compounds varied from 25% to 80%, except in K5, which was a special case aimed specifically at finding "type II" binders, where none of the compounds were predicted to be

  6. Multireference correlation consistent composite approach [MR-ccCA]: toward accurate prediction of the energetics of excited and transition state chemistry.

    PubMed

    Oyedepo, Gbenga A; Wilson, Angela K

    2010-08-26

    The correlation consistent Composite Approach, ccCA [ Deyonker , N. J. ; Cundari , T. R. ; Wilson , A. K. J. Chem. Phys. 2006 , 124 , 114104 ] has been demonstrated to predict accurate thermochemical properties of chemical species that can be described by a single configurational reference state, and at reduced computational cost, as compared with ab initio methods such as CCSD(T) used in combination with large basis sets. We have developed three variants of a multireference equivalent of this successful theoretical model. The method, called the multireference correlation consistent composite approach (MR-ccCA), is designed to predict the thermochemical properties of reactive intermediates, excited state species, and transition states to within chemical accuracy (e.g., 1 kcal/mol for enthalpies of formation) of reliable experimental values. In this study, we have demonstrated the utility of MR-ccCA: (1) in the determination of the adiabatic singlet-triplet energy separations and enthalpies of formation for the ground states for a set of diradicals and unsaturated compounds, and (2) in the prediction of energetic barriers to internal rotation, in ethylene and its heavier congener, disilene. Additionally, we have utilized MR-ccCA to predict the enthalpies of formation of the low-lying excited states of all the species considered. MR-ccCA is shown to give quantitative results without reliance upon empirically derived parameters, making it suitable for application to study novel chemical systems with significant nondynamical correlation effects.

  7. Accurate prediction of death by serial determination of galactose elimination capacity in primary biliary cirrhosis: a comparison with the Mayo model.

    PubMed

    Reichen, J; Widmer, T; Cotting, J

    1991-09-01

    We retrospectively analyzed the predictive accuracy of serial determinations of galactose elimination capacity in 61 patients with primary biliary cirrhosis. Death was predicted from the time that the regression line describing the decline in galactose elimination capacity vs. time intersected a value of 4 mg.min-1.kg-1. Thirty-one patients exhibited decreasing galactose elimination capacity; in 11 patients it remained stable and in 19 patients only one value was available. Among those patients with decreasing galactose elimination capacity, 10 died and three underwent liver transplantation; prediction of death was accurate to 7 +/- 19 mo. This criterion incorrectly predicted death in two patients with portal-vein thrombosis; otherwise, it did better than or as well as the Mayo clinic score. The latter was also tested on our patients and was found to adequately describe risk in yet another independent population of patients with primary biliary cirrhosis. Cox regression analysis selected only bilirubin and galactose elimination capacity, however, as independent predictors of death. We submit that serial determination of galactose elimination capacity in patients with primary biliary cirrhosis may be a useful adjunct to optimize the timing of liver transplantation and to evaluate new pharmacological treatment modalities of this disease.

  8. Effects of Assimilation Window Length and Radiatively Active Water Ice Clouds on Martian Thermal Tides and Martian Atmosphere Predictability

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Greybush, S. J.; Kalnay, E.; Hoffman, R. N.; Wilson, R.

    2013-12-01

    Martian therrnal tides are a particularly prominent feature that contribute much to the Martian atmospheric circulation and dust transport. To study the Mars diurnal features (or thermal tides), data assimilation based on the GFDL Mars Global Climate Model (MGCM) with the 4D-Local Ensemble Transform Kalman Filter (4D-LETKF) is used to perform a reanalysis of spacecraft temperature retrievals from the Thermal Emission Spectrometer (TES) and Mars Climate Sounder (MCS) instruments. Since the traditional 6-hr assimilation cycle induces spurious resonance in the Kelvin waves represented in both surface pressure and mid-level temperature, short assimilation window lengths (1-hour and 2-hour) are introduced in 4D-LETKF. In order to compare the performances of different assimilation window lengths, 10-sol forecasts based on the hour 00 and 12 reanalysis are evaluated and compared. The shorter windows show improved forecast root mean square difference with respect to observations, and not only remove the spurious resonance but also better compensate for the absence of radiatively active water ice clouds (RAC). The predictability of Martian atmosphere is also studied using multi-sol forecasts initiated from analyses employing different assimilation window lengths, and the effect of RAC on Martian atmospheric predictability is also discussed.

  9. Trait aggressiveness and hockey penalties: predicting hot tempers on the ice.

    PubMed

    Bushman, B J; Wells, G L

    1998-12-01

    Previous studies examining the validity of measures of trait aggressiveness either have been retrospective studies or have used laboratory aggression as the criterion behavior. Can a measure of trait aggressiveness predict nonlaboratory physical aggression? The Physical Aggression subscale of the Aggression Questionnaire was completed by 91 high school hockey players prior to the start of the season. At the end of the season, these trait aggressiveness scores were regressed on minutes in the penalty box for aggressive penalties (e.g., fighting, slashing, tripping) and minutes in the penalty box for nonaggressive penalties (e.g., delay of game, illegal equipment, too many players). As expected, preseason trait aggressiveness scores predicted aggressive penalty minutes (r = .33) but not nonaggressive penalty minutes (r = .04).

  10. Clouds enhance Greenland ice sheet meltwater runoff.

    PubMed

    Van Tricht, K; Lhermitte, S; Lenaerts, J T M; Gorodetskaya, I V; L'Ecuyer, T S; Noël, B; van den Broeke, M R; Turner, D D; van Lipzig, N P M

    2016-01-12

    The Greenland ice sheet has become one of the main contributors to global sea level rise, predominantly through increased meltwater runoff. The main drivers of Greenland ice sheet runoff, however, remain poorly understood. Here we show that clouds enhance meltwater runoff by about one-third relative to clear skies, using a unique combination of active satellite observations, climate model data and snow model simulations. This impact results from a cloud radiative effect of 29.5 (±5.2) W m(-2). Contrary to conventional wisdom, however, the Greenland ice sheet responds to this energy through a new pathway by which clouds reduce meltwater refreezing as opposed to increasing surface melt directly, thereby accelerating bare-ice exposure and enhancing meltwater runoff. The high sensitivity of the Greenland ice sheet to both ice-only and liquid-bearing clouds highlights the need for accurate cloud representations in climate models, to better predict future contributions of the Greenland ice sheet to global sea level rise.

  11. Clouds enhance Greenland ice sheet meltwater runoff

    PubMed Central

    Van Tricht, K.; Lhermitte, S.; Lenaerts, J. T. M.; Gorodetskaya, I. V.; L'Ecuyer, T. S.; Noël, B.; van den Broeke, M. R.; Turner, D. D.; van Lipzig, N. P. M.

    2016-01-01

    The Greenland ice sheet has become one of the main contributors to global sea level rise, predominantly through increased meltwater runoff. The main drivers of Greenland ice sheet runoff, however, remain poorly understood. Here we show that clouds enhance meltwater runoff by about one-third relative to clear skies, using a unique combination of active satellite observations, climate model data and snow model simulations. This impact results from a cloud radiative effect of 29.5 (±5.2) W m−2. Contrary to conventional wisdom, however, the Greenland ice sheet responds to this energy through a new pathway by which clouds reduce meltwater refreezing as opposed to increasing surface melt directly, thereby accelerating bare-ice exposure and enhancing meltwater runoff. The high sensitivity of the Greenland ice sheet to both ice-only and liquid-bearing clouds highlights the need for accurate cloud representations in climate models, to better predict future contributions of the Greenland ice sheet to global sea level rise. PMID:26756470

  12. Clouds enhance Greenland ice sheet meltwater runoff

    NASA Astrophysics Data System (ADS)

    Van Tricht, Kristof; Lhermitte, Stef; Lenaerts, Jan T. M.; Gorodetskaya, Irina V.; L'Ecuyer, Tristan S.; Noël, Brice; van den Broeke, Michiel R.; Turner, David D.; van Lipzig, Nicole P. M.

    2016-04-01

    The Greenland ice sheet has become one of the main contributors to global sea level rise, predominantly through increased meltwater runoff. The main drivers of Greenland ice sheet runoff, however, remain poorly understood. Here we show that clouds enhance meltwater runoff by about one-third relative to clear skies, using a unique combination of active satellite observations, climate model data and snow model simulations. This impact results from a cloud radiative effect of 29.5 (±5.2) W m-2. Contrary to conventional wisdom, however, the Greenland ice sheet responds to this energy through a new pathway by which clouds reduce meltwater refreezing as opposed to increasing surface melt directly, thereby accelerating bare-ice exposure and enhancing meltwater runoff. The high sensitivity of the Greenland ice sheet to both ice-only and liquid-bearing clouds highlights the need for accurate cloud representations in climate models, to better predict future contributions of the Greenland ice sheet to global sea level rise.

  13. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound–Kinase Activities: A Way toward Selective Promiscuity by Design?

    PubMed Central

    2016-01-01

    Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand–target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile. PMID:27482722

  14. Identification of fidgety movements and prediction of CP by the use of computer-based video analysis is more accurate when based on two video recordings.

    PubMed

    Adde, Lars; Helbostad, Jorunn; Jensenius, Alexander R; Langaas, Mette; Støen, Ragnhild

    2013-08-01

    This study evaluates the role of postterm age at assessment and the use of one or two video recordings for the detection of fidgety movements (FMs) and prediction of cerebral palsy (CP) using computer vision software. Recordings between 9 and 17 weeks postterm age from 52 preterm and term infants (24 boys, 28 girls; 26 born preterm) were used. Recordings were analyzed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analysis. Sensitivities, specificities, and area under curve were estimated for the first and second recording, or a mean of both. FMs were classified based on the Prechtl approach of general movement assessment. CP status was reported at 2 years. Nine children developed CP of whom all recordings had absent FMs. The mean variability of the centroid of motion (CSD) from two recordings was more accurate than using only one recording, and identified all children who were diagnosed with CP at 2 years. Age at assessment did not influence the detection of FMs or prediction of CP. The accuracy of computer vision techniques in identifying FMs and predicting CP based on two recordings should be confirmed in future studies.

  15. Tests of GCM pressure predictions for water ice stability using Mars Odyssey Neutron Spectrometer data

    NASA Astrophysics Data System (ADS)

    Wilson, J. T.; Eke, V. R.; Massey, R. J.; Elphic, R. C.; Feldman, W. C.; Maurice, S.; Teodoro, L. F. A.

    2015-10-01

    We have used the pixon image reconstruction t e c h n i q u e o n t h e M a r s O d y s s e y N e u t r o n Spectrometer epithermal neutron data to produce an improved global map of the hydrogen abundance on Mars. We will compare this to the predictions for surface hydration from the martian general circulation models, in order to provide both new constraints on, and tests of, the models.

  16. Development of Three-Dimensional Flow Code Package to Predict Performance and Stability of Aircraft with Leading Edge Ice Contamination

    NASA Technical Reports Server (NTRS)

    Strash, D. J.; Summa, J. M.

    1996-01-01

    In the work reported herein, a simplified, uncoupled, zonal procedure is utilized to assess the capability of numerically simulating icing effects on a Boeing 727-200 aircraft. The computational approach combines potential flow plus boundary layer simulations by VSAERO for the un-iced aircraft forces and moments with Navier-Stokes simulations by NPARC for the incremental forces and moments due to iced components. These are compared with wind tunnel force and moment data, supplied by the Boeing Company, examining longitudinal flight characteristics. Grid refinement improved the local flow features over previously reported work with no appreciable difference in the incremental ice effect. The computed lift curve slope with and without empennage ice matches the experimental value to within 1%, and the zero lift angle agrees to within 0.2 of a degree. The computed slope of the un-iced and iced aircraft longitudinal stability curve is within about 2% of the test data. This work demonstrates the feasibility of a zonal method for the icing analysis of complete aircraft or isolated components within the linear angle of attack range. In fact, this zonal technique has allowed for the viscous analysis of a complete aircraft with ice which is currently not otherwise considered tractable.

  17. SeaRISE: A Multidisciplinary Research Initiative to Predict Rapid Changes in Global Sea Level Caused by Collapse of Marine Ice Sheets

    NASA Technical Reports Server (NTRS)

    Bindschadler, Robert A. (Editor)

    1990-01-01

    The results of a workshop held to discuss the role of the polar ice sheets in global climate change are reported. The participants agreed that the most important aspect of the ice sheets' involvement in climate change is the potential of marine ice sheets to cause a rapid change in global sea level. To address this concern, a research initiative is called for that considers the full complexity of the coupled atmosphere-ocean-cryosphere-lithosphere system. This initiative, called SeaRISE (Sea-level Response to Ice Sheet Evolution) has the goal of predicting the contribution of marine ice sheets to rapid changes in global sea level in the next decade to few centuries. To attain this goal, a coordinated program of multidisciplinary investigations must be launched with the linked objectives of understanding the current state, internal dynamics, interactions, and history of this environmental system. The key questions needed to satisfy these objectives are presented and discussed along with a plan of action to make the SeaRISE project a reality.

  18. Spring Snow Depth on Arctic Sea Ice using the IceBridge Snow Depth Product (Invited)

    NASA Astrophysics Data System (ADS)

    Webster, M.; Rigor, I. G.; Nghiem, S. V.; Kurtz, N. T.; Farrell, S. L.

    2013-12-01

    Snow has dual roles in the growth and decay of Arctic sea ice. In winter, it insulates sea ice from colder air temperatures, slowing its growth. From spring into summer, the albedo of snow determines how much insolation is transmitted through the sea ice and into the underlying ocean, ultimately impacting the progression of the summer ice melt. Knowing the snow thickness and distribution are essential for understanding and modeling sea ice thermodynamics and the surface heat budget. Therefore, an accurate assessment of the snow cover is necessary for identifying its impacts in the changing Arctic. This study assesses springtime snow conditions on Arctic sea ice using airborne snow thickness measurements from Operation IceBridge (2009-2012). The 2012 data were validated with coordinated in situ measurements taken in March 2012 during the BRomine, Ozone, and Mercury EXperiment field campaign. We find a statistically significant correlation coefficient of 0.59 and RMS error of 5.8 cm. The comparison between the IceBridge snow thickness product and the 1937, 1954-1991 Soviet drifting ice station data suggests that the snow cover has thinned by 33% in the western Arctic and 44% in the Beaufort and Chukchi Seas. A rudimentary estimation shows that a thinner snow cover in the Beaufort and Chukchi Seas translates to a mid-December surface heat flux as high as 81 W/m2 compared to 32 W/m2. The relationship between the 2009-2012 thinner snow depth distribution and later sea ice freeze-up is statistically significant, with a correlation coefficient of 0.59. These results may help us better understand the surface energy budget in the changing Arctic, and may improve our ability to predict the future state of the sea ice cover.

  19. ION COMPOSITION ELUCIDATION (ICE)

    EPA Science Inventory



    Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer to simultaneously determine exact masses and relative isotopic abundances from mass peak profiles. These can be determined more accurately and at higher sensitivity ...

  20. Uncertainty Quantification for Large-Scale Ice Sheet Modeling

    SciTech Connect

    Ghattas, Omar

    2016-02-05

    This report summarizes our work to develop advanced forward and inverse solvers and uncertainty quantification capabilities for a nonlinear 3D full Stokes continental-scale ice sheet flow model. The components include: (1) forward solver: a new state-of-the-art parallel adaptive scalable high-order-accurate mass-conservative Newton-based 3D nonlinear full Stokes ice sheet flow simulator; (2) inverse solver: a new adjoint-based inexact Newton method for solution of deterministic inverse problems governed by the above 3D nonlinear full Stokes ice flow model; and (3) uncertainty quantification: a novel Hessian-based Bayesian method for quantifying uncertainties in the inverse ice sheet flow solution and propagating them forward into predictions of quantities of interest such as ice mass flux to the ocean.

  1. Dose Addition Models Based on Biologically Relevant Reductions in Fetal Testosterone Accurately Predict Postnatal Reproductive Tract Alterations by a Phthalate Mixture in Rats

    PubMed Central

    Howdeshell, Kembra L.; Rider, Cynthia V.; Wilson, Vickie S.; Furr, Johnathan R.; Lambright, Christy R.; Gray, L. Earl

    2015-01-01

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the current study were 2-fold: (1) to test whether a mixture model of dose addition based on the fetal T production data of individual phthalates would predict the effects of a 5 phthalate mixture on androgen-sensitive postnatal male reproductive tract development, and (2) to determine the biological relevance of the reductions in fetal T to induce abnormal postnatal reproductive tract development using data from the mixture study. We administered a dose range of the mixture (60, 40, 20, 10, and 5% of the top dose used in the previous fetal T production study consisting of 300 mg/kg per chemical of benzyl butyl (BBP), di(n)butyl (DBP), diethyl hexyl phthalate (DEHP), di-isobutyl phthalate (DiBP), and 100 mg dipentyl (DPP) phthalate/kg; the individual phthalates were present in equipotent doses based on their ability to reduce fetal T production) via gavage to Sprague Dawley rat dams on GD8-postnatal day 3. We compared observed mixture responses to predictions of dose addition based on the previously published potencies of the individual phthalates to reduce fetal T production relative to a reference chemical and published postnatal data for the reference chemical (called DAref). In addition, we predicted DA (called DAall) and response addition (RA) based on logistic regression analysis of all 5 individual phthalates when complete data were available. DA ref and DA all accurately predicted the observed mixture effect for 11 of 14 endpoints. Furthermore, reproductive tract malformations were seen in 17–100% of F1 males when fetal T production was reduced by about 25–72%, respectively. PMID:26350170

  2. Absolute Measurements of Macrophage Migration Inhibitory Factor and Interleukin-1-β mRNA Levels Accurately Predict Treatment Response in Depressed Patients

    PubMed Central

    Ferrari, Clarissa; Uher, Rudolf; Bocchio-Chiavetto, Luisella; Riva, Marco Andrea; Pariante, Carmine M.

    2016-01-01

    Background: Increased levels of inflammation have been associated with a poorer response to antidepressants in several clinical samples, but these findings have had been limited by low reproducibility of biomarker assays across laboratories, difficulty in predicting response probability on an individual basis, and unclear molecular mechanisms. Methods: Here we measured absolute mRNA values (a reliable quantitation of number of molecules) of Macrophage Migration Inhibitory Factor and interleukin-1β in a previously published sample from a randomized controlled trial comparing escitalopram vs nortriptyline (GENDEP) as well as in an independent, naturalistic replication sample. We then used linear discriminant analysis to calculate mRNA values cutoffs that best discriminated between responders and nonresponders after 12 weeks of antidepressants. As Macrophage Migration Inhibitory Factor and interleukin-1β might be involved in different pathways, we constructed a protein-protein interaction network by the Search Tool for the Retrieval of Interacting Genes/Proteins. Results: We identified cutoff values for the absolute mRNA measures that accurately predicted response probability on an individual basis, with positive predictive values and specificity for nonresponders of 100% in both samples (negative predictive value=82% to 85%, sensitivity=52% to 61%). Using network analysis, we identified different clusters of targets for these 2 cytokines, with Macrophage Migration Inhibitory Factor interacting predominantly with pathways involved in neurogenesis, neuroplasticity, and cell proliferation, and interleukin-1β interacting predominantly with pathways involved in the inflammasome complex, oxidative stress, and neurodegeneration. Conclusion: We believe that these data provide a clinically suitable approach to the personalization of antidepressant therapy: patients who have absolute mRNA values above the suggested cutoffs could be directed toward earlier access to more

  3. Comparison of full field and anomaly initialisation for decadal climate prediction: towards an optimal consistency between the ocean and sea-ice anomaly initialisation state

    NASA Astrophysics Data System (ADS)

    Volpi, Danila; Guemas, Virginie; Doblas-Reyes, Francisco J.

    2016-10-01

    Decadal prediction exploits sources of predictability from both the internal variability through the initialisation of the climate model from observational estimates, and the external radiative forcings. When a model is initialised with the observed state at the initial time step (Full Field Initialisation—FFI), the forecast run drifts towards the biased model climate. Distinguishing between the climate signal to be predicted and the model drift is a challenging task, because the application of a-posteriori bias correction has the risk of removing part of the variability signal. The anomaly initialisation (AI) technique aims at addressing the drift issue by answering the following question: if the model is allowed to start close to its own attractor (i.e. its biased world), but the phase of the simulated variability is constrained toward the contemporaneous observed one at the initialisation time, does the prediction skill improve? The relative merits of the FFI and AI techniques applied respectively to the ocean component and the ocean and sea ice components simultaneously in the EC-Earth global coupled model are assessed. For both strategies the initialised hindcasts show better skill than historical simulations for the ocean heat content and AMOC along the first two forecast years, for sea ice and PDO along the first forecast year, while for AMO the improvements are statistically significant for the first two forecast years. The AI in the ocean and sea ice components significantly improves the skill of the Arctic sea surface temperature over the FFI.

  4. Discovery of a general method of solving the Schrödinger and dirac equations that opens a way to accurately predictive quantum chemistry.

    PubMed

    Nakatsuji, Hiroshi

    2012-09-18

    Just as Newtonian law governs classical physics, the Schrödinger equation (SE) and the relativistic Dirac equation (DE) rule the world of chemistry. So, if we can solve these equations accurately, we can use computation to predict chemistry precisely. However, for approximately 80 years after the discovery of these equations, chemists believed that they could not solve SE and DE for atoms and molecules that included many electrons. This Account reviews ideas developed over the past decade to further the goal of predictive quantum chemistry. Between 2000 and 2005, I discovered a general method of solving the SE and DE accurately. As a first inspiration, I formulated the structure of the exact wave function of the SE in a compact mathematical form. The explicit inclusion of the exact wave function's structure within the variational space allows for the calculation of the exact wave function as a solution of the variational method. Although this process sounds almost impossible, it is indeed possible, and I have published several formulations and applied them to solve the full configuration interaction (CI) with a very small number of variables. However, when I examined analytical solutions for atoms and molecules, the Hamiltonian integrals in their secular equations diverged. This singularity problem occurred in all atoms and molecules because it originates from the singularity of the Coulomb potential in their Hamiltonians. To overcome this problem, I first introduced the inverse SE and then the scaled SE. The latter simpler idea led to immediate and surprisingly accurate solution for the SEs of the hydrogen atom, helium atom, and hydrogen molecule. The free complement (FC) method, also called the free iterative CI (free ICI) method, was efficient for solving the SEs. In the FC method, the basis functions that span the exact wave function are produced by the Hamiltonian of the system and the zeroth-order wave function. These basis functions are called complement

  5. In-situ aircraft observations of ice concentrations within clouds over the Antarctic Peninsula and Larsen Ice Shelf

    NASA Astrophysics Data System (ADS)

    Grosvenor, D. P.; Choularton, T. W.; Lachlan-Cope, T.; Gallagher, M. W.; Crosier, J.; Bower, K. N.; Ladkin, R. S.; Dorsey, J. R.

    2012-07-01

    In-situ aircraft observations of ice crystal concentrations in Antarctic clouds are presented for the first time. Orographic, layer and wave clouds around the Antarctic Peninsula and Larsen Ice shelf regions were penetrated by the British Antarctic Survey's Twin Otter Aircraft, which was equipped with modern cloud physics probes. The clouds studied were mostly in the free troposphere and hence ice crystals blown from the surface are unlikely to have been a major source for the ice phase. The temperature range covered by the experiments was 0 to -21°C. The clouds were found to contain supercooled liquid water in most regions and at heterogeneous ice formation temperatures ice crystal concentrations (60 s averages) were often less than 0.07 l-1, although values up to 0.22 l-1 were observed. Estimates of observed aerosol concentrations were used as input into the DeMott et al., 2010 ice nuclei (IN) parameterisation. The observed ice crystal number concentrations were generally in broad agreement with the IN predictions, although on the whole the predicted values were higher. Possible reasons for this are discussed and include the lack of IN observations in this region with which to characterise the parameterisation, and/or problems in relating ice concentration measurements to IN concentrations. Other IN parameterisations significantly overestimated the number of ice particles. Generally ice particle concentrations were much lower than found in clouds in middle latitudes for a given temperature. Higher ice crystal concentrations were sometimes observed at temperatures warmer than -9 °C, with values of several per litre reached. These were attributable to secondary ice particle production by the Hallett Mossop process. Even in this temperature range it was observed that there were regions with little or no ice that were dominated by supercooled liquid water. It is likely that in some cases this was due to a lack of seeding ice crystals to act as rimers to initiate

  6. In-situ aircraft observations of ice concentrations within clouds over the Antarctic Peninsula and Larsen Ice Shelf

    NASA Astrophysics Data System (ADS)

    Grosvenor, D. P.; Choularton, T. W.; Lachlan-Cope, T.; Gallagher, M. W.; Crosier, J.; Bower, K. N.; Ladkin, R. S.; Dorsey, J. R.

    2012-12-01

    In-situ aircraft observations of ice crystal concentrations in Antarctic clouds are presented for the first time. Orographic, layer and wave clouds around the Antarctic Peninsula and Larsen Ice shelf regions were penetrated by the British Antarctic Survey's Twin Otter aircraft, which was equipped with modern cloud physics probes. The clouds studied were mostly in the free troposphere and hence ice crystals blown from the surface are unlikely to have been a major source for the ice phase. The temperature range covered by the experiments was 0 to -21 °C. The clouds were found to contain supercooled liquid water in most regions and at heterogeneous ice formation temperatures ice crystal concentrations (60 s averages) were often less than 0.07 l-1, although values up to 0.22 l-1 were observed. Estimates of observed aerosol concentrations were used as input into the DeMott et al. (2010) ice nuclei (IN) parameterisation. The observed ice crystal number concentrations were generally in broad agreement with the IN predictions, although on the whole the predicted values were higher. Possible reasons for this are discussed and include the lack of IN observations in this region with which to characterise the parameterisation, and/or problems in relating ice concentration measurements to IN concentrations. Other IN parameterisations significantly overestimated the number of ice particles. Generally ice particle concentrations were much lower than found in clouds in middle latitudes for a given temperature. Higher ice crystal concentrations were sometimes observed at temperatures warmer than -9 °C, with values of several per litre reached. These were attributable to secondary ice particle production by the Hallett Mossop process. Even in this temperature range it was observed that there were regions with little or no ice that were dominated by supercooled liquid water. It is likely that in some cases this was due to a lack of seeding ice crystals to act as rimers to initiate

  7. The Need for Accurate Risk Prediction Models for Road Mapping, Shared Decision Making and Care Planning for the Elderly with Advanced Chronic Kidney Disease.

    PubMed

    Stryckers, Marijke; Nagler, Evi V; Van Biesen, Wim

    2016-11-01

    As people age, chronic kidney disease becomes more common, but it rarely leads to end-stage kidney disease. When it does, the choice between dialysis and conservative care can be daunting, as much depends on life expectancy and personal expectations of medical care. Shared decision making implies adequately informing patients about their options, and facilitating deliberation of the available information, such that decisions are tailored to the individual's values and preferences. Accurate estimations of one's risk of progression to end-stage kidney disease and death with or without dialysis are essential for shared decision making to be effective. Formal risk prediction models can help, provided they are externally validated, well-calibrated and discriminative; include unambiguous and measureable variables; and come with readily applicable equations or scores. Reliable, externally validated risk prediction models for progression of chronic kidney disease to end-stage kidney disease or mortality in frail elderly with or without chronic kidney disease are scant. Within this paper, we discuss a number of promising models, highlighting both the strengths and limitations physicians should understand for using them judiciously, and emphasize the need for external validation over new development for further advancing the field.

  8. How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II.

    PubMed

    Beckwith, Martha A; Ames, William; Vila, Fernando D; Krewald, Vera; Pantazis, Dimitrios A; Mantel, Claire; Pécaut, Jacques; Gennari, Marcello; Duboc, Carole; Collomb, Marie-Noëlle; Yano, Junko; Rehr, John J; Neese, Frank; DeBeer, Serena

    2015-10-14

    First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.

  9. The VACS Index Accurately Predicts Mortality and Treatment Response among Multi-Drug Resistant HIV Infected Patients Participating in the Options in Management with Antiretrovirals (OPTIMA) Study

    PubMed Central

    Brown, Sheldon T.; Tate, Janet P.; Kyriakides, Tassos C.; Kirkwood, Katherine A.; Holodniy, Mark; Goulet, Joseph L.; Angus, Brian J.; Cameron, D. William; Justice, Amy C.

    2014-01-01

    Objectives The VACS Index is highly predictive of all-cause mortality among HIV infected individuals within the first few years of combination antiretroviral therapy (cART). However, its accuracy among highly treatment experienced individuals and its responsiveness to treatment interventions have yet to be evaluated. We compared the accuracy and responsiveness of the VACS Index with a Restricted Index of age and traditional HIV biomarkers among patients enrolled in the OPTIMA study. Methods Using data from 324/339 (96%) patients in OPTIMA, we evaluated associations between indices and mortality using Kaplan-Meier estimates, proportional hazards models, Harrel’s C-statistic and net reclassification improvement (NRI). We also determined the association between study interventions and risk scores over time, and change in score and mortality. Results Both the Restricted Index (c = 0.70) and VACS Index (c = 0.74) predicted mortality from baseline, but discrimination was improved with the VACS Index (NRI = 23%). Change in score from baseline to 48 weeks was more strongly associated with survival for the VACS Index than the Restricted Index with respective hazard ratios of 0.26 (95% CI 0.14–0.49) and 0.39(95% CI 0.22–0.70) among the 25% most improved scores, and 2.08 (95% CI 1.27–3.38) and 1.51 (95%CI 0.90–2.53) for the 25% least improved scores. Conclusions The VACS Index predicts all-cause mortality more accurately among multi-drug resistant, treatment experienced individuals and is more responsive to changes in risk associated with treatment intervention than an index restricted to age and HIV biomarkers. The VACS Index holds promise as an intermediate outcome for intervention research. PMID:24667813

  10. Parameterizing Size Distribution in Ice Clouds

    SciTech Connect

    DeSlover, Daniel; Mitchell, David L.

    2009-09-25

    cloud optical properties formulated in terms of PSD parameters in combination with remote measurements of thermal radiances to characterize the small mode. This is possible since the absorption efficiency (Qabs) of small mode crystals is larger at 12 µm wavelength relative to 11 µm wavelength due to the process of wave resonance or photon tunneling more active at 12 µm. This makes the 12/11 µm absorption optical depth ratio (or equivalently the 12/11 µm Qabs ratio) a means for detecting the relative concentration of small ice particles in cirrus. Using this principle, this project tested and developed PSD schemes that can help characterize cirrus clouds at each of the three ARM sites: SGP, NSA and TWP. This was the main effort of this project. These PSD schemes and ice sedimentation velocities predicted from them have been used to test the new cirrus microphysics parameterization in the GCM known as the Community Climate Systems Model (CCSM) as part of an ongoing collaboration with NCAR. Regarding the second problem, we developed and did preliminary testing on a passive thermal method for retrieving the total water path (TWP) of Arctic mixed phase clouds where TWPs are often in the range of 20 to 130 g m-2 (difficult for microwave radiometers to accurately measure). We also developed a new radar method for retrieving the cloud ice water content (IWC), which can be vertically integrated to yield the ice water path (IWP). These techniques were combined to determine the IWP and liquid water path (LWP) in Arctic clouds, and hence the fraction of ice and liquid water. We have tested this approach using a case study from the ARM field campaign called M-PACE (Mixed-Phase Arctic Cloud Experiment). This research led to a new satellite remote sensing method that appears promising for detecting low levels of liquid water in high clouds typically between -20 and -36 oC. We hope to develop this method in future research.

  11. A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models

    NASA Astrophysics Data System (ADS)

    Lüpkes, Christof; Gryanik, Vladimir M.; Hartmann, JöRg; Andreas, Edgar L.

    2012-07-01

    A hierarchy of parametrizations of the neutral 10 m drag coefficients over polar sea ice with different morphology regimes is derived on the basis of a partitioning concept that splits the total surface drag into contributions of skin drag and form drag. The new derivation, which provides drag coefficients as a function of sea ice concentration and characteristic length scales of roughness elements, needs fewer assumptions than previous similar approaches. It is shown that form drag variability can explain the variability of surface drag in the marginal sea ice zone (MIZ) and in the summertime inner Arctic regions. In the MIZ, form drag is generated by floe edges; in the inner Arctic, it is generated by edges at melt ponds and leads due to the elevation of the ice surface relative to the open water surface. It is shown that an earlier fit of observed neutral drag coefficients is obtained as a special case within the new concept when specific simplifications are made which concern the floe and melt pond geometry. Due to the different surface morphologies in the MIZ and summertime Arctic, different functional dependencies of the drag coefficients on the sea ice concentration result. These differences cause only minor differences between the MIZ and summertime drag coefficients in average conditions, but they might be locally important for atmospheric momentum transport to sea ice. The new parametrization formulae can be used for present conditions but also for future climate scenarios with changing sea ice conditions.

  12. Modelling the feedbacks between mass balance, ice flow and debris transport to predict the response to climate change of debris-covered glaciers in the Himalaya

    NASA Astrophysics Data System (ADS)

    Rowan, Ann V.; Egholm, David L.; Quincey, Duncan J.; Glasser, Neil F.

    2015-11-01

    Many Himalayan glaciers are characterised in their lower reaches by a rock debris layer. This debris insulates the glacier surface from atmospheric warming and complicates the response to climate change compared to glaciers with clean-ice surfaces. Debris-covered glaciers can persist well below the altitude that would be sustainable for clean-ice glaciers, resulting in much longer timescales of mass loss and meltwater production. The properties and evolution of supraglacial debris present a considerable challenge to understanding future glacier change. Existing approaches to predicting variations in glacier volume and meltwater production rely on numerical models that represent the processes governing glaciers with clean-ice surfaces, and yield conflicting results. We developed a numerical model that couples the flow of ice and debris and includes important feedbacks between debris accumulation and glacier mass balance. To investigate the impact of debris transport on the response of a glacier to recent and future climate change, we applied this model to a large debris-covered Himalayan glacier-Khumbu Glacier in Nepal. Our results demonstrate that supraglacial debris prolongs the response of the glacier to warming and causes lowering of the glacier surface in situ, concealing the magnitude of mass loss when compared with estimates based on glacierised area. Since the Little Ice Age, Khumbu Glacier has lost 34% of its volume while its area has reduced by only 6%. We predict a decrease in glacier volume of 8-10% by AD2100, accompanied by dynamic and physical detachment of the debris-covered tongue from the active glacier within the next 150 yr. This detachment will accelerate rates of glacier decay, and similar changes are likely for other debris-covered glaciers in the Himalaya.

  13. An Intercomparison of Predicted Sea Ice Concentration from Global Ocean Forecast System & Arctic Cap Nowcast/Forecast System

    NASA Astrophysics Data System (ADS)

    Rosemond, K.

    2015-12-01

    The objective of this research is to provide an evaluation of improvements in marginal ice zone (MIZ) and pack ice estimations from the Global Ocean Forecast System (GOFS) model compared to the current operational model, the Arctic Cap Nowcast/Forecast System (ACNFS). This will be determined by an intercomparison between the subjectively estimated operational ice concentration data from the National Ice Center (NIC) MIZ analysis and the ice concentration estimates from GOFS and ACNFS. This will help ascertain which nowcast from the models compares best to the NIC operational data stream needed for vessel support. It will also provide a quantitative assessment of GOFS and ACNFS performance and be used in the Operational Evaluation (OPEVAL) report from the NIC to NRL. The intercomparison results are based on statistical evaluations through a series of map overlays from both models ACNFS, GOFS with the NIC's MIZ data. All data was transformed to a common grid and difference maps were generated to determine which model had the greatest difference compared to the MIZ ice concentrations. This was provided daily for both the freeze-up and meltout seasons. Results indicated the GOFS model surpassed the ACNFS model, however both models were comparable. These results will help US Navy and NWS Anchorage ice forecasters understand model biases and know which model guidance is likely to provide the best estimate of future ice conditions.The objective of this research is to provide an evaluation of improvements in marginal ice zone (MIZ) and pack ice estimations from the Global Ocean Forecast System (GOFS) model compared to the current operational model, the Arctic Cap Nowcast/Forecast System (ACNFS). This will be determined by an intercomparison between the subjectively estimated operational ice concentration data from the National Ice Center (NIC) MIZ analysis and the ice concentration estimates from GOFS and ACNFS. This will help ascertain which nowcast from the models

  14. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-03

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  15. Satellite remote sensing over ice

    NASA Technical Reports Server (NTRS)

    Thomas, R. H.

    1984-01-01

    Satellite remote sensing provides unique opportunities for observing ice-covered terrain. Passive-microwave data give information on snow extent on land, sea-ice extent and type, and zones of summer melting on the polar ice sheets, with the potential for estimating snow-accumulation rates on these ice sheets. All weather, high-resolution imagery of sea ice is obtained using synthetic aperture radars, and ice-movement vectors can be deduced by comparing sequential images of the same region. Radar-altimetry data provide highly detailed information on ice-sheet topography, with the potential for deducing thickening/thinning rates from repeat surveys. The coastline of Antarctica can be mapped accurately using altimetry data, and the size and spatial distribution of icebergs can be monitored. Altimetry data also distinguish open ocean from pack ice and they give an indication of sea-ice characteristics.

  16. Integrating trans-abdominal ultrasonography with fecal steroid metabolite monitoring to accurately diagnose pregnancy and predict the timing of parturition in the red panda (Ailurus fulgens styani).

    PubMed

    Curry, Erin; Browning, Lissa J; Reinhart, Paul; Roth, Terri L

    2017-02-23

    Red pandas (Ailurus fulgens styani) exhibit a variable gestation length and may experience a pseudopregnancy indistinguishable from true pregnancy; therefore, it is not possible to deduce an individual's true pregnancy status and parturition date based on breeding dates or fecal progesterone excretion patterns alone. The goal of this study was to evaluate the use of transabdominal ultrasonography for pregnancy diagnosis in red pandas. Two to three females were monitored over 4 consecutive years, generating a total of seven profiles (four pregnancies, two pseudopregnancies, and one lost pregnancy). Fecal samples were collected and assayed for progesterone (P4) and estrogen conjugate (EC) to characterize patterns associated with breeding activity and parturition events. Animals were trained for voluntary transabdominal ultrasound and examinations were performed weekly. Breeding behaviors and fecal EC data suggest that the estrus cycle of this species is 11-12 days in length. Fecal steroid metabolite analyses also revealed that neither P4 nor EC concentrations were suitable indicators of pregnancy in this species; however, a secondary increase in P4 occurred 69-71 days prior to parturition in all pregnant females, presumably coinciding with embryo implantation. Using ultrasonography, embryos were detected as early as 62 days post-breeding/50 days pre-partum and serial measurements of uterine lumen diameter were documented throughout four pregnancies. Advances in reproductive diagnostics, such as the implementation of ultrasonography, may facilitate improved husbandry of pregnant females and allow for the accurate prediction of parturition.

  17. FDG-PET measurement is more accurate than neuropsychological assessments to predict global cognitive deterioration in patients with mild cognitive impairment.

    PubMed

    Chételat, Gaël; Eustache, Francis; Viader, Fausto; De La Sayette, Vincent; Pélerin, Alice; Mézenge, Florence; Hannequin, Didier; Dupuy, Benoît; Baron, Jean-Claude; Desgranges, Béatrice

    2005-02-01

    The accurate prediction, at a pre-dementia stage of Alzheimer's disease (AD), of the subsequent clinical evolution of patients would be a major breakthrough from both therapeutic and research standpoints. Amnestic mild cognitive impairment (MCI) is presently the most common reference to address the pre-dementia stage of AD. However, previous longitudinal studies on patients with MCI assessing neuropsychological and PET markers of future conversion to AD are sparse and yield discrepant findings, while a comprehensive comparison of the relative accuracy of these two categories of measure is still lacking. In the present study, we assessed the global cognitive decline as measured by the Mattis scale in 18 patients with amnestic MCI over an 18-month follow-up period, studying which subtest of this scale showed significant deterioration over time. Using baseline measurements from neuropsychological evaluation of memory and PET, we then assessed significant markers of global cognitive change, that is, percent annual change in the Mattis scale total score, and searched for the best predictor of this global cognitive decline. Altogether, our results revealed significant decline over the 18-month follow-up period in the total score and the verbal initiation and memory-recall subscores of the Mattis scale. The percent annual change in the total Mattis score significantly correlated with age and baseline performances in delayed episodic memory recall as well as semantic autobiographical and category word fluencies. Regarding functional imaging, significant correlations were also found with baseline PET values in the right temporo-parietal and medial frontal areas. Age and right temporo-parietal PET values were the most significant predictors of subsequent global cognitive decline, and the only ones to survive stepwise regression analyses. Our findings are consistent with previous works showing predominant delayed recall and semantic memory impairment at a pre-dementia stage

  18. Ice, Ice, Baby!

    NASA Astrophysics Data System (ADS)

    Hamilton, C.

    2008-12-01

    The Center for Remote Sensing of Ice Sheets (CReSIS) has developed an outreach program based on hands-on activities called "Ice, Ice, Baby". These lessons are designed to teach the science principles of displacement, forces of motion, density, and states of matter. These properties are easily taught through the interesting topics of glaciers, icebergs, and sea level rise in K-8 classrooms. The activities are fun, engaging, and simple enough to be used at science fairs and family science nights. Students who have participated in "Ice, Ice, Baby" have successfully taught these to adults and students at informal events. The lessons are based on education standards which are available on our website www.cresis.ku.edu. This presentation will provide information on the activities, survey results from teachers who have used the material, and other suggested material that can be used before and after the activities.

  19. Arctic landfast sea ice

    NASA Astrophysics Data System (ADS)

    Konig, Christof S.

    Landfast ice is sea ice which forms and remains fixed along a coast, where it is attached either to the shore, or held between shoals or grounded icebergs. Landfast ice fundamentally modifies the momentum exchange between atmosphere and ocean, as compared to pack ice. It thus affects the heat and freshwater exchange between air and ocean and impacts on the location of ocean upwelling and downwelling zones. Further, the landfast ice edge is essential for numerous Arctic mammals and Inupiat who depend on them for their subsistence. The current generation of sea ice models is not capable of reproducing certain aspects of landfast ice formation, maintenance, and disintegration even when the spatial resolution would be sufficient to resolve such features. In my work I develop a new ice model that permits the existence of landfast sea ice even in the presence of offshore winds, as is observed in mature. Based on viscous-plastic as well as elastic-viscous-plastic ice dynamics I add tensile strength to the ice rheology and re-derive the equations as well as numerical methods to solve them. Through numerical experiments on simplified domains, the effects of those changes are demonstrated. It is found that the modifications enable landfast ice modeling, as desired. The elastic-viscous-plastic rheology leads to initial velocity fluctuations within the landfast ice that weaken the ice sheet and break it up much faster than theoretically predicted. Solving the viscous-plastic rheology using an implicit numerical method avoids those waves and comes much closer to theoretical predictions. Improvements in landfast ice modeling can only verified in comparison to observed data. I have extracted landfast sea ice data of several decades from several sources to create a landfast sea ice climatology that can be used for that purpose. Statistical analysis of the data shows several factors that significantly influence landfast ice distribution: distance from the coastline, ocean depth, as

  20. IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data

    PubMed Central

    Zhang, Wei; Wang, I-Ming; Wang, Changxi; Lin, Liya; Chai, Xianghua; Wu, Jinghua; Bett, Andrew J.; Dhanasekaran, Govindarajan; Casimiro, Danilo R.; Liu, Xiao

    2016-01-01

    Large-scale study of the properties of T-cell receptor (TCR) and B-cell receptor (BCR) repertoires through next-generation sequencing is providing excellent insights into the understanding of adaptive immune responses. Variable(Diversity)Joining [V(D)J] germline genes and alleles must be characterized in detail to facilitate repertoire analyses. However, most species do not have well-characterized TCR/BCR germline genes because of their high homology. Also, more germline alleles are required for humans and other species, which limits the capacity for studying immune repertoires. Herein, we developed “Immune Germline Prediction” (IMPre), a tool for predicting germline V/J genes and alleles using deep-sequencing data derived from TCR/BCR repertoires. We developed a new algorithm, “Seed_Clust,” for clustering, produced a multiway tree for assembly and optimized the sequence according to the characteristics of rearrangement. We trained IMPre on human samples of T-cell receptor beta (TRB) and immunoglobulin heavy chain and then tested it on additional human samples. Accuracy of 97.7, 100, 92.9, and 100% was obtained for TRBV, TRBJ, IGHV, and IGHJ, respectively. Analyses of subsampling performance for these samples showed IMPre to be robust using different data quantities. Subsequently, IMPre was tested on samples from rhesus monkeys and human long sequences: the highly accurate results demonstrated IMPre to be stable with animal and multiple data types. With rapid accumulation of high-throughput sequence data for TCR and BCR repertoires, IMPre can be applied broadly for obtaining novel genes and a large number of novel alleles. IMPre is available at https://github.com/zhangwei2015/IMPre. PMID:27867380

  1. Cosmological constraints from the CFHTLenS shear measurements using a new, accurate, and flexible way of predicting non-linear mass clustering

    NASA Astrophysics Data System (ADS)

    Angulo, Raul E.; Hilbert, Stefan

    2015-03-01

    We explore the cosmological constraints from cosmic shear using a new way of modelling the non-linear matter correlation functions. The new formalism extends the method of Angulo & White, which manipulates outputs of N-body simulations to represent the 3D non-linear mass distribution in different cosmological scenarios. We show that predictions from our approach for shear two-point correlations at 1-300 arcmin separations are accurate at the ˜10 per cent level, even for extreme changes in cosmology. For moderate changes, with target cosmologies similar to that preferred by analyses of recent Planck data, the accuracy is close to ˜5 per cent. We combine this approach with a Monte Carlo Markov chain sampler to explore constraints on a Λ cold dark matter model from the shear correlation functions measured in the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS). We obtain constraints on the parameter combination σ8(Ωm/0.27)0.6 = 0.801 ± 0.028. Combined with results from cosmic microwave background data, we obtain marginalized constraints on σ8 = 0.81 ± 0.01 and Ωm = 0.29 ± 0.01. These results are statistically compatible with previous analyses, which supports the validity of our approach. We discuss the advantages of our method and the potential it offers, including a path to model in detail (i) the effects of baryons, (ii) high-order shear correlation functions, and (iii) galaxy-galaxy lensing, among others, in future high-precision cosmological analyses.

  2. A New Sea Ice Model: Pancakes to Metrics

    NASA Technical Reports Server (NTRS)

    Coon, M.; Kwok, R.; Pruis, M.; Levy, G.; Schreyer, H. L.; Sulsky, D.; Toudal, L.

    2007-01-01

    We are developing, testing, and validating a new sea ice dynamics model that treats the ice cover as an elastic/decohesive material in the permanent pack and includes the correct frazil/pancake behavior in the marginal zone. Two salient features of present ice dynamics models are that they do not: 1) reproduce the oriented fracture patterns of openings and closings in the pack ice, and 2) accurately model the effects of frazil/pancake ice formation in the ice margin. These poorly modeled areas account for a substantial portion of the ice growth, turbulent heat flux to the atmosphere, salt flux to the ocean, and energy dissipation due to slippage, ridging, and rafting, in the Arctic. Existing sea ice models have shown limited success in predicting the degree to which a lead will open for prescribed or observed forcing conditions. An important aspect of the new model we are developing is that the existence of cracks, along with their orientation, opening, and closing, is predicted. To put this effort in perspective a short history of ice dynamics modeling and data collection is presented. The RGPS data set is used to validate the model. As part of the testing and validation of the model, we are working on a new metric for comparing linear features (leads and ridges) in the data and model to be used in data assimilation for this model. The model framework is presented as well as some results showing the creation and development of leads in a simulation of ice dynamics in the Beaufort Sea. Other presentations by the authors will show other results from this effort.

  3. Inception of ice accretion by ice crystal impact

    NASA Astrophysics Data System (ADS)

    Löwe, Jens; Kintea, Daniel; Baumert, Arne; Bansmer, Stephan; Roisman, Ilia V.; Tropea, Cameron

    2016-09-01

    In this experimental and theoretical study the ice accretion phenomena on a heated cylinder in Braunschweig Icing Wind Tunnel are investigated. The ice crystal size, velocity, the liquid-to-total mass ratio are accurately controlled. The evolution of the cylinder temperature, the time required for the inception of the ice accretion, and the ice accretion rate are measured for various operating conditions. The surface temperature of the solid target is determined by balancing the heating power in the wall and the cooling effect of the stream of ice particles. We have discovered that the inception of the ice crystal accretion is determined by the instant when the surface temperature of the heated target reduces to the freezing temperature. This result will help to model the phenomena of ice crystal accretion.

  4. Change Detection of the Amery Ice Shelf Front (2004-2012) Using ENVISAT ASAR Data

    NASA Astrophysics Data System (ADS)

    Zhao, C.; Cheng, X.; Liu, Y.

    2012-12-01

    Antarctic ice shelves are prominent constituent parts of ice sheets due to their ice-ocean-atmosphere interface and their vulnerability to regional and global changes in atmospheric and oceanic temperatures. The majority of mass loss from the Antarctic ice sheet occurs at the ice shelves via either iceberg calving or basal melting. To fully understand the complex process of ice shelf mass balance, it is necessary to monitor the ice shelf changes over an extended period of time. The Amery Ice Shelf is the largest ice shelf in East Antarctica. Understanding the changes of the Amery Ice Shelf front are crucial for making accurate predictions about the response of ice sheets to global climate change. Here we use the time series of ENVISAT images from 2004 to 2012 and the ice flow lines in Antarctic to monitor the changes of 11 test areas in the Amery Ice Shelf front (Fig. 1). Each image was linearly stretched to enhance the edges and then filtered according to an efficient image denoising scheme. We then extracted the coastlines semi-automatically by combining an artificial drawing method with an improved watershed algorithm. The 11 test areas are chosen according to the ice flow lines of the Antarctic. The results show that the Amery Ice Shelf has been expanding obviously. The rate in the middle of the Amery Ice Shelf front is higher than that on both sides of the front. The highest average propagation rate is 3.36 m/day and the lowest rate is 1.65 m/day in the past 9 years. The rates of 11 test areas during 2009 and 2010 are generally lower than those in other periods. It indicates that the propagation rate would be influenced by the climate environment. Additionally, the short-term environmental forces, such as calving events, tidal bending, ocean swell and so on would influence the ice shelf propagation. In conclusion, the rapid propagation of the Amery Ice Shelf has confirmed the fact that the East Antarctic has been expanding. Once some large iceberg calving

  5. Processes causing electrification of ice crystals in thunderclouds

    NASA Astrophysics Data System (ADS)

    Vonnegut, B.; Moore, C. B.

    Jayaratne and Saunders (1991) have performed a useful service by reporting their laboratory experiments demonstrating, contrary to the findings of Odencrantz and Buecher (1967), that ice crystal charging does not take place in an unmixed cloud of ice crystals. Jayaratne and Saunders' further cold box experiments showing that the ice crystals become electrified when a fan in the cold box is turned on, support their view that an ice-ice charging process takes place on the surfaces of the moving ice-covered fan-blades. Their conclusion, that this phenomenon might be capable of producing each second the several coulombs of charged cloud particles necessary to maintain the electrification of a thundercloud, appears justified. However, because their paper is lacking in experimental details and because it is unknown whether the conditions in their cold chamber accurately duplicate those in a thunderstorm, this point is not possible to resolve. There is good reason to doubt J and S's final conclusion, that "… in thunderstorms, ice crystal charges are similarly acquired by collision processes RATHER THAN BY ANY OTHER MECHANISM". It is puzzling to understand why the authors have chosen to ignore ion attachment, an important ice crystal charging process that does not involve collisions between ice crystals. Beginning with Gish and Wait (1950), numerous investigators have demonstrated that ion currents flow to the tops of thunderclouds as predicted by Wilson (1920). Marshall et al. (1989) and Byrne et al. (1989) have found that ice particles at cloud top carry appreciable charges that appear to be derived from the Wilson current. In an average storm there can be little doubt that this mechanism too could be producing charged ice crystals at the required rate of about a coulomb per second (Vonnegut, 1990).

  6. Prospecting for Martian Ice

    NASA Technical Reports Server (NTRS)

    McBride, S. A.; Allen, C. C.; Bell, M. S.

    2005-01-01

    During high Martian obliquity, ice is stable to lower latitudes than predicted by models of present conditions and observed by the Gamma Ray Spectrometer (approx. 60 deg N). An ice-rich layer deposited at mid-latitudes could persist to the present day; ablation of the top 1 m of ice leaving a thin insulating cover could account for lack of its detection by GRS. The presence of an ice-layer in the mid-latitudes is suggested by a network of polygons, interpreted as ice-wedge cracks. This study focuses on an exceptional concentration of polygons in Western Utopia (section of Casius quadrangle, roughly 40 deg - 50 deg N, 255 deg - 300 deg W). We attempt to determine the thickness and age of this ice layer through crater-polygons relations.

  7. Ice stream activity scaled to ice sheet volume during Laurentide Ice Sheet deglaciation.

    PubMed

    Stokes, C R; Margold, M; Clark, C D; Tarasov, L

    2016-02-18

    The contribution of the Greenland and West Antarctic ice sheets to sea level has increased in recent decades, largely owing to the thinning and retreat of outlet glaciers and ice streams. This dynamic loss is a serious concern, with some modelling studies suggesting that the collapse of a major ice sheet could be imminent or potentially underway in West Antarctica, but others predicting a more limited response. A major problem is that observations used to initialize and calibrate models typically span only a few decades, and, at the ice-sheet scale, it is unclear how the entire drainage network of ice streams evolves over longer timescales. This represents one of the largest sources of uncertainty when predicting the contributions of ice sheets to sea-level rise. A key question is whether ice streams might increase and sustain rates of mass loss over centuries or millennia, beyond those expected for a given ocean-climate forcing. Here we reconstruct the activity of 117 ice streams that operated at various times during deglaciation of the Laurentide Ice Sheet (from about 22,000 to 7,000 years ago) and show that as they activated and deactivated in different locations, their overall number decreased, they occupied a progressively smaller percentage of the ice sheet perimeter and their total discharge decreased. The underlying geology and topography clearly influenced ice stream activity, but--at the ice-sheet scale--their drainage network adjusted and was linked to changes in ice sheet volume. It is unclear whether these findings can be directly translated to modern ice sheets. However, contrary to the view that sees ice streams as unstable entities that can accelerate ice-sheet deglaciation, we conclude that ice streams exerted progressively less influence on ice sheet mass balance during the retreat of the Laurentide Ice Sheet.

  8. Modeling Commercial Turbofan Engine Icing Risk With Ice Crystal Ingestion

    NASA Technical Reports Server (NTRS)

    Jorgenson, Philip C. E.; Veres, Joseph P.

    2013-01-01

    flight. The computational tool was utilized to help guide a portion of the PSL testing, and was used to predict ice accretion could also occur at significantly lower altitudes. The predictions were qualitatively verified by subsequent testing of the engine in the PSL. The PSL test has helped to calibrate the engine icing computational tool to assess the risk of ice accretion. The results from the computer simulation identified prevalent trends in wet bulb temperature, ice particle melt ratio, and engine inlet temperature as a function of altitude for predicting engine icing risk due to ice crystal ingestion.

  9. Predictability of Ice Concentration Anomalies in the High Latitudes of the North Atlantic Using a Statistical Approach

    DTIC Science & Technology

    1988-12-01

    However, effects discussed by Ramage (1984), such as insolation, heating from the ship and cloud cover biases are not taken into account. 4. Duplication...Long-term climatic changes, or trends, may adversely influence the statistical analyses of data. Since Oort (1987) detected long-term cooling of SST...84 Naval Oceanography Command D.tachment, Asheville, N. C., Sea Ice Climatic Atlas: Volume II Arctic East, pp. I-,47 Oort A. H., and others

  10. Did glacially induced TPW end the ice age? A reanalysis

    NASA Astrophysics Data System (ADS)

    Chan, Ngai-Ham; Mitrovica, Jerry X.; Daradich, Amy

    2015-09-01

    Previous studies of Earth rotation perturbations due to ice-age loading have predicted a slow secular drift of the rotation axis relative to the surface geography (i.e. true polar wander, TPW) of order of several degrees over the Plio-Pleistocene. It has been argued that this drift and the change in the geographic distribution of solar insolation that it implies may have been responsible for important transitions in ice-age climate, including the termination of ice-age cycles.We use a revised rotational stability theory that incorporates a more accurate treatment of the Earth's background ellipticity to reconsider this issue, and demonstrate that the net displacement of the pole predicted in earlier studies disappears. This more muted polar motion is due to two factors: first, the revised theory no longer predicts the permanent shift in the rotation axis, or the so-called `unidirectional TPW', that appears in the traditional stability theory; and, second, the increased background ellipticity incorporated in the revised predictions acts to reduce the normal mode amplitudes governing the motion of the pole. We conclude that ice-age-induced TPW was not responsible for the termination of the ice age. This does not preclude the possibility that TPW induced by mantle convective flow may have played a role in major Plio-Pleistocene climate transitions, including the onset of Northern Hemisphere glaciation.

  11. Consider an Ice Stream.

    NASA Astrophysics Data System (ADS)

    Bindschadler, R.

    2002-12-01

    Forty years ago, John Nye was one of the leaders who introduced the rigors of classical physics to glaciology. His elegant treatments frequently took advantage of the then recent discovery that ice could be approximated as a plastic material. With this viewpoint, Nye was able to explain the shape of ice sheets and glaciers, to predict the expected pattern of stress and velocity within a glacier, and to derive the advance and retreat of a glacier from the record of accumulation and ablation. These advances have given generations of glaciologists tools to interpret the excellent observational record of glacier behavior and variation. In the 1980s, glaciologist, weaned on these works of Nye and of other similarly adept colleagues, carried their lessons to West Antarctica to study ice streams, the vast conveyor belts of ice that discharged nearly as much Antarctic ice as the much larger East Antarctic ice sheet. Ice streams were a glaciological conundrum. Despite the gently sloping surface, these broad features roared along, moving fastest when the gravitational impetus was least. After two decades of research, ice streams still have not given up all their secrets, yet much is now known. Internal deformation is negligible. Basal friction is frequently nil leaving the shattered margins as the primary means to avoid rapid wastage of the ice sheet. Within the margins, the resistive force results from a delicate balance of heat and evolving ice fabrics. Nevertheless, the bed beneath an ice stream cannot be ignored. It is ultimately the state of the underlying marine sediment that determines whether the ice stream can slide at all. There too, the heat balance is critical with an influx of water required to keep the bed wet enough to let the streams glide along. Ice stream research has been the portal through which glaciologists have seen and identified the complexities of West Antarctic ice sheet dynamics. Remarkably, nearly all time scales seem important. Ice stream

  12. Microbial abundance in surface ice on the Greenland Ice Sheet

    PubMed Central

    Stibal, Marek; Gözdereliler, Erkin; Cameron, Karen A.; Box, Jason E.; Stevens, Ian T.; Gokul, Jarishma K.; Schostag, Morten; Zarsky, Jakub D.; Edwards, Arwyn; Irvine-Fynn, Tristram D. L.; Jacobsen, Carsten S.

    2015-01-01

    Measuring microbial abundance in glacier ice and identifying its controls is essential for a better understanding and quantification of biogeochemical processes in glacial ecosystems. However, cell enumeration of glacier ice samples is challenging due to typically low cell numbers and the presence of interfering mineral particles. We quantified for the first time the abundance of microbial cells in surface ice from geographically distinct sites on the Greenland Ice Sheet (GrIS), using three enumeration methods: epifluorescence microscopy (EFM), flow cytometry (FCM), and quantitative polymerase chain reaction (qPCR). In addition, we reviewed published data on microbial abundance in glacier ice and tested the three methods on artificial ice samples of realistic cell (102–107 cells ml−1) and mineral particle (0.1–100 mg ml−1) concentrations, simulating a range of glacial ice types, from clean subsurface ice to surface ice to sediment-laden basal ice. We then used multivariate statistical analysis to identify factors responsible for the variation in microbial abundance on the ice sheet. EFM gave the most accurate and reproducible results of the tested methodologies, and was therefore selected as the most suitable technique for cell enumeration of ice containing dust. Cell numbers in surface ice samples, determined by EFM, ranged from ~ 2 × 103 to ~ 2 × 106 cells ml−1 while dust concentrations ranged from 0.01 to 2 mg ml−1. The lowest abundances were found in ice sampled from the accumulation area of the ice sheet and in samples affected by fresh snow; these samples may be considered as a reference point of the cell abundance of precipitants that are deposited on the ice sheet surface. Dust content was the most significant variable to explain the variation in the abundance data, which suggests a direct association between deposited dust particles and cells and/or by their provision of limited nutrients to microbial communities on the GrIS. PMID:25852678

  13. On the Ice Nucleation Spectrum

    NASA Technical Reports Server (NTRS)

    Barahona, D.

    2012-01-01

    This work presents a novel formulation of the ice nucleation spectrum, i.e. the function relating the ice crystal concentration to cloud formation conditions and aerosol properties. The new formulation is physically-based and explicitly accounts for the dependency of the ice crystal concentration on temperature, supersaturation, cooling rate, and particle size, surface area and composition. This is achieved by introducing the concepts of ice nucleation coefficient (the number of ice germs present in a particle) and nucleation probability dispersion function (the distribution of ice nucleation coefficients within the aerosol population). The new formulation is used to generate ice nucleation parameterizations for the homogeneous freezing of cloud droplets and the heterogeneous deposition ice nucleation on dust and soot ice nuclei. For homogeneous freezing, it was found that by increasing the dispersion in the droplet volume distribution the fraction of supercooled droplets in the population increases. For heterogeneous ice nucleation the new formulation consistently describes singular and stochastic behavior within a single framework. Using a fundamentally stochastic approach, both cooling rate independence and constancy of the ice nucleation fraction over time, features typically associated with singular behavior, were reproduced. Analysis of the temporal dependency of the ice nucleation spectrum suggested that experimental methods that measure the ice nucleation fraction over few seconds would tend to underestimate the ice nuclei concentration. It is shown that inferring the aerosol heterogeneous ice nucleation properties from measurements of the onset supersaturation and temperature may carry significant error as the variability in ice nucleation properties within the aerosol population is not accounted for. This work provides a simple and rigorous ice nucleation framework where theoretical predictions, laboratory measurements and field campaign data can be

  14. Ice thickness in the Northwest Passage

    NASA Astrophysics Data System (ADS)

    Haas, Christian; Howell, Stephen E. L.

    2015-09-01

    Recently, the feasibility of commercial shipping in the ice-prone Northwest Passage (NWP) has attracted a lot of attention. However, very little ice thickness information actually exists. We present results of the first ever airborne electromagnetic ice thickness surveys over the NWP carried out in April and May 2011 and 2015 over first-year and multiyear ice. These show modal thicknesses between 1.8 and 2.0 m in all regions. Mean thicknesses over 3 m and thick, deformed ice were observed over some multiyear ice regimes shown to originate from the Arctic Ocean. Thick ice features more than 100 m wide and thicker than 4 m occurred frequently. Results indicate that even in today's climate, ice conditions must still be considered severe. These results have important implications for the prediction of ice breakup and summer ice conditions, and the assessment of sea ice hazards during the summer shipping season.

  15. Impacts of alternative fuels in aviation on microphysical aerosol properties and predicted ice nuclei concentration at aircraft cruise altitude

    NASA Astrophysics Data System (ADS)

    Weinzierl, B.; D'Ascoli, E.; Sauer, D. N.; Kim, J.; Scheibe, M.; Schlager, H.; Moore, R.; Anderson, B. E.; Ullrich, R.; Mohler, O.; Hoose, C.

    2015-12-01

    In the past decades air traffic has been substantially growing affecting air quality and climate. According to the International Civil Aviation Authority (ICAO), in the next few years world passenger and freight traffic is expected to increase annually by 6-7% and 4-5%, respectively. One possibility to reduce aviation impacts on the atmosphere and climate might be the replacement of fossil fuels by alternative fuels. However, so far the effects of alternative fuels on particle emissions from aircraft engines and their ability to form contrails remain uncertain. To study the effects of alternative fuels on particle emissions and the formation of contrails, the Alternative Fuel Effects on Contrails and Cruise Emissions (ACCESS) field experiment was conducted in California. In May 2014, the DLR Falcon 20 and the NASA HU-25 jet aircraft were instrumented with an extended aerosol and trace gas payload probing different types of fuels including JP-8 and JP-8 blended with HEFA (Hydroprocessed Esters and Fatty Acids) while the NASA DC8 aircraft acted as the source aircraft for ACCESS-2. Emission measurements were taken in the DC8 exhaust plumes at aircraft cruise level between 9-12 km altitude and at distances between 50 m and 20 km behind the DC8 engines. Here, we will present results from the ACCESS-2 aerosol measurements which show a 30-60% reduction of the non-volatile (mainly black carbon) particle number concentration in the aircraft exhaust for the HEFA-blend compared to conventional JP-8 fuel. Size-resolved particle emission indices show the largest reductions for larger particle sizes suggesting that the HEFA blend contains fewer and smaller black carbon particles. We will combine the airborne measurements with a parameterization of deposition nucleation developed during a number of ice nucleation experiments at the AIDA chamber in Karlsruhe and discuss the impact of alternative fuels on the abundance of potential ice nuclei at cruise conditions.

  16. Interspecies scaling of urinary excretory amounts of nine drugs belonging to different therapeutic areas with diverse chemical structures - accurate prediction of the human urinary excretory amounts.

    PubMed

    Bhamidipati, Ravi Kanth; Mullangi, Ramesh; Srinivas, Nuggehally R

    2017-02-01

    1. The human urinary excretory amounts of total drug (parent + metabolites) were predicted for nine drugs with diverse chemical structures using simple allometry. The drugs used for scaling were cephapirin, olanzapine, labetolol, carisbamate, voriconazole, tofacitinib, nevirapine, ropinirole, and cyclindole. 2. The traditional allometric scaling was attempted using Y = aW(b) relationship. The corresponding predicted urinary amounts were converted into % recovery by using appropriate human dose. Appropriate statistical tests comprising of fold-difference (predicted/observed values) and error calculations (MAE and RMSE) were performed. 3. The interspecies scaling of all nine drugs tested showed excellent correlation (r > 0.9672). The predictions for eight out of nine drugs (exception was cephaphirin) were contained within 0.80-1.25 fold-differences. The MAE and RMSE were within ± 18% and 14.64%, respectively. 4. The present work supported the potential application of prospective allometry scaling to predict the urinary excretory amounts of the total drug and gauge any issues for the renal handling of the total drug.

  17. [Tail Plane Icing

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The Aviation Safety Program initiated by NASA in 1997 has put greater emphasis in safety related research activities. Ice-contaminated-tailplane stall (ICTS) has been identified by the NASA Lewis Icing Technology Branch as an important activity for aircraft safety related research. The ICTS phenomenon is characterized as a sudden, often uncontrollable aircraft nose- down pitching moment, which occurs due to increased angle-of-attack of the horizontal tailplane resulting in tailplane stall. Typically, this phenomenon occurs when lowering the flaps during final approach while operating in or recently departing from icing conditions. Ice formation on the tailplane leading edge can reduce tailplane angle-of-attack range and cause flow separation resulting in a significant reduction or complete loss of aircraft pitch control. In 1993, the Federal Aviation Authority (FAA) and NASA embarked upon a four-year research program to address the problem of tailplane stall and to quantify the effect of tailplane ice accretion on aircraft performance and handling characteristics. The goals of this program, which was completed in March 1998, were to collect aerodynamic data for an aircraft tail with and without ice contamination and to develop analytical methods for predicting the effects of tailplane ice contamination. Extensive dry air and icing tunnel tests which resulted in a database of the aerodynamic effects associated with tailplane ice contamination. Although the FAA/NASA tailplane icing program generated some answers regarding ice-contaminated-tailplane stall (ICTS) phenomena, NASA researchers have found many open questions that warrant further investigation into ICTS. In addition, several aircraft manufacturers have expressed interest in a second research program to expand the database to other tail configurations and to develop experimental and computational methodologies for evaluating the ICTS phenomenon. In 1998, the icing branch at NASA Lewis initiated a second

  18. Sea Ice

    NASA Technical Reports Server (NTRS)

    Parkinson, Claire L.; Cavalieri, Donald J.

    2005-01-01

    Sea ice covers vast areas of the polar oceans, with ice extent in the Northern Hemisphere ranging from approximately 7 x 10(exp 6) sq km in September to approximately 15 x 10(exp 6) sq km in March and ice extent in the Southern Hemisphere ranging from approximately 3 x 10(exp 6) sq km in February to approximately 18 x 10(exp 6) sq km in September. These ice covers have major impacts on the atmosphere, oceans, and ecosystems of the polar regions, and so as changes occur in them there are potential widespread consequences. Satellite data reveal considerable interannual variability in both polar sea ice covers, and many studies suggest possible connections between the ice and various oscillations within the climate system, such as the Arctic Oscillation, North Atlantic Oscillation, and Antarctic Oscillation, or Southern Annular Mode. Nonetheless, statistically significant long-term trends are also apparent, including overall trends of decreased ice coverage in the Arctic and increased ice coverage in the Antarctic from late 1978 through the end of 2003, with the Antarctic ice increases following marked decreases in the Antarctic ice during the 1970s. For a detailed picture of the seasonally varying ice cover at the start of the 21st century, this chapter includes ice concentration maps for each month of 2001 for both the Arctic and the Antarctic, as well as an overview of what the satellite record has revealed about the two polar ice covers from the 1970s through 2003.

  19. CFD Analysis of the Aerodynamics of a Business-Jet Airfoil with Leading-Edge Ice Accretion

    NASA Technical Reports Server (NTRS)

    Chi, X.; Zhu, B.; Shih, T. I.-P.; Addy, H. E.; Choo, Y. K.

    2004-01-01

    For rime ice - where the ice buildup has only rough and jagged surfaces but no protruding horns - this study shows two dimensional CFD analysis based on the one-equation Spalart-Almaras (S-A) turbulence model to predict accurately the lift, drag, and pressure coefficients up to near the stall angle. For glaze ice - where the ice buildup has two or more protruding horns near the airfoil's leading edge - CFD predictions were much less satisfactory because of the large separated region produced by the horns even at zero angle of attack. This CFD study, based on the WIND and the Fluent codes, assesses the following turbulence models by comparing predictions with available experimental data: S-A, standard k-epsilon, shear-stress transport, v(exp 2)-f, and differential Reynolds stress.

  20. Over Ice

    NASA Video Gallery

    All about NASA's IceBridge P-3B plane and its IceBridge retrofit. Upgraded with 21st century "special modifications", the aircraft is less a cold war relic and more like the Space Agency's Millenni...

  1. Accurate prediction of higher-level electronic structure energies for large databases using neural networks, Hartree-Fock energies, and small subsets of the database.

    PubMed

    Malshe, M; Pukrittayakamee, A; Raff, L M; Hagan, M; Bukkapatnam, S; Komanduri, R

    2009-09-28

    A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68,308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be

  2. Accurate prediction of higher-level electronic structure energies for large databases using neural networks, Hartree-Fock energies, and small subsets of the database

    NASA Astrophysics Data System (ADS)

    Malshe, M.; Pukrittayakamee, A.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.

    2009-09-01

    A novel method is presented that significantly reduces the computational bottleneck of executing high-level, electronic structure calculations of the energies and their gradients for a large database that adequately samples the configuration space of importance for systems containing more than four atoms that are undergoing multiple, simultaneous reactions in several energetically open channels. The basis of the method is the high-degree of correlation that generally exists between the Hartree-Fock (HF) and higher-level electronic structure energies. It is shown that if the input vector to a neural network (NN) includes both the configuration coordinates and the HF energies of a small subset of the database, MP4(SDQ) energies with the same basis set can be predicted for the entire database using only the HF and MP4(SDQ) energies for the small subset and the HF energies for the remainder of the database. The predictive error is shown to be less than or equal to the NN fitting error if a NN is fitted to the entire database of higher-level electronic structure energies. The general method is applied to the computation of MP4(SDQ) energies of 68 308 configurations that comprise the database for the simultaneous, unimolecular decomposition of vinyl bromide into six different reaction channels. The predictive accuracy of the method is investigated by employing successively smaller subsets of the database to train the NN to predict the MP4(SDQ) energies of the remaining configurations of the database. The results indicate that for this system, the subset can be as small as 8% of the total number of configurations in the database without loss of accuracy beyond that expected if a NN is employed to fit the higher-level energies for the entire database. The utilization of this procedure is shown to save about 78% of the total computational time required for the execution of the MP4(SDQ) calculations. The sampling error involved with selection of the subset is shown to be

  3. Ice crystal ingestion by turbofans

    NASA Astrophysics Data System (ADS)

    Rios Pabon, Manuel A.

    This Thesis will present the problem of inflight icing in general and inflight icing caused by the ingestion of high altitude ice crystals produced by high energy mesoscale convective complexes in particular, and propose a new device to prevent it based on dielectric barrier discharge plasma. Inflight icing is known to be the cause of 583 air accidents and more than 800 deaths in more than a decade. The new ice crystal ingestion problem has caused more than 100 flights to lose engine power since the 1990's, and the NTSB identified it as one of the causes of the Air France flight 447 accident in 1-Jun2008. The mechanics of inflight icing not caused by ice crystals are well established. Aircraft surfaces exposed to supercooled liquid water droplets will accrete ice in direct proportion of the droplet catch and the freezing heat transfer process. The multiphase flow droplet catch is predicted by the simple sum of forces on each spherical droplet and a droplet trajectory calculation based on Lagrangian or Eulerian analysis. The most widely used freezing heat transfer model for inflight icing caused by supercooled droplets was established by Messinger. Several computer programs implement these analytical models to predict inflight icing, with LEWICE being based on Lagrangian analysis and FENSAP being based on Eulerian analysis as the best representatives among them. This Thesis presents the multiphase fluid mechanics particular to ice crystals, and explains how it differs from the established droplet multiphase flow, and the obstacles in implementing the former in computational analysis. A new modification of the Messinger thermal model is proposed to account for ice accretion produced by ice crystal impingement. Because there exist no computational and experimental ways to fully replicate ice crystal inflight icing, and because existing ice protections systems consume vast amounts of energy, a new ice protection device based on dielectric barrier discharge plasma is

  4. Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis.

    PubMed

    Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

    2011-04-01

    Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore

  5. An experimental and theoretical study of the ice accretion process during artificial and natural icing conditions

    NASA Technical Reports Server (NTRS)

    Kirby, Mark S.; Hansman, R. John

    1988-01-01

    Real-time measurements of ice growth during artificial and natural icing conditions were conducted using an ultrasonic pulse-echo technique. This technique allows ice thickness to be measured with an accuracy of + or - 0.5 mm; in addition, the ultrasonic signal characteristics may be used to detect the presence of liquid on the ice surface and hence discern wet and dry ice growth behavior. Ice growth was measured on the stagnation line of a cylinder exposed to artificial icing conditions in the NASA Lewis Icing Research Tunnel (IRT), and similarly for a cylinder exposed in flight to natural icing conditions. Ice thickness was observed to increase approximately linearly with exposure time during the initial icing period. The ice accretion rate was found to vary with cloud temperature during wet ice growth, and liquid runback from the stagnation region was inferred. A steady-state energy balance model for the icing surface was used to compare heat transfer characteristics for IRT and natural icing conditions. Ultrasonic measurements of wet and dry ice growth observed in the IRT and in flight were compared with icing regimes predicted by a series of heat transfer coefficients. The heat transfer magnitude was generally inferred to be higher for the IRT than for the natural icing conditions encountered in flight. An apparent variation in the heat transfer magnitude was also observed for flights conducted through different natural icing-cloud formations.

  6. Use of dose-dependent absorption into target tissues to more accurately predict cancer risk at low oral doses of hexavalent chromium.

    PubMed

    Haney, J

    2015-02-01

    The mouse dose at the lowest water concentration used in the National Toxicology Program hexavalent chromium (CrVI) drinking water study (NTP, 2008) is about 74,500 times higher than the approximate human dose corresponding to the 35-city geometric mean reported in EWG (2010) and over 1000 times higher than that based on the highest reported tap water concentration. With experimental and environmental doses differing greatly, it is a regulatory challenge to extrapolate high-dose results to environmental doses orders of magnitude lower in a meaningful and toxicologically predictive manner. This seems particularly true for the low-dose extrapolation of results for oral CrVI-induced carcinogenesis since dose-dependent differences in the dose fraction absorbed by mouse target tissues are apparent (Kirman et al., 2012). These data can be used for a straightforward adjustment of the USEPA (2010) draft oral slope factor (SFo) to be more predictive of risk at environmentally-relevant doses. More specifically, the evaluation of observed and modeled differences in the fraction of dose absorbed by target tissues at the point-of-departure for the draft SFo calculation versus lower doses suggests that the draft SFo be divided by a dose-specific adjustment factor of at least an order of magnitude to be less over-predictive of risk at more environmentally-relevant doses.

  7. A Second New Species of Ice Crawlers from China (Insecta: Grylloblattodea), with Thorax Evolution and the Prediction of Potential Distribution

    PubMed Central

    Bai, Ming; Jarvis, Karl; Wang, Shu-Yong; Song, Ke-Qing; Wang, Yan-Ping; Wang, Zhi-Liang; Li, Wen-Zhu; Wang, Wei; Yang, Xing-Ke

    2010-01-01

    Modern grylloblattids are one of the least diverse of the modern insect orders. The thorax changes in morphology might be associated with the changes of the function of the forelegs, wing loss, changes in behavior and adaptation to habitat. As temperature is the main barrier for migration of modern grylloblattids, the range of each species is extremely limited. The potential distribution areas of grylloblattids remain unclear. A second new species of ice crawlers (Insecta: Grylloblattodea), Grylloblattella cheni Bai, Wang et Yang sp. nov., is described from China. The distribution map and key to species of Grylloblattella are given. A comparison of the thorax of extant and extinct Grylloblattodea is presented, with an emphasis on the pronotum using geometric morphometric analysis, which may reflect thorax adaptation and the evolution of Grylloblattodea. Potential global distribution of grylloblattids is inferred. Highly diversified pronota of extinct Grylloblattodea may reflect diverse habitats and niches. The relatively homogeneous pronota of modern grylloblattids might be explained by two hypotheses: synapomorphy or convergent evolution. Most fossils of Grylloblattodea contain an obviously longer meso- and metathorax than prothorax. The length of the meso- and metathorax of modern grylloblattids is normally shorter than the prothorax. This may be associated with the wing loss, which is accompanied by muscle reduction and changes to the thoracic skeleton system. Threats to grylloblattids and several conservation comments are also provided. PMID:20877572

  8. Normal Tissue Complication Probability Estimation by the Lyman-Kutcher-Burman Method Does Not Accurately Predict Spinal Cord Tolerance to Stereotactic Radiosurgery

    SciTech Connect

    Daly, Megan E.; Luxton, Gary; Choi, Clara Y.H.; Gibbs, Iris C.; Chang, Steven D.; Adler, John R.; Soltys, Scott G.

    2012-04-01

    Purpose: To determine whether normal tissue complication probability (NTCP) analyses of the human spinal cord by use of the Lyman-Kutcher-Burman (LKB) model, supplemented by linear-quadratic modeling to account for the effect of fractionation, predict the risk of myelopathy from stereotactic radiosurgery (SRS). Methods and Materials: From November 2001 to July 2008, 24 spinal hemangioblastomas in 17 patients were treated with SRS. Of the tumors, 17 received 1 fraction with a median dose of 20 Gy (range, 18-30 Gy) and 7 received 20 to 25 Gy in 2 or 3 sessions, with cord maximum doses of 22.7 Gy (range, 17.8-30.9 Gy) and 22.0 Gy (range, 20.2-26.6 Gy), respectively. By use of conventional values for {alpha}/{beta}, volume parameter n, 50% complication probability dose TD{sub 50}, and inverse slope parameter m, a computationally simplified implementation of the LKB model was used to calculate the biologically equivalent uniform dose and NTCP for each treatment. Exploratory calculations were performed with alternate values of {alpha}/{beta} and n. Results: In this study 1 case (4%) of myelopathy occurred. The LKB model using radiobiological parameters from Emami and the logistic model with parameters from Schultheiss overestimated complication rates, predicting 13 complications (54%) and 18 complications (75%), respectively. An increase in the volume parameter (n), to assume greater parallel organization, improved the predictive value of the models. Maximum-likelihood LKB fitting of {alpha}/{beta} and n yielded better predictions (0.7 complications), with n = 0.023 and {alpha}/{beta} = 17.8 Gy. Conclusions: The spinal cord tolerance to the dosimetry of SRS is higher than predicted by the LKB model using any set of accepted parameters. Only a high {alpha}/{beta} value in the LKB model and only a large volume effect in the logistic model with Schultheiss data could explain the low number of complications observed. This finding emphasizes that radiobiological models

  9. The role of sediment supply in esker formation and ice tunnel evolution

    NASA Astrophysics Data System (ADS)

    Burke, Matthew J.; Brennand, Tracy A.; Sjogren, Darren B.

    2015-05-01

    Meltwater is an important part of the glacier system as it can directly influence ice sheet dynamics. Although it is important that ice sheet models incorporate accurate information about subglacial meltwater processes, the relative inaccessibility of contemporary ice sheet beds makes direct investigation challenging. Former ice sheet beds contain a wealth of meltwater landforms such as eskers that, if accurately interpreted, can provide detailed insight into the hydrology of former ice sheets. Eskers are the casts of ice-walled channels and are a common landform within the footprint of the last Laurentide and Cordilleran Ice Sheets. In south-western Alberta, esker distribution suggests that both water and sediment supply may have been important controls; the longest esker ridge segments are located within meltwater valleys partially filled by glaciofluvial sediments, whereas the shortest esker ridge segments are located in areas dominated by clast-poor till. Through detailed esker ridge planform and crest-type mapping, and near surface geophysics we reveal morpho-sedimentary relationships that suggest esker sedimentation was dynamic, but that esker distribution and architecture were primarily governed by sediment supply. Through comparison of these data with data from eskers elsewhere, we suggest three formative scenarios: 1) where sediment supply and flow powers were high, coarse sediment loads result in rapid deposition, and rates of thermo-mechanical ice tunnel growth is exceeded by the rate of ice tunnel closure due to sediment infilling. High sedimentation rates reduce ice tunnel cross-sectional area, cause an increase in meltwater flow velocity and force ice tunnel growth. Thus, ice tunnel growth is fastest where sedimentation rate is highest; this positive feedback results in a non-uniform ice tunnel geometry, and favours macroform development and non-uniform ridge geometry. 2) Where sediment supply is limited, but flow power high, the rate of sedimentation

  10. A Newly Updated Database of Elevation-changes of the Greenand Ice Sheet to Study Surface Processes and Ice Dynamics

    NASA Astrophysics Data System (ADS)

    Schenk, A. F.; Csatho, B. M.; van den Broeke, M.; Kuipers Munneke, P.

    2015-12-01

    This paper reports about important upgrades of the Greenland Ice Sheet (GrIS) surface elevation and elevation-change database obtained with our Surface Elevation And Change detection (SERAC) software suite. We have developed SERAC to derive information from laser altimetry data, particularly time series of elevation changes and their partitioning into changes caused by ice dynamics. This allows direct investigation of ice dynamic processes that is much needed for improving the predictive power of ice sheet models. SERAC is different from most other change detection methods. It is based on detecting changes of surface patches, about 1 km by 1 km in size, rather than deriving elevation changes from individual laser points. The current database consists of ~100,000 time series with satellite laser altimetry data from ICESat, airborne laser observations obtained by NASA's Airborne Topographic Mapper (ATM) and the Land, Vegetation and Ice Sensor (LVIS). The upgrade is significant, because not only new observations from 2013 and 2014 have been added but also a number of improvements lead to a more comprehensive and consistent record of elevation-changes. First, we used the model that gives in addition to ice sheet also information about ice caps and glaciers (Rastner et al., 2012) for deciding if a laser point is on the ice sheet or ice cap. Then we added small gaps that exist in the ICESat GLA12 data set because the ice sheet mask is not wide enough. The new database is now more complete and will facilitate more accurate comparisons of mass balance studies obtained from the Gravity Recovery and Climate Experiment system (GRACE). For determining the part of a time series caused by ice dynamics we used the new firn compaction model and Surface Mass Balance (SMB) estimates from RACMO2.3. The new database spans the time period from 1993 to 2014. Adding new observations amounts to a spatial densification of the old record and at the same time extends the time domain by two

  11. Lost in translation: preclinical studies on 3,4-methylenedioxymethamphetamine provide information on mechanisms of action, but do not allow accurate prediction of adverse events in humans

    PubMed Central

    Green, AR; King, MV; Shortall, SE; Fone, KCF

    2012-01-01

    3,4-Methylenedioxymethamphetamine (MDMA) induces both acute adverse effects and long-term neurotoxic loss of brain 5-HT neurones in laboratory animals. However, when choosing doses, most preclinical studies have paid little attention to the pharmacokinetics of the drug in humans or animals. The recreational use of MDMA and current clinical investigations of the drug for therapeutic purposes demand better translational pharmacology to allow accurate risk assessment of its ability to induce adverse events. Recent pharmacokinetic studies on MDMA in animals and humans are reviewed and indicate that the risks following MDMA ingestion should be re-evaluated. Acute behavioural and body temperature changes result from rapid MDMA-induced monoamine release, whereas long-term neurotoxicity is primarily caused by metabolites of the drug. Therefore acute physiological changes in humans are fairly accurately mimicked in animals by appropriate dosing, although allometric dosing calculations have little value. Long-term changes require MDMA to be metabolized in a similar manner in experimental animals and humans. However, the rate of metabolism of MDMA and its major metabolites is slower in humans than rats or monkeys, potentially allowing endogenous neuroprotective mechanisms to function in a species specific manner. Furthermore acute hyperthermia in humans probably limits the chance of recreational users ingesting sufficient MDMA to produce neurotoxicity, unlike in the rat. MDMA also inhibits the major enzyme responsible for its metabolism in humans thereby also assisting in preventing neurotoxicity. These observations question whether MDMA alone produces long-term 5-HT neurotoxicity in human brain, although when taken in combination with other recreational drugs it may induce neurotoxicity. LINKED ARTICLES This article is commented on by Parrott, pp. 1518–1520 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476-5381.2012.01941.x and to view the the

  12. Race-specific genetic risk score is more accurate than nonrace-specific genetic risk score for predicting prostate cancer and high-grade diseases.

    PubMed

    Na, Rong; Ye, Dingwei; Qi, Jun; Liu, Fang; Lin, Xiaoling; Helfand, Brian T; Brendler, Charles B; Conran, Carly; Gong, Jian; Wu, Yishuo; Gao, Xu; Chen, Yaqing; Zheng, S Lilly; Mo, Zengnan; Ding, Qiang; Sun, Yinghao; Xu, Jianfeng

    2016-01-01

    Genetic risk score (GRS) based on disease risk-associated single nucleotide polymorphisms (SNPs) is an informative tool that can be used to provide inherited information for specific diseases in addition to family history. However, it is still unknown whether only SNPs that are implicated in a specific racial group should be used when calculating GRSs. The objective of this study is to compare the performance of race-specific GRS and nonrace-specific GRS for predicting prostate cancer (PCa) among 1338 patients underwent prostate biopsy in Shanghai, China. A race-specific GRS was calculated with seven PCa risk-associated SNPs implicated in East Asians (GRS7), and a nonrace-specific GRS was calculated based on 76 PCa risk-associated SNPs implicated in at least one racial group (GRS76). The means of GRS7 and GRS76 were 1.19 and 1.85, respectively, in the study population. Higher GRS7 and GRS76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRS7 had a better area under the receiver-operating curve (AUC) than GRS76 for discriminating PCa (0.602 vs 0.573) and high-grade PCa (0.603 vs 0.575) but did not reach statistical significance. GRS7 had a better (up to 13% at different cutoffs) positive predictive value (PPV) than GRS76. In conclusion, a race-specific GRS is more robust and has a better performance when predicting PCa in East Asian men than a GRS calculated using SNPs that are not shown to be associated with East Asians.

  13. The CUPIC algorithm: an accurate model for the prediction of sustained viral response under telaprevir or boceprevir triple therapy in cirrhotic patients.

    PubMed

    Boursier, J; Ducancelle, A; Vergniol, J; Veillon, P; Moal, V; Dufour, C; Bronowicki, J-P; Larrey, D; Hézode, C; Zoulim, F; Fontaine, H; Canva, V; Poynard, T; Allam, S; De Lédinghen, V

    2015-12-01

    Triple therapy using boceprevir or telaprevir remains the reference treatment for genotype 1 chronic hepatitis C in countries where new interferon-free regimens have not yet become available. Antiviral treatment is highly required in cirrhotic patients, but they represent a difficult-to-treat population. We aimed to develop a simple algorithm for the prediction of sustained viral response (SVR) in cirrhotic patients treated with triple therapy. A total of 484 cirrhotic patients from the ANRS CO20 CUPIC cohort treated with triple therapy were randomly distributed into derivation and validation sets. A total of 52.1% of patients achieved SVR. In the derivation set, a D0 score for the prediction of SVR before treatment initiation included the following independent predictors collected at day 0: prior treatment response, gamma-GT, platelets, telaprevir treatment, viral load. To refine the prediction at the early phase of the treatment, a W4 score included as additional parameter the viral load collected at week 4. The D0 and W4 scores were combined in the CUPIC algorithm defining three subgroups: 'no treatment initiation or early stop at week 4', 'undetermined' and 'SVR highly probable'. In the validation set, the rates of SVR in these three subgroups were, respectively, 11.1%, 50.0% and 82.2% (P < 0.001). By replacing the variable 'prior treatment response' with 'IL28B genotype', another algorithm was derived for treatment-naïve patients with similar results. The CUPIC algorithm is an easy-to-use tool that helps physicians weigh their decision between immediately treating cirrhotic patients using boceprevir/telaprevir triple therapy or waiting for new drugs to become available in their country.

  14. A model of basal hydrological networks, ice-infiltrated sediments, and effective stress

    NASA Astrophysics Data System (ADS)

    Papamarcos, S. S.; Rempel, A. W.

    2011-12-01

    angle of convergence at shallower gradients (2 Pa/m) can be as low as 57 degrees from the direction of ice flow. These preliminary calculations are being extended to further explore the factors that determine the structure of steady-state drainage networks, and their response to transient events. The effective stress conditions at the base of an ice sheet regulate frictional controls on sliding velocities. Predictive models that treat both the effective stress in basal conduits as well as the conditions in the surrounding bed are required to provide a more accurate description of how subglacial hydrology affects the movement of the overlying ice.

  15. Regional seasonal forecasts of the Arctic sea ice in two coupled climate models

    NASA Astrophysics Data System (ADS)

    Chevallier, Matthieu; Guémas, Virginie; Salas y Mélia, David; Doblas-Reyes, Francisco

    2015-04-01

    The predictive capabilities of two state-of-the-art coupled atmosphere-ocean global climate models (CNRM-CM5.1 and EC-Earth v2.3) in seasonal forecasting of the Arctic sea ice will be presented with a focus on regional skill. 5-month hindcasts of September sea ice area in the Arctic peripherial seas (Barents-Kara seas, Laptev-East Siberian seas, Chukchi sea and Beaufort sea) and March sea ice area in the marginal ice zones (Barents, Greenland, Labrador, Bering and Okhotsk sea) have been produced over the period 1990-2009. Systems mainly differ with respect to the initialization strategy, the ensemble generation techniques and the sea ice components. Predictive skill, assessed in terms of actual and potential predictability, is comparable in the two systems for both summer and winter hindcasts. Most interestingly, the multi-model prediction is often better than individual predictions in several sub-basins, including the Barents sea in the winter and most shelf seas in the summer. Systematic biases are also reduced using the multi-model predictions. Results from this study show that a regional zoom of global seasonal forecasts could be useful for operational needs. This study also show that the multi-model approach may be the step forward in producing accurate and reliable seasonal forecasts based on coupled global climate models.

  16. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

    PubMed Central

    Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690

  17. Pyroelectricity of water ice.

    PubMed

    Wang, Hanfu; Bell, Richard C; Iedema, Martin J; Schenter, Gregory K; Wu, Kai; Cowin, James P

    2008-05-22

    Water ice usually is thought to have zero pyroelectricity by symmetry. However, biasing it with ions breaks the symmetry because of the induced partial dipole alignment. This unmasks a large pyroelectricity. Ions were soft-landed upon 1 mum films of water ice at temperatures greater than 160 K. When cooled below 140-150 K, the dipole alignment locks in. Work function measurements of these films then show high and reversible pyroelectric activity from 30 to 150 K. For an initial approximately 10 V induced by the deposited ions at 160 K, the observed bias below 150 K varies approximately as 10 Vx(T/150 K)2. This implies that water has pyroelectric coefficients as large as that of many commercial pyroelectrics, such as lead zirconate titanate (PZT). The pyroelectricity of water ice, not previously reported, is in reasonable agreement with that predicted using harmonic analysis of a model system of SPC ice. The pyroelectricity is observed in crystalline and compact amorphous ice, deuterated or not. This implies that for water ice between 0 and 150 K (such as astrophysical ices), temperature changes can induce strong electric fields (approximately 10 MV/m) that can influence their chemistry, ion trajectories, or binding.

  18. NASA Iced Aerodynamics and Controls Current Research

    NASA Technical Reports Server (NTRS)

    Addy, Gene

    2009-01-01

    This slide presentation reviews the state of current research in the area of aerodynamics and aircraft control with ice conditions by the Aviation Safety Program, part of the Integrated Resilient Aircraft Controls Project (IRAC). Included in the presentation is a overview of the modeling efforts. The objective of the modeling is to develop experimental and computational methods to model and predict aircraft response during adverse flight conditions, including icing. The Aircraft icing modeling efforts includes the Ice-Contaminated Aerodynamics Modeling, which examines the effects of ice contamination on aircraft aerodynamics, and CFD modeling of ice-contaminated aircraft aerodynamics, and Advanced Ice Accretion Process Modeling which examines the physics of ice accretion, and works on computational modeling of ice accretions. The IRAC testbed, a Generic Transport Model (GTM) and its use in the investigation of the effects of icing on its aerodynamics is also reviewed. This has led to a more thorough understanding and models, both theoretical and empirical of icing physics and ice accretion for airframes, advanced 3D ice accretion prediction codes, CFD methods for iced aerodynamics and better understanding of aircraft iced aerodynamics and its effects on control surface effectiveness.

  19. Accurate prediction of diradical chemistry from a single-reference density-matrix method: Model application to the bicyclobutane to gauche-1,3-butadiene isomerization

    SciTech Connect

    Bertels, Luke W.; Mazziotti, David A.

    2014-07-28

    Multireference correlation in diradical molecules can be captured by a single-reference 2-electron reduced-density-matrix (2-RDM) calculation with only single and double excitations in the 2-RDM parametrization. The 2-RDM parametrization is determined by N-representability conditions that are non-perturbative in their treatment of the electron correlation. Conventional single-reference wave function methods cannot describe the entanglement within diradical molecules without employing triple- and potentially even higher-order excitations of the mean-field determinant. In the isomerization of bicyclobutane to gauche-1,3-butadiene the parametric 2-RDM (p2-RDM) method predicts that the diradical disrotatory transition state is 58.9 kcal/mol above bicyclobutane. This barrier is in agreement with previous multireference calculations as well as recent Monte Carlo and higher-order coupled cluster calculations. The p2-RDM method predicts the Nth natural-orbital occupation number of the transition state to be 0.635, revealing its diradical character. The optimized geometry from the p2-RDM method differs in important details from the complete-active-space self-consistent-field geometry used in many previous studies including the Monte Carlo calculation.

  20. Accurate Prediction of Glucuronidation of Structurally Diverse Phenolics by Human UGT1A9 Using Combined Experimental and In Silico Approaches

    PubMed Central

    Wu, Baojian; Wang, Xiaoqiang; Zhang, Shuxing; Hu, Ming

    2012-01-01

    Purpose The catalytic selectivity of human UGT1A9, an important membrane-bound enzyme catalyzing glucuronidation of xenobiotics were determined experimentally using 145 phenolics, and analyzed by 3D-QSAR methods. Methods The catalytic efficiency of UGT1A9 was determined by kinetic profiling. Quantitative structure activity relationships were analyzed using the CoMFA and CoMSIA techniques. Molecular alignment of the substrate structures was made by superimposing the glucuronidation site and its adjacent aromatic ring to achieve maximal steric overlap. For a substrate with multiple active glucuronidation sites, each site was considered as a separate substrate. Results The 3D-QSAR analyses produced statistically reliable models with good predictive power (CoMFA: q2 = 0.548, r2= 0.949, r2pred = 0.775; CoMSIA: q2 = 0.579, r2= 0.876, r2pred = 0.700). The contour coefficient maps were applied to elucidate structural features among substrates that are responsible for the selectivity differences. Furthermore, the contour coefficient maps were overlaid in the catalytic pocket of a homology model of UGT1A9; this enabled us to identify the UGT1A9 catalytic pocket with a high degree of confidence. Conclusion The CoMFA/CoMSIA models can predict the substrate selectivity and in vitro clearance of UGT1A9. Our findings also provide a possible molecular basis for understanding UGT1A9 functions and its substrate selectivity. PMID:22302521

  1. Is scoring system of computed tomography based metric parameters can accurately predicts shock wave lithotripsy stone-free rates and aid in the development of treatment strategies?

    PubMed Central

    Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim

    2016-01-01

    Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192

  2. SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

    PubMed

    Schunter, C; Garza, J C; Macpherson, E; Pascual, M

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA-seq is one such technique for the discovery of SNPs and development of markers for large-scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black-faced blenny), a small rocky-shore fish from the Mediterranean Sea. RNA-seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time-consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.

  3. Ice Fog and Light Snow Measurements Using a High-Resolution Camera System

    NASA Astrophysics Data System (ADS)

    Kuhn, Thomas; Gultepe, Ismail

    2016-09-01

    Ice fog, diamond dust, and light snow usually form over extremely cold weather conditions, and they affect both visibility and Earth's radiative energy budget. Prediction of these hydrometeors using models is difficult because of limited knowledge of the microphysical properties at the small size ranges due to measurement issues. These phenomena need to be better represented in forecast and climate models; therefore, in addition to remote sensing accurate measurements using ground-based instrumentation are required. An imaging instrument, aimed at measuring ice fog and light snow particles, has been built and is presented here. The ice crystal imaging (ICI) probe samples ice particles into a vertical, tapered inlet with an inlet flow rate of 11 L min-1. A laser beam across the vertical air flow containing the ice crystals allows for their detection by a photodetector collecting the scattered light. Detected particles are then imaged with high optical resolution. An illuminating LED flash and image capturing are triggered by the photodetector. In this work, ICI measurements collected during the fog remote sensing and modeling (FRAM) project, which took place during Winter of 2010-2011 in Yellowknife, NWT, Canada, are summarized and challenges related to measuring small ice particles are described. The majority of ice particles during the 2-month-long campaign had sizes between 300 and 800 μm. During ice fog events the size distribution measured had a lower mode diameter of 300 μm compared to the overall campaign average with mode at 500 μm.

  4. Slush Fund: Ice's Multiphase Evolution and Its Role in Shaping Europa

    NASA Astrophysics Data System (ADS)

    Buffo, Jacob; Schmidt, Britney E.

    2016-10-01

    The role of Europa's ice shell in mediating ocean-surface interaction, constraining potential habitability of the underlying hydrosphere, and dictating the surface morphology of the moon has been discussed in the literature for years, yet the dynamics and characteristics of the shell itself remain largely unconstrained. These discrepancies likely arise from underrepresented physics and varying a priori assumptions built into the current ice shell models. Presented here is a two-phase reactive porous media model of Europa's ice shell evolution, inspired by successful contemporary sea ice models, designed to capture the multiphase nature of forming ice as well as eliminate the need for a priori assumptions about ice shell structure and properties. The design of the model is such that it temporally and spatially constructs the ice shell from a first principles approach, allowing for accurate simulation of the shell's thermodynamic and compositional properties from the beginning of its formation up to its current state. This methodology provides explicit predictions of the