Science.gov

Sample records for accurate code predictions

  1. 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.

  2. Aeroacoustic Prediction Codes

    NASA Technical Reports Server (NTRS)

    Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

    2000-01-01

    This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor

  3. The FLUKA Code: An Accurate Simulation Tool for Particle Therapy

    PubMed Central

    Battistoni, Giuseppe; Bauer, Julia; Boehlen, Till T.; Cerutti, Francesco; Chin, Mary P. W.; Dos Santos Augusto, Ricardo; Ferrari, Alfredo; Ortega, Pablo G.; Kozłowska, Wioletta; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R.; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis

    2016-01-01

    Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with both 4He and 12C ion beams. Accurate description of ionization energy losses and of particle scattering and interactions lead to the excellent agreement of calculated depth–dose profiles with those measured at leading European hadron therapy centers, both with proton and ion beams. In order to support the application of FLUKA in hospital-based environments, Flair, the FLUKA graphical interface, has been enhanced with the capability of translating CT DICOM images into voxel-based computational phantoms in a fast and well-structured way. The interface is capable of importing also radiotherapy treatment data described in DICOM RT standard. In addition, the interface is equipped with an intuitive PET scanner geometry generator and automatic recording of coincidence events. Clinically, similar cases will be presented both in terms of absorbed dose and biological dose calculations describing the various available features. PMID:27242956

  4. The FLUKA Code: An Accurate Simulation Tool for Particle Therapy.

    PubMed

    Battistoni, Giuseppe; Bauer, Julia; Boehlen, Till T; Cerutti, Francesco; Chin, Mary P W; Dos Santos Augusto, Ricardo; Ferrari, Alfredo; Ortega, Pablo G; Kozłowska, Wioletta; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis

    2016-01-01

    Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with both (4)He and (12)C ion beams. Accurate description of ionization energy losses and of particle scattering and interactions lead to the excellent agreement of calculated depth-dose profiles with those measured at leading European hadron therapy centers, both with proton and ion beams. In order to support the application of FLUKA in hospital-based environments, Flair, the FLUKA graphical interface, has been enhanced with the capability of translating CT DICOM images into voxel-based computational phantoms in a fast and well-structured way. The interface is capable of importing also radiotherapy treatment data described in DICOM RT standard. In addition, the interface is equipped with an intuitive PET scanner geometry generator and automatic recording of coincidence events. Clinically, similar cases will be presented both in terms of absorbed dose and biological dose calculations describing the various available features.

  5. Dopamine reward prediction error coding.

    PubMed

    Schultz, Wolfram

    2016-03-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards-an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less reward than predicted (negative prediction error). The dopamine signal increases nonlinearly with reward value and codes formal economic utility. Drugs of addiction generate, hijack, and amplify the dopamine reward signal and induce exaggerated, uncontrolled dopamine effects on neuronal plasticity. The striatum, amygdala, and frontal cortex also show reward prediction error coding, but only in subpopulations of neurons. Thus, the important concept of reward prediction errors is implemented in neuronal hardware.

  6. Dopamine reward prediction error coding

    PubMed Central

    Schultz, Wolfram

    2016-01-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards—an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less reward than predicted (negative prediction error). The dopamine signal increases nonlinearly with reward value and codes formal economic utility. Drugs of addiction generate, hijack, and amplify the dopamine reward signal and induce exaggerated, uncontrolled dopamine effects on neuronal plasticity. The striatum, amygdala, and frontal cortex also show reward prediction error coding, but only in subpopulations of neurons. Thus, the important concept of reward prediction errors is implemented in neuronal hardware. PMID:27069377

  7. 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.

  8. Predictive coding of multisensory timing

    PubMed Central

    Shi, Zhuanghua; Burr, David

    2016-01-01

    The sense of time is foundational for perception and action, yet it frequently departs significantly from physical time. In the paper we review recent progress on temporal contextual effects, multisensory temporal integration, temporal recalibration, and related computational models. We suggest that subjective time arises from minimizing prediction errors and adaptive recalibration, which can be unified in the framework of predictive coding, a framework rooted in Helmholtz’s ‘perception as inference’. PMID:27695705

  9. Neural Elements for Predictive Coding

    PubMed Central

    Shipp, Stewart

    2016-01-01

    Predictive coding theories of sensory brain function interpret the hierarchical construction of the cerebral cortex as a Bayesian, generative model capable of predicting the sensory data consistent with any given percept. Predictions are fed backward in the hierarchy and reciprocated by prediction error in the forward direction, acting to modify the representation of the outside world at increasing levels of abstraction, and so to optimize the nature of perception over a series of iterations. This accounts for many ‘illusory’ instances of perception where what is seen (heard, etc.) is unduly influenced by what is expected, based on past experience. This simple conception, the hierarchical exchange of prediction and prediction error, confronts a rich cortical microcircuitry that is yet to be fully documented. This article presents the view that, in the current state of theory and practice, it is profitable to begin a two-way exchange: that predictive coding theory can support an understanding of cortical microcircuit function, and prompt particular aspects of future investigation, whilst existing knowledge of microcircuitry can, in return, influence theoretical development. As an example, a neural inference arising from the earliest formulations of predictive coding is that the source populations of forward and backward pathways should be completely separate, given their functional distinction; this aspect of circuitry – that neurons with extrinsically bifurcating axons do not project in both directions – has only recently been confirmed. Here, the computational architecture prescribed by a generalized (free-energy) formulation of predictive coding is combined with the classic ‘canonical microcircuit’ and the laminar architecture of hierarchical extrinsic connectivity to produce a template schematic, that is further examined in the light of (a) updates in the microcircuitry of primate visual cortex, and (b) rapid technical advances made possible by

  10. A more accurate nonequilibrium air radiation code - NEQAIR second generation

    NASA Technical Reports Server (NTRS)

    Moreau, Stephane; Laux, Christophe O.; Chapman, Dean R.; Maccormack, Robert W.

    1992-01-01

    Two experiments, one an equilibrium flow in a plasma torch at Stanford, the other a nonequilibrium flow in a SDIO/IST Bow-Shock-Ultra-Violet missile flight, have provided the basis for modifying, enhancing, and testing the well-known radiation code, NEQAIR. The original code, herein termed NEQAIR1, lacked computational efficiency, accurate data for some species and the flexibility to handle a variety of species. The modified code, herein termed NEQAIR2, incorporates recent findings in the spectroscopic and radiation models. It can handle any number of species and radiative bands in a gas whose thermodynamic state can be described by up to four temperatures. It provides a new capability of computing very fine spectra in a reasonable CPU time, while including transport phenomena along the line of sight and the characteristics of instruments that were used in the measurements. Such a new tool should allow more accurate testing and diagnosis of the different physical models used in numerical simulations of radiating, low density, high energy flows.

  11. Accurate documentation, correct coding, and compliance: it's your best defense!

    PubMed

    Coles, T S; Babb, E F

    1999-07-01

    This article focuses on the need for physicians to maintain an awareness of regulatory policy and the law impacting the federal government's medical insurance programs, and to internalize and apply this knowledge in their practices. Basic information concerning selected fraud and abuse statutes and the civil monetary penalties and sanctions for noncompliance is discussed. The application of accurate documentation and correct coding principles, as well as the rationale for implementating an effective compliance plan in order to prevent fraud and abuse and/or minimize disciplinary action from government regulatory agencies, are emphasized.

  12. Canonical microcircuits for predictive coding

    PubMed Central

    Bastos, Andre M.; Usrey, W. Martin; Adams, Rick A.; Mangun, George R.; Fries, Pascal; Friston, Karl J.

    2013-01-01

    Summary This review considers the influential notion of a canonical (cortical) microcircuit in light of recent theories about neuronal processing. Specifically, we conciliate quantitative studies of microcircuitry and the functional logic of neuronal computations. We revisit the established idea that message passing among hierarchical cortical areas implements a form of Bayesian inference – paying careful attention to the implications for intrinsic connections among neuronal populations. By deriving canonical forms for these computations, one can associate specific neuronal populations with specific computational roles. This analysis discloses a remarkable correspondence between the microcircuitry of the cortical column and the connectivity implied by predictive coding. Furthermore, it provides some intuitive insights into the functional asymmetries between feedforward and feedback connections and the characteristic frequencies over which they operate. PMID:23177956

  13. A review of predictive coding algorithms.

    PubMed

    Spratling, M W

    2017-03-01

    Predictive coding is a leading theory of how the brain performs probabilistic inference. However, there are a number of distinct algorithms which are described by the term "predictive coding". This article provides a concise review of these different predictive coding algorithms, highlighting their similarities and differences. Five algorithms are covered: linear predictive coding which has a long and influential history in the signal processing literature; the first neuroscience-related application of predictive coding to explaining the function of the retina; and three versions of predictive coding that have been proposed to model cortical function. While all these algorithms aim to fit a generative model to sensory data, they differ in the type of generative model they employ, in the process used to optimise the fit between the model and sensory data, and in the way that they are related to neurobiology.

  14. 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

  15. 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…

  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 coding in sepsis: clinical significance and financial implications.

    PubMed

    Chin, Y T; Scattergood, N; Thornber, M; Thomas, S

    2016-09-01

    Sepsis is a major healthcare problem and leading cause of death worldwide. UK hospital mortality statistics and payments for patient episodes of care are calculated on clinical coding data. The accuracy of these data depends on the quality of coding. This study aimed to investigate whether patients with significant bacteraemia are coded for sepsis and to estimate the financial costs of miscoding. Of 54 patients over a one-month period with a significant bacteraemia, only 19% had been coded for sepsis. This is likely to lead to falsely high calculated hospital mortality. Furthermore, this resulted in an underpayment of £21,000 for one month alone.

  18. Predictive depth coding of wavelet transformed images

    NASA Astrophysics Data System (ADS)

    Lehtinen, Joonas

    1999-10-01

    In this paper, a new prediction based method, predictive depth coding, for lossy wavelet image compression is presented. It compresses a wavelet pyramid composition by predicting the number of significant bits in each wavelet coefficient quantized by the universal scalar quantization and then by coding the prediction error with arithmetic coding. The adaptively found linear prediction context covers spatial neighbors of the coefficient to be predicted and the corresponding coefficients on lower scale and in the different orientation pyramids. In addition to the number of significant bits, the sign and the bits of non-zero coefficients are coded. The compression method is tested with a standard set of images and the results are compared with SFQ, SPIHT, EZW and context based algorithms. Even though the algorithm is very simple and it does not require any extra memory, the compression results are relatively good.

  19. RRTMGP: A fast and accurate radiation code for the next decade

    NASA Astrophysics Data System (ADS)

    Mlawer, E. J.; Pincus, R.; Wehe, A.; Delamere, J.

    2015-12-01

    Atmospheric radiative processes are key drivers of the Earth's climate and must be accurately represented in global circulations models (GCMs) to allow faithful simulations of the planet's past, present, and future. The radiation code RRTMG is widely utilized by global modeling centers for both climate and weather predictions, but it has become increasingly out-of-date. The code's structure is not well suited for the current generation of computer architectures and its stored absorption coefficients are not consistent with the most recent spectroscopic information. We are developing a new broadband radiation code for the current generation of computational architectures. This code, called RRTMGP, will be a completely restructured and modern version of RRTMG. The new code preserves the strengths of the existing RRTMG parameterization, especially the high accuracy of the k-distribution treatment of absorption by gases, but the entire code is being rewritten to provide highly efficient computation across a range of architectures. Our redesign includes refactoring the code into discrete kernels corresponding to fundamental computational elements (e.g. gas optics), optimizing the code for operating on multiple columns in parallel, simplifying the subroutine interface, revisiting the existing gas optics interpolation scheme to reduce branching, and adding flexibility with respect to run-time choices of streams, need for consideration of scattering, aerosol and cloud optics, etc. The result of the proposed development will be a single, well-supported and well-validated code amenable to optimization across a wide range of platforms. Our main emphasis is on highly-parallel platforms including Graphical Processing Units (GPUs) and Many-Integrated-Core processors (MICs), which experience shows can accelerate broadband radiation calculations by as much as a factor of fifty. RRTMGP will provide highly efficient and accurate radiative fluxes calculations for coupled global

  20. 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.

  1. 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.

  2. An efficient sliding window strategy for accurate location of eukaryotic protein coding regions.

    PubMed

    Rao, Nini; Lei, Xu; Guo, Jianxiu; Huang, Hao; Ren, Zhenglong

    2009-04-01

    The sliding window is one of important factors that seriously affect the accuracy of coding region prediction and location for the methods based on power spectrum technique. It is very difficult to select the appropriate sliding step and the window length for different organisms. In this study, a novel sliding window strategy is proposed on the basis of power spectrum analysis for the accurate location of eukaryotic protein coding regions. The proposed sliding window strategy is very simple and the sliding step of window is changeable. Our tests show that the average location error for the novel method is 12 bases. Compared with the previous location error of 54 bases using the fixed sliding step, the novel sliding window strategy increased the location accuracy greatly. Further, the consumed CPU time to run the novel strategy is much shorter than the strategy of the fixed length sliding step. So, the computational complexity for the novel method is decreased greatly.

  3. Code-excited linear predictive coding of multispectral MR images

    NASA Astrophysics Data System (ADS)

    Hu, Jian-Hong; Wang, Yao; Cahill, Patrick

    1996-02-01

    This paper reports a multispectral code excited linear predictive coding method for the compression of well-registered multispectral MR images. Different linear prediction models and the adaptation schemes have been compared. The method which uses forward adaptive autoregressive (AR) model has proven to achieve a good compromise between performance, complexity and robustness. This approach is referred to as the MFCELP method. Given a set of multispectral images, the linear predictive coefficients are updated over non-overlapping square macroblocks. Each macro-block is further divided into several micro-blocks and, the best excitation signals for each microblock are determined through an analysis-by-synthesis procedure. To satisfy the high quality requirement for medical images, the error between the original images and the synthesized ones are further specified using a vector quantizer. The MFCELP method has been applied to 26 sets of clinical MR neuro images (20 slices/set, 3 spectral bands/slice, 256 by 256 pixels/image, 12 bits/pixel). It provides a significant improvement over the discrete cosine transform (DCT) based JPEG method, a wavelet transform based embedded zero-tree wavelet (EZW) coding method, as well as the MSARMA method we developed before.

  4. Fast prediction algorithm for multiview video coding

    NASA Astrophysics Data System (ADS)

    Abdelazim, Abdelrahman; Mein, Stephen James; Varley, Martin Roy; Ait-Boudaoud, Djamel

    2013-03-01

    The H.264/multiview video coding (MVC) standard has been developed to enable efficient coding for three-dimensional and multiple viewpoint video sequences. The inter-view statistical dependencies are utilized and an inter-view prediction is employed to provide more efficient coding; however, this increases the overall encoding complexity. Motion homogeneity is exploited here to selectively enable inter-view prediction, and to reduce complexity in the motion estimation (ME) and the mode selection processes. This has been accomplished by defining situations that relate macro-blocks' motion characteristics to the mode selection and the inter-view prediction processes. When comparing the proposed algorithm to the H.264/MVC reference software and other recent work, the experimental results demonstrate a significant reduction in ME time while maintaining similar rate-distortion performance.

  5. 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.

  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. Predictive Coding Strategies for Developmental Neurorobotics

    PubMed Central

    Park, Jun-Cheol; Lim, Jae Hyun; Choi, Hansol; Kim, Dae-Shik

    2012-01-01

    In recent years, predictive coding strategies have been proposed as a possible means by which the brain might make sense of the truly overwhelming amount of sensory data available to the brain at any given moment of time. Instead of the raw data, the brain is hypothesized to guide its actions by assigning causal beliefs to the observed error between what it expects to happen and what actually happens. In this paper, we present a variety of developmental neurorobotics experiments in which minimalist prediction error-based encoding strategies are utilize to elucidate the emergence of infant-like behavior in humanoid robotic platforms. Our approaches will be first naively Piagian, then move onto more Vygotskian ideas. More specifically, we will investigate how simple forms of infant learning, such as motor sequence generation, object permanence, and imitation learning may arise if minimizing prediction errors are used as objective functions. PMID:22586416

  8. 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

  9. 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.

  10. Visual mismatch negativity: a predictive coding view

    PubMed Central

    Stefanics, Gábor; Kremláček, Jan; Czigler, István

    2014-01-01

    An increasing number of studies investigate the visual mismatch negativity (vMMN) or use the vMMN as a tool to probe various aspects of human cognition. This paper reviews the theoretical underpinnings of vMMN in the light of methodological considerations and provides recommendations for measuring and interpreting the vMMN. The following key issues are discussed from the experimentalist's point of view in a predictive coding framework: (1) experimental protocols and procedures to control “refractoriness” effects; (2) methods to control attention; (3) vMMN and veridical perception. PMID:25278859

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

    PubMed Central

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-01-01

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  1. 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

  2. On scalable lossless video coding based on sub-pixel accurate MCTF

    NASA Astrophysics Data System (ADS)

    Yea, Sehoon; Pearlman, William A.

    2006-01-01

    We propose two approaches to scalable lossless coding of motion video. They achieve SNR-scalable bitstream up to lossless reconstruction based upon the subpixel-accurate MCTF-based wavelet video coding. The first approach is based upon a two-stage encoding strategy where a lossy reconstruction layer is augmented by a following residual layer in order to obtain (nearly) lossless reconstruction. The key advantages of our approach include an 'on-the-fly' determination of bit budget distribution between the lossy and the residual layers, freedom to use almost any progressive lossy video coding scheme as the first layer and an added feature of near-lossless compression. The second approach capitalizes on the fact that we can maintain the invertibility of MCTF with an arbitrary sub-pixel accuracy even in the presence of an extra truncation step for lossless reconstruction thanks to the lifting implementation. Experimental results show that the proposed schemes achieve compression ratios not obtainable by intra-frame coders such as Motion JPEG-2000 thanks to their inter-frame coding nature. Also they are shown to outperform the state-of-the-art non-scalable inter-frame coder H.264 (JM) lossless mode, with the added benefit of bitstream embeddedness.

  3. 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

  4. 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

  5. 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.

  6. The Helicopter Antenna Radiation Prediction Code (HARP)

    NASA Technical Reports Server (NTRS)

    Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

    1990-01-01

    The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

  7. 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

  8. 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.

  9. 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

  10. SMARTIES: User-friendly codes for fast and accurate calculations of light scattering by spheroids

    NASA Astrophysics Data System (ADS)

    Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.

    2016-05-01

    We provide a detailed user guide for SMARTIES, a suite of MATLAB codes for the calculation of the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. SMARTIES is a MATLAB implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. The theory behind the improvements in numerical accuracy and convergence is briefly summarized, with reference to the original publications. Instructions of use, and a detailed description of the code structure, its range of applicability, as well as guidelines for further developments by advanced users are discussed in separate sections of this user guide. The code may be useful to researchers seeking a fast, accurate and reliable tool to simulate the near-field and far-field optical properties of elongated particles, but will also appeal to other developers of light-scattering software seeking a reliable benchmark for non-spherical particles with a challenging aspect ratio and/or refractive index contrast.

  11. 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

  12. 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.

  13. 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.

  14. Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.; Dyson, Rodger W.

    1999-01-01

    The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that

  15. Impact of hierarchies of clinical codes on predicting future days in hospital.

    PubMed

    Yang Xie; Neubauer, Sandra; Schreier, Gunter; Redmond, Stephen J; Lovell, Nigel H

    2015-01-01

    Health insurance claims contain valuable information for predicting the future health of a population. Nowadays, with many mature machine learning algorithms, models can be implemented to predict future medical costs and hospitalizations. However, it is well-known that the way in which the data are represented significantly affects the performance of machine learning algorithms. In health insurance claims, key clinical information mainly comes from the associated clinical codes, such as diagnosis codes and procedure codes, which are hierarchically structured. In this study, it is investigated whether the hierarchies of such clinical codes can be utilized to improve predictive performance in the context of predicting future days in hospital. Empirical investigations were done on data sets of different sizes, considering that the frequency of the appearance of lower-level (more specific) clinical codes could vary significantly in populations of different sizes. The use of bagged trees with feature sets that include only basic demographic features, low-level, medium-level, high-level clinical codes, and a full feature set were compared. The main finding from this study is that different hierarchies of clinical codes do not have a significant impact on the predictive power. Some other findings include: 1) Sample size greatly affects the predictive outcome (more observations result in more stable and more accurate outcomes); 2) Combined use of enriched demographic features and clinical features give better performance as compared to using them separately.

  16. Picturewise inter-view prediction selection for multiview video coding

    NASA Astrophysics Data System (ADS)

    Huo, Junyan; Chang, Yilin; Li, Ming; Yang, Haitao

    2010-11-01

    Inter-view prediction is introduced in multiview video coding (MVC) to exploit the inter-view correlation. Statistical analyses show that the coding gain benefited from inter-view prediction is unequal among pictures. On the basis of this observation, a picturewise interview prediction selection scheme is proposed. This scheme employs a novel inter-view prediction selection criterion to determine whether it is necessary to apply inter-view prediction to the current coding picture. This criterion is derived from the available coding information of the temporal reference pictures. Experimental results show that the proposed scheme can improve the performance of MVC with a comprehensive consideration of compression efficiency, computational complexity, and random access ability.

  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. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  5. Predictive Bias and Sensitivity in NRC Fuel Performance Codes

    SciTech Connect

    Geelhood, Kenneth J.; Luscher, Walter G.; Senor, David J.; Cunningham, Mitchel E.; Lanning, Donald D.; Adkins, Harold E.

    2009-10-01

    The latest versions of the fuel performance codes, FRAPCON-3 and FRAPTRAN were examined to determine if the codes are intrinsically conservative. Each individual model and type of code prediction was examined and compared to the data that was used to develop the model. In addition, a brief literature search was performed to determine if more recent data have become available since the original model development for model comparison.

  6. 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?

  7. 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.

  8. 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).

  9. 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.

  10. 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).

  11. Efficient Coding of the Prediction Residual.

    DTIC Science & Technology

    1979-12-27

    Page I. Average of Fundamental and Formant Frequencies and Formant Amplitudes of Vowels by 76 Speakers .. ........... ... 28 II. Representation of IPA...0, 1, ..., M-1 p - Order of the LPC filter F1, F2, ... - Formant frequencies r,(m) - Output of the ith bandpass filter m = 0, 1, ..., M-l; z = 1, 2...correlation coefficients and other parameters that represent the formant frequency characteristics. The other waveform is the prediction residual. Figure

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Fast and accurate search for non-coding RNA pseudoknot structures in genomes

    PubMed Central

    Huang, Zhibin; Wu, Yong; Robertson, Joseph; Feng, Liang; Malmberg, Russell L.; Cai, Liming

    2008-01-01

    Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph. Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high

  17. 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

  18. Piecewise Mapping in HEVC Lossless Intra-prediction Coding.

    PubMed

    Sanchez, Victor; Auli-Llinas, Francesc; Serra-Sagrista, Joan

    2016-05-19

    The lossless intra-prediction coding modality of the High Efficiency Video Coding (HEVC) standard provides high coding performance while allowing frame-by-frame basis access to the coded data. This is of interest in many professional applications such as medical imaging, automotive vision and digital preservation in libraries and archives. Various improvements to lossless intra-prediction coding have been proposed recently, most of them based on sample-wise prediction using Differential Pulse Code Modulation (DPCM). Other recent proposals aim at further reducing the energy of intra-predicted residual blocks. However, the energy reduction achieved is frequently minimal due to the difficulty of correctly predicting the sign and magnitude of residual values. In this paper, we pursue a novel approach to this energy-reduction problem using piecewise mapping (pwm) functions. Specifically, we analyze the range of values in residual blocks and apply accordingly a pwm function to map specific residual values to unique lower values. We encode appropriate parameters associated with the pwm functions at the encoder, so that the corresponding inverse pwm functions at the decoder can map values back to the same residual values. These residual values are then used to reconstruct the original signal. This mapping is, therefore, reversible and introduces no losses. We evaluate the pwm functions on 4×4 residual blocks computed after DPCM-based prediction for lossless coding of a variety of camera-captured and screen content sequences. Evaluation results show that the pwm functions can attain maximum bit-rate reductions of 5.54% and 28.33% for screen content material compared to DPCM-based and block-wise intra-prediction, respectively. Compared to Intra- Block Copy, piecewise mapping can attain maximum bit-rate reductions of 11.48% for camera-captured material.

  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. A spectrally accurate boundary-layer code for infinite swept wings

    NASA Astrophysics Data System (ADS)

    Pruett, C. David

    1994-12-01

    This report documents the development, validation, and application of a spectrally accurate boundary-layer code, WINGBL2, which has been designed specifically for use in stability analyses of swept-wing configurations. Currently, we consider only the quasi-three-dimensional case of an infinitely long wing of constant cross section. The effects of streamwise curvature, streamwise pressure gradient, and wall suction and/or blowing are taken into account in the governing equations and boundary conditions. The boundary-layer equations are formulated both for the attachment-line flow and for the evolving boundary layer. The boundary-layer equations are solved by marching in the direction perpendicular to the leading edge, for which high-order (up to fifth) backward differencing techniques are used. In the wall-normal direction, a spectral collocation method, based upon Chebyshev polynomial approximations, is exploited. The accuracy, efficiency, and user-friendliness of WINGBL2 make it well suited for applications to linear stability theory, parabolized stability equation methodology, direct numerical simulation, and large-eddy simulation. The method is validated against existing schemes for three test cases, including incompressible swept Hiemenz flow and Mach 2.4 flow over an airfoil swept at 70 deg to the free stream.

  1. A spectrally accurate boundary-layer code for infinite swept wings

    NASA Technical Reports Server (NTRS)

    Pruett, C. David

    1994-01-01

    This report documents the development, validation, and application of a spectrally accurate boundary-layer code, WINGBL2, which has been designed specifically for use in stability analyses of swept-wing configurations. Currently, we consider only the quasi-three-dimensional case of an infinitely long wing of constant cross section. The effects of streamwise curvature, streamwise pressure gradient, and wall suction and/or blowing are taken into account in the governing equations and boundary conditions. The boundary-layer equations are formulated both for the attachment-line flow and for the evolving boundary layer. The boundary-layer equations are solved by marching in the direction perpendicular to the leading edge, for which high-order (up to fifth) backward differencing techniques are used. In the wall-normal direction, a spectral collocation method, based upon Chebyshev polynomial approximations, is exploited. The accuracy, efficiency, and user-friendliness of WINGBL2 make it well suited for applications to linear stability theory, parabolized stability equation methodology, direct numerical simulation, and large-eddy simulation. The method is validated against existing schemes for three test cases, including incompressible swept Hiemenz flow and Mach 2.4 flow over an airfoil swept at 70 deg to the free stream.

  2. 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.

  3. Roadmap Toward a Predictive Performance-based Commercial Energy Code

    SciTech Connect

    Rosenberg, Michael I.; Hart, Philip R.

    2014-10-01

    Energy codes have provided significant increases in building efficiency over the last 38 years, since the first national energy model code was published in late 1975. The most commonly used path in energy codes, the prescriptive path, appears to be reaching a point of diminishing returns. The current focus on prescriptive codes has limitations including significant variation in actual energy performance depending on which prescriptive options are chosen, a lack of flexibility for designers and developers, and the inability to handle control optimization that is specific to building type and use. This paper provides a high level review of different options for energy codes, including prescriptive, prescriptive packages, EUI Target, outcome-based, and predictive performance approaches. This paper also explores a next generation commercial energy code approach that places a greater emphasis on performance-based criteria. A vision is outlined to serve as a roadmap for future commercial code development. That vision is based on code development being led by a specific approach to predictive energy performance combined with building specific prescriptive packages that are designed to be both cost-effective and to achieve a desired level of performance. Compliance with this new approach can be achieved by either meeting the performance target as demonstrated by whole building energy modeling, or by choosing one of the prescriptive packages.

  4. A trellis-searched APC (adaptive predictive coding) speech coder

    SciTech Connect

    Malone, K.T. ); Fischer, T.R. . Dept. of Electrical and Computer Engineering)

    1990-01-01

    In this paper we formulate a speech coding system that incorporates trellis coded vector quantization (TCVQ) and adaptive predictive coding (APC). A method for optimizing'' the TCVQ codebooks is presented and experimental results concerning survivor path mergings are reported. Simulation results are given for encoding rates of 16 and 9.6 kbps for a variety of coder parameters. The quality of the encoded speech is deemed excellent at an encoding rate of 16 kbps and very good at 9.6 kbps. 13 refs., 2 figs., 4 tabs.

  5. 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.

  6. Analysis of view synthesis prediction architectures in modern coding standards

    NASA Astrophysics Data System (ADS)

    Tian, Dong; Zou, Feng; Lee, Chris; Vetro, Anthony; Sun, Huifang

    2013-09-01

    Depth-based 3D formats are currently being developed as extensions to both AVC and HEVC standards. The availability of depth information facilitates the generation of intermediate views for advanced 3D applications and displays, and also enables more efficient coding of the multiview input data through view synthesis prediction techniques. This paper outlines several approaches that have been explored to realize view synthesis prediction in modern video coding standards such as AVC and HEVC. The benefits and drawbacks of various architectures are analyzed in terms of performance, complexity, and other design considerations. It is hence concluded that block-based VSP prediction for multiview video signals provides attractive coding gains with comparable complexity as traditional motion/disparity compensation.

  7. More About Vector Adaptive/Predictive Coding Of Speech

    NASA Technical Reports Server (NTRS)

    Jedrey, Thomas C.; Gersho, Allen

    1992-01-01

    Report presents additional information about digital speech-encoding and -decoding system described in "Vector Adaptive/Predictive Encoding of Speech" (NPO-17230). Summarizes development of vector adaptive/predictive coding (VAPC) system and describes basic functions of algorithm. Describes refinements introduced enabling receiver to cope with errors. VAPC algorithm implemented in integrated-circuit coding/decoding processors (codecs). VAPC and other codecs tested under variety of operating conditions. Tests designed to reveal effects of various background quiet and noisy environments and of poor telephone equipment. VAPC found competitive with and, in some respects, superior to other 4.8-kb/s codecs and other codecs of similar complexity.

  8. Dream to Predict? REM Dreaming as Prospective Coding

    PubMed Central

    Llewellyn, Sue

    2016-01-01

    The dream as prediction seems inherently improbable. The bizarre occurrences in dreams never characterize everyday life. Dreams do not come true! But assuming that bizarreness negates expectations may rest on a misunderstanding of how the predictive brain works. In evolutionary terms, the ability to rapidly predict what sensory input implies—through expectations derived from discerning patterns in associated past experiences—would have enhanced fitness and survival. For example, food and water are essential for survival, associating past experiences (to identify location patterns) predicts where they can be found. Similarly, prediction may enable predator identification from what would have been only a fleeting and ambiguous stimulus—without prior expectations. To confront the many challenges associated with natural settings, visual perception is vital for humans (and most mammals) and often responses must be rapid. Predictive coding during wake may, therefore, be based on unconscious imagery so that visual perception is maintained and appropriate motor actions triggered quickly. Speed may also dictate the form of the imagery. Bizarreness, during REM dreaming, may result from a prospective code fusing phenomena with the same meaning—within a particular context. For example, if the context is possible predation, from the perspective of the prey two different predators can both mean the same (i.e., immediate danger) and require the same response (e.g., flight). Prospective coding may also prune redundancy from memories, to focus the image on the contextually-relevant elements only, thus, rendering the non-relevant phenomena indeterminate—another aspect of bizarreness. In sum, this paper offers an evolutionary take on REM dreaming as a form of prospective coding which identifies a probabilistic pattern in past events. This pattern is portrayed in an unconscious, associative, sensorimotor image which may support cognition in wake through being mobilized as a

  9. Fast coding unit selection method for high efficiency video coding intra prediction

    NASA Astrophysics Data System (ADS)

    Xiong, Jian

    2013-07-01

    The high efficiency video coding (HEVC) video coding standard under development can achieve higher compression performance than previous standards, such as MPEG-4, H.263, and H.264/AVC. To improve coding performance, a quad-tree coding structure and a robust rate-distortion (RD) optimization technique is used to select an optimum coding mode. Since the RD costs of all possible coding modes are computed to decide an optimum mode, high computational complexity is induced in the encoder. A fast learning-based coding unit (CU) size selection method is presented for HEVC intra prediction. The proposed algorithm is based on theoretical analysis that shows the non-normalized histogram of oriented gradient (n-HOG) can be used to help select CU size. A codebook is constructed offline by clustering n-HOGs of training sequences for each CU size. The optimum size is determined by comparing the n-HOG of the current CU with the learned codebooks. Experimental results show that the CU size selection scheme speeds up intra coding significantly with negligible loss of peak signal-to-noise ratio.

  10. The NASA-LeRC wind turbine sound prediction code

    NASA Technical Reports Server (NTRS)

    Viterna, L. A.

    1981-01-01

    Since regular operation of the DOE/NASA MOD-1 wind turbine began in October 1979 about 10 nearby households have complained of noise from the machine. Development of the NASA-LeRC with turbine sound prediction code began in May 1980 as part of an effort to understand and reduce the noise generated by MOD-1. Tone sound levels predicted with this code are in generally good agreement with measured data taken in the vicinity MOD-1 wind turbine (less than 2 rotor diameters). Comparison in the far field indicates that propagation effects due to terrain and atmospheric conditions may be amplifying the actual sound levels by about 6 dB. Parametric analysis using the code has shown that the predominant contributions to MOD-1 rotor noise are: (1) the velocity deficit in the wake of the support tower; (2) the high rotor speed; and (3) off column operation.

  11. The NASA-LeRC wind turbine sound prediction code

    NASA Technical Reports Server (NTRS)

    Viterna, L. A.

    1981-01-01

    Development of the wind turbine sound prediction code began as part of an effort understand and reduce the noise generated by Mod-1. Tone sound levels predicted with this code are in good agreement with measured data taken in the vicinity Mod-1 wind turbine (less than 2 rotor diameters). Comparison in the far field indicates that propagation effects due to terrain and atmospheric conditions may amplify the actual sound levels by 6 dB. Parametric analysis using the code shows that the predominant contributors to Mod-1 rotor noise are (1) the velocity deficit in the wake of the support tower, (2) the high rotor speed, and (3) off-optimum operation.

  12. Predictive coding of music--brain responses to rhythmic incongruity.

    PubMed

    Vuust, Peter; Ostergaard, Leif; Pallesen, Karen Johanne; Bailey, Christopher; Roepstorff, Andreas

    2009-01-01

    During the last decades, models of music processing in the brain have mainly discussed the specificity of brain modules involved in processing different musical components. We argue that predictive coding offers an explanatory framework for functional integration in musical processing. Further, we provide empirical evidence for such a network in the analysis of event-related MEG-components to rhythmic incongruence in the context of strong metric anticipation. This is seen in a mismatch negativity (MMNm) and a subsequent P3am component, which have the properties of an error term and a subsequent evaluation in a predictive coding framework. There were both quantitative and qualitative differences in the evoked responses in expert jazz musicians compared with rhythmically unskilled non-musicians. We propose that these differences trace a functional adaptation and/or a genetic pre-disposition in experts which allows for a more precise rhythmic prediction.

  13. 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.

  14. User's manual for the ALS base heating prediction code, volume 2

    NASA Technical Reports Server (NTRS)

    Reardon, John E.; Fulton, Michael S.

    1992-01-01

    The Advanced Launch System (ALS) Base Heating Prediction Code is based on a generalization of first principles in the prediction of plume induced base convective heating and plume radiation. It should be considered to be an approximate method for evaluating trends as a function of configuration variables because the processes being modeled are too complex to allow an accurate generalization. The convective methodology is based upon generalizing trends from four nozzle configurations, so an extension to use the code with strap-on boosters, multiple nozzle sizes, and variations in the propellants and chamber pressure histories cannot be precisely treated. The plume radiation is more amenable to precise computer prediction, but simplified assumptions are required to model the various aspects of the candidate configurations. Perhaps the most difficult area to characterize is the variation of radiation with altitude. The theory in the radiation predictions is described in more detail. This report is intended to familiarize a user with the interface operation and options, to summarize the limitations and restrictions of the code, and to provide information to assist in installing the code.

  15. Coding Psychological Constructs in Text Using Mechanical Turk: A Reliable, Accurate, and Efficient Alternative

    PubMed Central

    Tosti-Kharas, Jennifer; Conley, Caryn

    2016-01-01

    In this paper we evaluate how to effectively use the crowdsourcing service, Amazon's Mechanical Turk (MTurk), to content analyze textual data for use in psychological research. MTurk is a marketplace for discrete tasks completed by workers, typically for small amounts of money. MTurk has been used to aid psychological research in general, and content analysis in particular. In the current study, MTurk workers content analyzed personally-written textual data using coding categories previously developed and validated in psychological research. These codes were evaluated for reliability, accuracy, completion time, and cost. Results indicate that MTurk workers categorized textual data with comparable reliability and accuracy to both previously published studies and expert raters. Further, the coding tasks were performed quickly and cheaply. These data suggest that crowdsourced content analysis can help advance psychological research. PMID:27303321

  16. Reflectance Prediction Modelling for Residual-Based Hyperspectral Image Coding

    PubMed Central

    Xiao, Rui; Gao, Junbin; Bossomaier, Terry

    2016-01-01

    A Hyperspectral (HS) image provides observational powers beyond human vision capability but represents more than 100 times the data compared to a traditional image. To transmit and store the huge volume of an HS image, we argue that a fundamental shift is required from the existing “original pixel intensity”-based coding approaches using traditional image coders (e.g., JPEG2000) to the “residual”-based approaches using a video coder for better compression performance. A modified video coder is required to exploit spatial-spectral redundancy using pixel-level reflectance modelling due to the different characteristics of HS images in their spectral and shape domain of panchromatic imagery compared to traditional videos. In this paper a novel coding framework using Reflectance Prediction Modelling (RPM) in the latest video coding standard High Efficiency Video Coding (HEVC) for HS images is proposed. An HS image presents a wealth of data where every pixel is considered a vector for different spectral bands. By quantitative comparison and analysis of pixel vector distribution along spectral bands, we conclude that modelling can predict the distribution and correlation of the pixel vectors for different bands. To exploit distribution of the known pixel vector, we estimate a predicted current spectral band from the previous bands using Gaussian mixture-based modelling. The predicted band is used as the additional reference band together with the immediate previous band when we apply the HEVC. Every spectral band of an HS image is treated like it is an individual frame of a video. In this paper, we compare the proposed method with mainstream encoders. The experimental results are fully justified by three types of HS dataset with different wavelength ranges. The proposed method outperforms the existing mainstream HS encoders in terms of rate-distortion performance of HS image compression. PMID:27695102

  17. Modifying scoping codes to accurately calculate TMI-cores with lifetimes greater than 500 effective full-power days

    SciTech Connect

    Bai, D.; Levine, S.L. ); Luoma, J.; Mahgerefteh, M. )

    1992-01-01

    The Three Mile Island unit 1 core reloads have been designed using fast but accurate scoping codes, PSUI-LEOPARD and ADMARC. PSUI-LEOPARD has been normalized to EPRI-CPM2 results and used to calculate the two-group constants, whereas ADMARC is a modern two-dimensional, two-group diffusion theory nodal code. Problems in accuracy were encountered for cycles 8 and higher as the core lifetime was increased beyond 500 effective full-power days. This is because the heavier loaded cores in both {sup 235}U and {sup 10}B have harder neutron spectra, which produces a change in the transport effect in the baffle reflector region, and the burnable poison (BP) simulations were not accurate enough for the cores containing the increased amount of {sup 10}B required in the BP rods. In the authors study, a technique has been developed to take into account the change in the transport effect in the baffle region by modifying the fast neutron diffusion coefficient as a function of cycle length and core exposure or burnup. A more accurate BP simulation method is also developed, using integral transport theory and CPM2 data, to calculate the BP contribution to the equivalent fuel assembly (supercell) two-group constants. The net result is that the accuracy of the scoping codes is as good as that produced by CASMO/SIMULATE or CPM2/SIMULATE when comparing with measured data.

  18. GenDecoder: genetic code prediction for metazoan mitochondria

    PubMed Central

    Abascal, Federico; Zardoya, Rafael; Posada, David

    2006-01-01

    Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from . PMID:16845034

  19. The multiform motor cortical output: Kinematic, predictive and response coding.

    PubMed

    Sartori, Luisa; Betti, Sonia; Chinellato, Eris; Castiello, Umberto

    2015-09-01

    Observing actions performed by others entails a subliminal activation of primary motor cortex reflecting the components encoded in the observed action. One of the most debated issues concerns the role of this output: Is it a mere replica of the incoming flow of information (kinematic coding), is it oriented to anticipate the forthcoming events (predictive coding) or is it aimed at responding in a suitable fashion to the actions of others (response coding)? The aim of the present study was to disentangle the relative contribution of these three levels and unify them into an integrated view of cortical motor coding. We combined transcranial magnetic stimulation (TMS) and electromyography recordings at different timings to probe the excitability of corticospinal projections to upper and lower limb muscles of participants observing a soccer player performing: (i) a penalty kick straight in their direction and then coming to a full stop, (ii) a penalty kick straight in their direction and then continuing to run, (iii) a penalty kick to the side and then continuing to run. The results show a modulation of the observer's corticospinal excitability in different effectors at different times reflecting a multiplicity of motor coding. The internal replica of the observed action, the predictive activation, and the adaptive integration of congruent and non-congruent responses to the actions of others can coexist in a not mutually exclusive way. Such a view offers reconciliation among different (and apparently divergent) frameworks in action observation literature, and will promote a more complete and integrated understanding of recent findings on motor simulation, motor resonance and automatic imitation.

  20. Multispectral code excited linear prediction coding and its application in magnetic resonance images.

    PubMed

    Hu, J H; Wang, Y; Cahill, P T

    1997-01-01

    This paper reports a multispectral code excited linear prediction (MCELP) method for the compression of multispectral images. Different linear prediction models and adaptation schemes have been compared. The method that uses a forward adaptive autoregressive (AR) model has been proven to achieve a good compromise between performance, complexity, and robustness. This approach is referred to as the MFCELP method. Given a set of multispectral images, the linear predictive coefficients are updated over nonoverlapping three-dimensional (3-D) macroblocks. Each macroblock is further divided into several 3-D micro-blocks, and the best excitation signal for each microblock is determined through an analysis-by-synthesis procedure. The MFCELP method has been applied to multispectral magnetic resonance (MR) images. To satisfy the high quality requirement for medical images, the error between the original image set and the synthesized one is further specified using a vector quantizer. This method has been applied to images from 26 clinical MR neuro studies (20 slices/study, three spectral bands/slice, 256x256 pixels/band, 12 b/pixel). The MFCELP method provides a significant visual improvement over the discrete cosine transform (DCT) based Joint Photographers Expert Group (JPEG) method, the wavelet transform based embedded zero-tree wavelet (EZW) coding method, and the vector tree (VT) coding method, as well as the multispectral segmented autoregressive moving average (MSARMA) method we developed previously.

  1. Efficient temporal and interlayer parameter prediction for weighted prediction in scalable high efficiency video coding

    NASA Astrophysics Data System (ADS)

    Tsang, Sik-Ho; Chan, Yui-Lam; Siu, Wan-Chi

    2017-01-01

    Weighted prediction (WP) is an efficient video coding tool that was introduced since the establishment of the H.264/AVC video coding standard, for compensating the temporal illumination change in motion estimation and compensation. WP parameters, including a multiplicative weight and an additive offset for each reference frame, are required to be estimated and transmitted to the decoder by slice header. These parameters cause extra bits in the coded video bitstream. High efficiency video coding (HEVC) provides WP parameter prediction to reduce the overhead. Therefore, WP parameter prediction is crucial to research works or applications, which are related to WP. Prior art has been suggested to further improve the WP parameter prediction by implicit prediction of image characteristics and derivation of parameters. By exploiting both temporal and interlayer redundancies, we propose three WP parameter prediction algorithms, enhanced implicit WP parameter, enhanced direct WP parameter derivation, and interlayer WP parameter, to further improve the coding efficiency of HEVC. Results show that our proposed algorithms can achieve up to 5.83% and 5.23% bitrate reduction compared to the conventional scalable HEVC in the base layer for SNR scalability and 2× spatial scalability, respectively.

  2. Biocomputational prediction of small non-coding RNAs in Streptomyces

    PubMed Central

    Pánek, Josef; Bobek, Jan; Mikulík, Karel; Basler, Marek; Vohradský, Jiří

    2008-01-01

    Background The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, have remained unstudied. This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs. Results Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a Streptomyces 6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs. Conclusion Streptomyces is the largest genus of Actinomyces, whose sRNAs have not been studied. The Actinomyces is a group of bacterial species with unique genomes and phenotypes. Therefore, in Actinomyces, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted Streptomyces sRNAs demonstrated by this study serve as the first evidence of the uniqueness of Actinomyces sRNAs. PMID:18477385

  3. Sonic boom predictions using a modified Euler code

    NASA Technical Reports Server (NTRS)

    Siclari, Michael J.

    1992-01-01

    The environmental impact of a next generation fleet of high-speed civil transports (HSCT) is of great concern in the evaluation of the commercial development of such a transport. One of the potential environmental impacts of a high speed civilian transport is the sonic boom generated by the aircraft and its effects on the population, wildlife, and structures in the vicinity of its flight path. If an HSCT aircraft is restricted from flying overland routes due to excessive booms, the commercial feasibility of such a venture may be questionable. NASA has taken the lead in evaluating and resolving the issues surrounding the development of a high speed civilian transport through its High-Speed Research Program (HSRP). The present paper discusses the usage of a Computational Fluid Dynamics (CFD) nonlinear code in predicting the pressure signature and ultimately the sonic boom generated by a high speed civilian transport. NASA had designed, built, and wind tunnel tested two low boom configurations for flight at Mach 2 and Mach 3. Experimental data was taken at several distances from these models up to a body length from the axis of the aircraft. The near field experimental data serves as a test bed for computational fluid dynamic codes in evaluating their accuracy and reliability for predicting the behavior of future HSCT designs. Sonic boom prediction methodology exists which is based on modified linear theory. These methods can be used reliably if near field signatures are available at distances from the aircraft where nonlinear and three dimensional effects have diminished in importance. Up to the present time, the only reliable method to obtain this data was via the wind tunnel with costly model construction and testing. It is the intent of the present paper to apply a modified three dimensional Euler code to predict the near field signatures of the two low boom configurations recently tested by NASA.

  4. AGR-1 Safety Test Predictions using the PARFUME code

    SciTech Connect

    Blaise Collin

    2012-05-01

    The PARFUME modeling code was used to predict failure probability of TRISO-coated fuel particles and diffusion of fission products through these particles during safety tests following the first irradiation test of the Advanced Gas Reactor program (AGR-1). These calculations support the AGR-1 Safety Testing Experiment, which is part of the PIE effort on AGR-1. Modeling of the AGR-1 Safety Test Predictions includes a 620-day irradiation followed by a 300-hour heat-up phase of selected AGR-1 compacts. Results include fuel failure probability, palladium penetration, and fractional release of fission products. Results show that no particle failure is predicted during irradiation or heat-up, and that fractional release of fission products is limited during irradiation but that it significantly increases during heat-up.

  5. A predictive coding account of MMN reduction in schizophrenia.

    PubMed

    Wacongne, Catherine

    2016-04-01

    The mismatch negativity (MMN) is thought to be an index of the automatic activation of a specialized network for active prediction and deviance detection in the auditory cortex. It is consistently reduced in schizophrenic patients and has received a lot of interest as a clinical and translational tool. The main neuronal hypothesis regarding the mechanisms leading to a reduced MMN in schizophrenic patients is a dysfunction of NMDA receptors (NMDA-R). However, this hypothesis has never been implemented in a neuronal model. In this paper, we examine the consequences of NMDA-R dysfunction in a neuronal model of MMN based on predictive coding principle. I also investigate how predictive processes may interact with synaptic adaptation in MMN generations and examine the consequences of this interaction for the use of MMN paradigms in schizophrenia research.

  6. BALOO: A Fast and Versatile Code for Accurate Multireference Variational/Perturbative Calculations.

    PubMed

    Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo; Barone, Vincenzo

    2015-05-12

    We present the new BALOO package for performing multireference variational/perturbative computations for medium- to large-size systems. To this end we have introduced a number of conceptual and technical improvements including full parallelization of the code, use and manipulation of a large panel of reference orbitals, implementation of diagrammatic perturbation treatment, and computation of properties by density matrix perturbed to the first-order. A number of test cases are analyzed with special reference to electronic transitions and magnetic properties to show the versatility, effectiveness, and accuracy of BALOO.

  7. Development of a massively parallel parachute performance prediction code

    SciTech Connect

    Peterson, C.W.; Strickland, J.H.; Wolfe, W.P.; Sundberg, W.D.; McBride, D.D.

    1997-04-01

    The Department of Energy has given Sandia full responsibility for the complete life cycle (cradle to grave) of all nuclear weapon parachutes. Sandia National Laboratories is initiating development of a complete numerical simulation of parachute performance, beginning with parachute deployment and continuing through inflation and steady state descent. The purpose of the parachute performance code is to predict the performance of stockpile weapon parachutes as these parachutes continue to age well beyond their intended service life. A new massively parallel computer will provide unprecedented speed and memory for solving this complex problem, and new software will be written to treat the coupled fluid, structure and trajectory calculations as part of a single code. Verification and validation experiments have been proposed to provide the necessary confidence in the computations.

  8. 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.

  9. Specification and Prediction of the Radiation Environment Using Data Assimilative VERB code

    NASA Astrophysics Data System (ADS)

    Shprits, Yuri; Kellerman, Adam

    2016-07-01

    We discuss how data assimilation can be used for the reconstruction of long-term evolution, bench-marking of the physics based codes and used to improve the now-casting and focusing of the radiation belts and ring current. We also discuss advanced data assimilation methods such as parameter estimation and smoothing. We present a number of data assimilation applications using the VERB 3D code. The 3D data assimilative VERB allows us to blend together data from GOES, RBSP A and RBSP B. 1) Model with data assimilation allows us to propagate data to different pitch angles, energies, and L-shells and blends them together with the physics-based VERB code in an optimal way. We illustrate how to use this capability for the analysis of the previous events and for obtaining a global and statistical view of the system. 2) The model predictions strongly depend on initial conditions that are set up for the model. Therefore, the model is as good as the initial conditions that it uses. To produce the best possible initial conditions, data from different sources (GOES, RBSP A, B, our empirical model predictions based on ACE) are all blended together in an optimal way by means of data assimilation, as described above. The resulting initial conditions do not have gaps. This allows us to make more accurate predictions. Real-time prediction framework operating on our website, based on GOES, RBSP A, B and ACE data, and 3D VERB, is presented and discussed.

  10. Interpersonal predictive coding, not action perception, is impaired in autism

    PubMed Central

    von der Lühe, T.; Manera, V.; Barisic, I.; Becchio, C.; Vogeley, K.

    2016-01-01

    This study was conducted to examine interpersonal predictive coding in individuals with high-functioning autism (HFA). Healthy and HFA participants observed point-light displays of two agents (A and B) performing separate actions. In the ‘communicative’ condition, the action performed by agent B responded to a communicative gesture performed by agent A. In the ‘individual’ condition, agent A's communicative action was substituted by a non-communicative action. Using a simultaneous masking-detection task, we demonstrate that observing agent A's communicative gesture enhanced visual discrimination of agent B for healthy controls, but not for participants with HFA. These results were not explained by differences in attentional factors as measured via eye-tracking, or by differences in the recognition of the point-light actions employed. Our findings, therefore, suggest that individuals with HFA are impaired in the use of social information to predict others' actions and provide behavioural evidence that such deficits could be closely related to impairments of predictive coding. PMID:27069050

  11. 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.

  12. 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

  13. Accurate dose assessment system for an exposed person utilising radiation transport calculation codes in emergency response to a radiological accident.

    PubMed

    Takahashi, F; Shigemori, Y; Seki, A

    2009-01-01

    A system has been developed to assess radiation dose distribution inside the body of exposed persons in a radiological accident by utilising radiation transport calculation codes-MCNP and MCNPX. The system consists mainly of two parts, pre-processor and post-processor of the radiation transport calculation. Programs for the pre-processor are used to set up a 'problem-dependent' input file, which defines the accident condition and dosimetric quantities to be estimated. The program developed for the post-processor part can effectively indicate dose information based upon the output file of the code. All of the programs in the dosimetry system can be executed with a generally used personal computer and accurately give the dose profile to an exposed person in a radiological accident without complicated procedures. An experiment using a physical phantom was carried out to verify the availability of the dosimetry system with the developed programs in a gamma ray irradiation field.

  14. Evaluation of a Second-Order Accurate Navier-Stokes Code for Detached Eddy Simulation Past a Circular Cylinder

    NASA Technical Reports Server (NTRS)

    Vatsa, Veer N.; Singer, Bart A.

    2003-01-01

    We evaluate the applicability of a production computational fluid dynamics code for conducting detached eddy simulation for unsteady flows. A second-order accurate Navier-Stokes code developed at NASA Langley Research Center, known as TLNS3D, is used for these simulations. We focus our attention on high Reynolds number flow (Re = 5 x 10(sup 4) - 1.4 x 10(sup 5)) past a circular cylinder to simulate flows with large-scale separations. We consider two types of flow situations: one in which the flow at the separation point is laminar, and the other in which the flow is already turbulent when it detaches from the surface of the cylinder. Solutions are presented for two- and three-dimensional calculations using both the unsteady Reynolds-averaged Navier-Stokes paradigm and the detached eddy simulation treatment. All calculations use the standard Spalart-Allmaras turbulence model as the base model.

  15. 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.

  16. 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.

  17. TTVFast: An efficient and accurate code for transit timing inversion problems

    SciTech Connect

    Deck, Katherine M.; Agol, Eric; Holman, Matthew J.; Nesvorný, David

    2014-06-01

    Transit timing variations (TTVs) have proven to be a powerful technique for confirming Kepler planet candidates, for detecting non-transiting planets, and for constraining the masses and orbital elements of multi-planet systems. These TTV applications often require the numerical integration of orbits for computation of transit times (as well as impact parameters and durations); frequently tens of millions to billions of simulations are required when running statistical analyses of the planetary system properties. We have created a fast code for transit timing computation, TTVFast, which uses a symplectic integrator with a Keplerian interpolator for the calculation of transit times. The speed comes at the expense of accuracy in the calculated times, but the accuracy lost is largely unnecessary, as transit times do not need to be calculated to accuracies significantly smaller than the measurement uncertainties on the times. The time step can be tuned to give sufficient precision for any particular system. We find a speed-up of at least an order of magnitude relative to dynamical integrations with high precision using a Bulirsch-Stoer integrator.

  18. Accurate imaging of moving targets via random sensor arrays and Kerdock codes

    NASA Astrophysics Data System (ADS)

    Strohmer, Thomas; Wang, Haichao

    2013-08-01

    The detection and parameter estimation of moving targets is one of the most important tasks in radar. Arrays of randomly distributed antennas have been popular for this purpose for about half a century. Yet, surprisingly little rigorous mathematical theory exists for random arrays that addresses fundamental questions such as how many targets can be recovered, at what resolution, at which noise level, and with which algorithm. In a different line of research in radar, mathematicians and engineers have invested significant effort into the design of radar transmission waveforms which satisfy various desirable properties. In this paper we bring these two seemingly unrelated areas together. Using tools from compressive sensing we derive a theoretical framework for the imaging of targets in the azimuth-range-Doppler domain via random antenna arrays. In one manifestation of our theory we use Kerdock codes as transmission waveforms and exploit some of their peculiar properties in our analysis. Our paper provides two main contributions. (i) We derive the first rigorous mathematical theory for the detection of moving targets using random sensor arrays. (ii) The transmitted waveforms satisfy a variety of properties that are very desirable and important from a practical viewpoint. Thus our approach does not just lead to useful theoretical insights, but is also of practical importance. Various extensions of our results are derived and numerical simulations confirming our theory are presented.

  19. An atlas of human long non-coding RNAs with accurate 5' ends.

    PubMed

    Hon, Chung-Chau; Ramilowski, Jordan A; Harshbarger, Jayson; Bertin, Nicolas; Rackham, Owen J L; Gough, Julian; Denisenko, Elena; Schmeier, Sebastian; Poulsen, Thomas M; Severin, Jessica; Lizio, Marina; Kawaji, Hideya; Kasukawa, Takeya; Itoh, Masayoshi; Burroughs, A Maxwell; Noma, Shohei; Djebali, Sarah; Alam, Tanvir; Medvedeva, Yulia A; Testa, Alison C; Lipovich, Leonard; Yip, Chi-Wai; Abugessaisa, Imad; Mendez, Mickaël; Hasegawa, Akira; Tang, Dave; Lassmann, Timo; Heutink, Peter; Babina, Magda; Wells, Christine A; Kojima, Soichi; Nakamura, Yukio; Suzuki, Harukazu; Daub, Carsten O; de Hoon, Michiel J L; Arner, Erik; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R

    2017-03-09

    Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.

  20. TTVFast: An Efficient and Accurate Code for Transit Timing Inversion Problems

    NASA Astrophysics Data System (ADS)

    Deck, Katherine M.; Agol, Eric; Holman, Matthew J.; Nesvorný, David

    2014-06-01

    Transit timing variations (TTVs) have proven to be a powerful technique for confirming Kepler planet candidates, for detecting non-transiting planets, and for constraining the masses and orbital elements of multi-planet systems. These TTV applications often require the numerical integration of orbits for computation of transit times (as well as impact parameters and durations); frequently tens of millions to billions of simulations are required when running statistical analyses of the planetary system properties. We have created a fast code for transit timing computation, TTVFast, which uses a symplectic integrator with a Keplerian interpolator for the calculation of transit times. The speed comes at the expense of accuracy in the calculated times, but the accuracy lost is largely unnecessary, as transit times do not need to be calculated to accuracies significantly smaller than the measurement uncertainties on the times. The time step can be tuned to give sufficient precision for any particular system. We find a speed-up of at least an order of magnitude relative to dynamical integrations with high precision using a Bulirsch-Stoer integrator.

  1. DCT/DST-based transform coding for intra prediction in image/video coding.

    PubMed

    Saxena, Ankur; Fernandes, Felix C

    2013-10-01

    In this paper, we present a DCT/DST based transform scheme that applies either the conventional DCT or type-7 DST for all the video-coding intra-prediction modes: vertical, horizontal, and oblique. Our approach is applicable to any block-based intra prediction scheme in a codec that employs transforms along the horizontal and vertical direction separably. Previously, Han, Saxena, and Rose showed that for the intra-predicted residuals of horizontal and vertical modes, the DST is the optimal transform with performance close to the KLT. Here, we prove that this is indeed the case for the other oblique modes. The optimal choice of using DCT or DST is based on intra-prediction modes and requires no additional signaling information or rate-distortion search. The DCT/DST scheme presented in this paper was adopted in the HEVC standardization in March 2011. Further simplifications, especially to reduce implementation complexity, which remove the mode-dependency between DCT and DST, and simply always use DST for the 4 × 4 intra luma blocks, were adopted in the HEVC standard in July 2012. Simulation results conducted for the DCT/DST algorithm are shown in the reference software for the ongoing HEVC standardization. Our results show that the DCT/DST scheme provides significant BD-rate improvement over the conventional DCT based scheme for intra prediction in video sequences.

  2. Arc Jet Facility Test Condition Predictions Using the ADSI Code

    NASA Technical Reports Server (NTRS)

    Palmer, Grant; Prabhu, Dinesh; Terrazas-Salinas, Imelda

    2015-01-01

    The Aerothermal Design Space Interpolation (ADSI) tool is used to interpolate databases of previously computed computational fluid dynamic solutions for test articles in a NASA Ames arc jet facility. The arc jet databases are generated using an Navier-Stokes flow solver using previously determined best practices. The arc jet mass flow rates and arc currents used to discretize the database are chosen to span the operating conditions possible in the arc jet, and are based on previous arc jet experimental conditions where possible. The ADSI code is a database interpolation, manipulation, and examination tool that can be used to estimate the stagnation point pressure and heating rate for user-specified values of arc jet mass flow rate and arc current. The interpolation is performed in the other direction (predicting mass flow and current to achieve a desired stagnation point pressure and heating rate). ADSI is also used to generate 2-D response surfaces of stagnation point pressure and heating rate as a function of mass flow rate and arc current (or vice versa). Arc jet test data is used to assess the predictive capability of the ADSI code.

  3. Probability Distribution Estimation for Autoregressive Pixel-Predictive Image Coding.

    PubMed

    Weinlich, Andreas; Amon, Peter; Hutter, Andreas; Kaup, André

    2016-03-01

    Pixelwise linear prediction using backward-adaptive least-squares or weighted least-squares estimation of prediction coefficients is currently among the state-of-the-art methods for lossless image compression. While current research is focused on mean intensity prediction of the pixel to be transmitted, best compression requires occurrence probability estimates for all possible intensity values. Apart from common heuristic approaches, we show how prediction error variance estimates can be derived from the (weighted) least-squares training region and how a complete probability distribution can be built based on an autoregressive image model. The analysis of image stationarity properties further allows deriving a novel formula for weight computation in weighted least-squares proofing and generalizing ad hoc equations from the literature. For sparse intensity distributions in non-natural images, a modified image model is presented. Evaluations were done in the newly developed C++ framework volumetric, artificial, and natural image lossless coder (Vanilc), which can compress a wide range of images, including 16-bit medical 3D volumes or multichannel data. A comparison with several of the best available lossless image codecs proofs that the method can achieve very competitive compression ratios. In terms of reproducible research, the source code of Vanilc has been made public.

  4. 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

  5. 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

  6. 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.

  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.

    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.

  8. Fast Prediction of HCCI Combustion with an Artificial Neural Network Linked to a Fluid Mechanics Code

    SciTech Connect

    Aceves, S M; Flowers, D L; Chen, J; Babaimopoulos, A

    2006-08-29

    We have developed an artificial neural network (ANN) based combustion model and have integrated it into a fluid mechanics code (KIVA3V) to produce a new analysis tool (titled KIVA3V-ANN) that can yield accurate HCCI predictions at very low computational cost. The neural network predicts ignition delay as a function of operating parameters (temperature, pressure, equivalence ratio and residual gas fraction). KIVA3V-ANN keeps track of the time history of the ignition delay during the engine cycle to evaluate the ignition integral and predict ignition for each computational cell. After a cell ignites, chemistry becomes active, and a two-step chemical kinetic mechanism predicts composition and heat generation in the ignited cells. KIVA3V-ANN has been validated by comparison with isooctane HCCI experiments in two different engines. The neural network provides reasonable predictions for HCCI combustion and emissions that, although typically not as good as obtained with the more physically representative multi-zone model, are obtained at a much reduced computational cost. KIVA3V-ANN can perform reasonably accurate HCCI calculations while requiring only 10% more computational effort than a motored KIVA3V run. It is therefore considered a valuable tool for evaluation of engine maps or other performance analysis tasks requiring multiple individual runs.

  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. 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

  11. Fast motion prediction algorithm for multiview video coding

    NASA Astrophysics Data System (ADS)

    Abdelazim, Abdelrahman; Zhang, Guang Y.; Mein, Stephen J.; Varley, Martin R.; Ait-Boudaoud, Djamel

    2011-06-01

    Multiview Video Coding (MVC) is an extension to the H.264/MPEG-4 AVC video compression standard developed with joint efforts by MPEG/VCEG to enable efficient encoding of sequences captured simultaneously from multiple cameras using a single video stream. Therefore the design is aimed at exploiting inter-view dependencies in addition to reducing temporal redundancies. However, this further increases the overall encoding complexity In this paper, the high correlation between a macroblock and its enclosed partitions is utilised to estimate motion homogeneity, and based on the result inter-view prediction is selectively enabled or disabled. Moreover, if the MVC is divided into three layers in terms of motion prediction; the first being the full and sub-pixel motion search, the second being the mode selection process and the third being repetition of the first and second for inter-view prediction, the proposed algorithm significantly reduces the complexity in the three layers. To assess the proposed algorithm, a comprehensive set of experiments were conducted. The results show that the proposed algorithm significantly reduces the motion estimation time whilst maintaining similar Rate Distortion performance, when compared to both the H.264/MVC reference software and recently reported work.

  12. A CMOS Imager with Focal Plane Compression using Predictive Coding

    NASA Technical Reports Server (NTRS)

    Leon-Salas, Walter D.; Balkir, Sina; Sayood, Khalid; Schemm, Nathan; Hoffman, Michael W.

    2007-01-01

    This paper presents a CMOS image sensor with focal-plane compression. The design has a column-level architecture and it is based on predictive coding techniques for image decorrelation. The prediction operations are performed in the analog domain to avoid quantization noise and to decrease the area complexity of the circuit, The prediction residuals are quantized and encoded by a joint quantizer/coder circuit. To save area resources, the joint quantizerlcoder circuit exploits common circuitry between a single-slope analog-to-digital converter (ADC) and a Golomb-Rice entropy coder. This combination of ADC and encoder allows the integration of the entropy coder at the column level. A prototype chip was fabricated in a 0.35 pm CMOS process. The output of the chip is a compressed bit stream. The test chip occupies a silicon area of 2.60 mm x 5.96 mm which includes an 80 X 44 APS array. Tests of the fabricated chip demonstrate the validity of the design.

  13. 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/.

  14. 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.

  15. Retrieving the Molecular Composition of Planet-Forming Material: An Accurate Non-LTE Radiative Transfer Code for JWST

    NASA Astrophysics Data System (ADS)

    Pontoppidan, Klaus

    Based on the observed distributions of exoplanets and dynamical models of their evolution, the primary planet-forming regions of protoplanetary disks are thought to span distances of 1-20 AU from typical stars. A key observational challenge of the next decade will be to understand the links between the formation of planets in protoplanetary disks and the chemical composition of exoplanets. Potentially habitable planets in particular are likely formed by solids growing within radii of a few AU, augmented by unknown contributions from volatiles formed at larger radii of 10-50 AU. The basic chemical composition of these inner disk regions is characterized by near- to far-infrared (2-200 micron) emission lines from molecular gas at temperatures of 50-1500 K. A critical step toward measuring the chemical composition of planet-forming regions is therefore to convert observed infrared molecular line fluxes, profiles and images to gas temperatures, densities and molecular abundances. However, current techniques typically employ approximate radiative transfer methods and assumptions of local thermodynamic equilibrium (LTE) to retrieve abundances, leading to uncertainties of orders of magnitude and inconclusive comparisons to chemical models. Ultimately, the scientific impact of the high quality spectroscopic data expected from the James Webb Space Telescope (JWST) will be limited by the availability of radiative transfer tools for infrared molecular lines. We propose to develop a numerically accurate, non-LTE 3D line radiative transfer code, needed to interpret mid-infrared molecular line observations of protoplanetary and debris disks in preparation for the James Webb Space Telescope (JWST). This will be accomplished by adding critical functionality to the existing Monte Carlo code LIME, which was originally developed to support (sub)millimeter interferometric observations. In contrast to existing infrared codes, LIME calculates the exact statistical balance of arbitrary

  16. Numerical Prediction of SERN Performance using WIND code

    NASA Technical Reports Server (NTRS)

    Engblom, W. A.

    2003-01-01

    Computational results are presented for the performance and flow behavior of single-expansion ramp nozzles (SERNs) during overexpanded operation and transonic flight. Three-dimensional Reynolds-Averaged Navier Stokes (RANS) results are obtained for two vehicle configurations, including the NASP Model 5B and ISTAR RBCC (a variant of X-43B) using the WIND code. Numerical predictions for nozzle integrated forces and pitch moments are directly compared to experimental data for the NASP Model 5B, and adequate-to-excellent agreement is found. The sensitivity of SERN performance and separation phenomena to freestream static pressure and Mach number is demonstrated via a matrix of cases for both vehicles. 3-D separation regions are shown to be induced by either lateral (e.g., sidewall) shocks or vertical (e.g., cowl trailing edge) shocks. Finally, the implications of this work to future preliminary design efforts involving SERNs are discussed.

  17. 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.

  18. 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

  19. 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.

  20. AGR-2 safety test predictions using the PARFUME code

    SciTech Connect

    Collin, Blaise P.

    2014-09-01

    This report documents calculations performed to predict failure probability of TRISO-coated fuel particles and diffusion of fission products through these particles during safety tests following the second irradiation test of the Advanced Gas Reactor program (AGR-2). The calculations include the modeling of the AGR-2 irradiation that occurred from June 2010 to October 2013 in the Advanced Test Reactor (ATR) and the modeling of a safety testing phase to support safety tests planned at Oak Ridge National Laboratory and at Idaho National Laboratory (INL) for a selection of AGR-2 compacts. The heat-up of AGR-2 compacts is a critical component of the AGR-2 fuel performance evaluation, and its objectives are to identify the effect of accident test temperature, burnup, and irradiation temperature on the performance of the fuel at elevated temperature. Safety testing of compacts will be followed by detailed examinations of the fuel particles to further evaluate fission product retention and behavior of the kernel and coatings. The modeling was performed using the particle fuel model computer code PARFUME developed at INL. PARFUME is an advanced gas-cooled reactor fuel performance modeling and analysis code (Miller 2009). It has been developed as an integrated mechanistic code that evaluates the thermal, mechanical, and physico-chemical behavior of fuel particles during irradiation to determine the failure probability of a population of fuel particles given the particle-to-particle statistical variations in physical dimensions and material properties that arise from the fuel fabrication process, accounting for all viable mechanisms that can lead to particle failure. The code also determines the diffusion of fission products from the fuel through the particle coating layers, and through the fuel matrix to the coolant boundary. The subsequent release of fission products is calculated at the compact level (release of fission products from the compact). PARFUME calculates the

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

    PubMed

    Zhu, Yafeng; Engström, Pär G; Tellgren-Roth, Christian; Baudo, Charles D; Kennell, John C; Sun, Sheng; Billmyre, R Blake; Schröder, Markus S; Andersson, Anna; Holm, Tina; Sigurgeirsson, Benjamin; Wu, Guangxi; Sankaranarayanan, Sundar Ram; Siddharthan, Rahul; Sanyal, Kaustuv; Lundeberg, Joakim; Nystedt, Björn; Boekhout, Teun; Dawson, Thomas L; Heitman, Joseph; Scheynius, Annika; Lehtiö, Janne

    2017-01-18

    Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.

  7. Benchmark studies of the Bending Corrected Rotating Linear Model (BCRLM) reactive scattering code: Implications for accurate quantum calculations

    SciTech Connect

    Hayes, E.F.; Darakjian, Z. . Dept. of Chemistry); Walker, R.B. )

    1990-01-01

    The Bending Corrected Rotating Linear Model (BCRLM), developed by Hayes and Walker, is a simple approximation to the true multidimensional scattering problem for reaction of the type: A + BC {yields} AB + C. While the BCRLM method is simpler than methods designed to obtain accurate three dimensional quantum scattering results, this turns out to be a major advantage in terms of our benchmarking studies. The computer code used to obtain BCRLM scattering results is written for the most part in standard FORTRAN and has been reported to several scalar, vector, and parallel architecture computers including the IBM 3090-600J, the Cray XMP and YMP, the Ardent Titan, IBM RISC System/6000, Convex C-1 and the MIPS 2000. Benchmark results will be reported for each of these machines with an emphasis on comparing the scalar, vector, and parallel performance for the standard code with minimum modifications. Detailed analysis of the mapping of the BCRLM approach onto both shared and distributed memory parallel architecture machines indicates the importance of introducing several key changes in the basic strategy and algorithums used to calculate scattering results. This analysis of the BCRLM approach provides some insights into optimal strategies for mapping three dimensional quantum scattering methods, such as the Parker-Pack method, onto shared or distributed memory parallel computers.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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].

  15. 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.

  16. Predictive Coding: A Fresh View of Inhibition in the Retina

    NASA Astrophysics Data System (ADS)

    Srinivasan, M. V.; Laughlin, S. B.; Dubs, A.

    1982-11-01

    Interneurons exhibiting centre--surround antagonism within their receptive fields are commonly found in peripheral visual pathways. We propose that this organization enables the visual system to encode spatial detail in a manner that minimizes the deleterious effects of intrinsic noise, by exploiting the spatial correlation that exists within natural scenes. The antagonistic surround takes a weighted mean of the signals in neighbouring receptors to generate a statistical prediction of the signal at the centre. The predicted value is subtracted from the actual centre signal, thus minimizing the range of outputs transmitted by the centre. In this way the entire dynamic range of the interneuron can be devoted to encoding a small range of intensities, thus rendering fine detail detectable against intrinsic noise injected at later stages in processing. This predictive encoding scheme also reduces spatial redundancy, thereby enabling the array of interneurons to transmit a larger number of distinguishable images, taking into account the expected structure of the visual world. The profile of the required inhibitory field is derived from statistical estimation theory. This profile depends strongly upon the signal: noise ratio and weakly upon the extent of lateral spatial correlation. The receptive fields that are quantitatively predicted by the theory resemble those of X-type retinal ganglion cells and show that the inhibitory surround should become weaker and more diffuse at low intensities. The latter property is unequivocally demonstrated in the first-order interneurons of the fly's compound eye. The theory is extended to the time domain to account for the phasic responses of fly interneurons. These comparisons suggest that, in the early stages of processing, the visual system is concerned primarily with coding the visual image to protect against subsequent intrinsic noise, rather than with reconstructing the scene or extracting specific features from it. The treatment

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Optimal coding of vectorcardiographic sequences using spatial prediction.

    PubMed

    Augustyniak, Piotr

    2007-05-01

    This paper discusses principles, implementation details, and advantages of sequence coding algorithm applied to the compression of vectocardiograms (VCG). The main novelty of the proposed method is the automatic management of distortion distribution controlled by the local signal contents in both technical and medical aspects. As in clinical practice, the VCG loops representing P, QRS, and T waves in the three-dimensional (3-D) space are considered here as three simultaneous sequences of objects. Because of the similarity of neighboring loops, encoding the values of prediction error significantly reduces the data set volume. The residual values are de-correlated with the discrete cosine transform (DCT) and truncated at certain energy threshold. The presented method is based on the irregular temporal distribution of medical data in the signal and takes advantage of variable sampling frequency for automatically detected VCG loops. The features of the proposed algorithm are confirmed by the results of the numerical experiment carried out for a wide range of real records. The average data reduction ratio reaches a value of 8.15 while the percent root-mean-square difference (PRD) distortion ratio for the most important sections of signal does not exceed 1.1%.

  3. 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

  4. 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

  5. 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

  6. 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 .

  7. Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins.

    PubMed

    Warden, Charles D; Kim, Seong-Ho; Yi, Soojin V

    2008-02-13

    Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Affinity regression predicts the recognition code of nucleic acid binding proteins

    PubMed Central

    Pelossof, Raphael; Singh, Irtisha; Yang, Julie L.; Weirauch, Matthew T.; Hughes, Timothy R.; Leslie, Christina S.

    2016-01-01

    Predicting the affinity profiles of nucleic acid-binding proteins directly from the protein sequence is a major unsolved problem. We present a statistical approach for learning the recognition code of a family of transcription factors (TFs) or RNA-binding proteins (RBPs) from high-throughput binding assays. Our method, called affinity regression, trains on protein binding microarray (PBM) or RNA compete experiments to learn an interaction model between proteins and nucleic acids, using only protein domain and probe sequences as inputs. By training on mouse homeodomain PBM profiles, our model correctly identifies residues that confer DNA-binding specificity and accurately predicts binding motifs for an independent set of divergent homeodomains. Similarly, learning from RNA compete profiles for diverse RBPs, our model can predict the binding affinities of held-out proteins and identify key RNA-binding residues. More broadly, we envision applying our method to model and predict biological interactions in any setting where there is a high-throughput ‘affinity’ readout. PMID:26571099

  18. 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

  19. Analytic solution to verify code predictions of two-phase flow in a boiling water reactor core channel. [CONDOR code

    SciTech Connect

    Chen, K.F.; Olson, C.A.

    1983-09-01

    One reliable method that can be used to verify the solution scheme of a computer code is to compare the code prediction to a simplified problem for which an analytic solution can be derived. An analytic solution for the axial pressure drop as a function of the flow was obtained for the simplified problem of homogeneous equilibrium two-phase flow in a vertical, heated channel with a cosine axial heat flux shape. This analytic solution was then used to verify the predictions of the CONDOR computer code, which is used to evaluate the thermal-hydraulic performance of boiling water reactors. The results show excellent agreement between the analytic solution and CONDOR prediction.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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)).

  7. Dynamic Forces in Spur Gears - Measurement, Prediction, and Code Validation

    NASA Technical Reports Server (NTRS)

    Oswald, Fred B.; Townsend, Dennis P.; Rebbechi, Brian; Lin, Hsiang Hsi

    1996-01-01

    Measured and computed values for dynamic loads in spur gears were compared to validate a new version of the NASA gear dynamics code DANST-PC. Strain gage data from six gear sets with different tooth profiles were processed to determine the dynamic forces acting between the gear teeth. Results demonstrate that the analysis code successfully simulates the dynamic behavior of the gears. Differences between analysis and experiment were less than 10 percent under most conditions.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Development of a shock noise prediction code for high-speed helicopters - The subsonically moving shock

    NASA Technical Reports Server (NTRS)

    Tadghighi, H.; Holz, R.; Farassat, F.; Lee, Yung-Jang

    1991-01-01

    A previously defined airfoil subsonic shock-noise prediction formula whose result depends on a mapping of the time-dependent shock surface to a time-independent computational domain is presently coded and incorporated in the NASA-Langley rotor-noise prediction code, WOPWOP. The structure and algorithms used in the shock-noise prediction code are presented; special care has been taken to reduce computation time while maintaining accuracy. Numerical examples of shock-noise prediction are presented for hover and forward flight. It is confirmed that shock noise is an important component of the quadrupole source.

  13. 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.

  14. 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

  15. Divide sampling-based hybrid temporal-spatial prediction coding for H.264/AVC

    NASA Astrophysics Data System (ADS)

    Li, Hongwei; Song, Rui; Wu, Chengke; Zhang, Jie

    2011-11-01

    A divide sampling-based hybrid temporal-spatial prediction coding algorithm is designed to further improve the coding performance of the conventional H.264/AVC coding. In the proposed algorithm, a frame is first divided into four equal-sized subframes, and the first subframe is coded using the rate distortion optimization model with inter- or intraprediction adaptively. Then, the optimal prediction method of the macroblock in other subframes is selected flexibly and reasonably from intraprediction, the fast interprediction, and the spatial interpolation prediction. The simulation results show that compared with the conventional H.264/AVC coding, the average bit rate is reduced by 6.15% under the same peak signal-to-noise ratio (PSNR), the average PSNR is increased by 0.22 dB under the same bit rate, and the average coding time is saved by 12.40% in the proposed algorithm.

  16. 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.

  17. 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.

  18. 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.

  19. 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

    To go beyond qualitative models of the biological substrate of object recognition, we ask: can a single ventral stream neuronal linking hypothesis quantitatively account for core object recognition performance over a broad range of tasks? We measured human performance in 64 object recognition tests using thousands of challenging images that explore shape similarity and identity preserving object variation. We then used multielectrode arrays to measure neuronal population responses to those same images in visual areas V4 and inferior temporal (IT) cortex of monkeys and simulated V1 population responses. We tested leading candidate linking hypotheses and control hypotheses, each postulating how ventral stream neuronal responses underlie object recognition behavior. Specifically, for each hypothesis, we computed the predicted performance on the 64 tests and compared it with the measured pattern of human performance. All tested hypotheses based on low- and mid-level visually evoked activity (pixels, V1, and V4) were very poor predictors of the human behavioral pattern. However, simple learned weighted sums of distributed average IT firing rates exactly predicted the behavioral pattern. More elaborate linking hypotheses relying on IT trial-by-trial correlational structure, finer IT temporal codes, or ones that strictly respect the known spatial substructures of IT (“face patches”) did not improve predictive power. Although these results do not reject those more elaborate hypotheses, they suggest a simple, sufficient quantitative model: each object recognition task is learned from the spatially distributed mean firing rates (100 ms) of ∼60,000 IT neurons and is executed as a simple weighted sum of those firing rates. SIGNIFICANCE STATEMENT We sought to go beyond qualitative models of visual object recognition and determine whether a single neuronal linking hypothesis can quantitatively account for core object recognition behavior. To achieve this, we designed a

  20. 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

    To go beyond qualitative models of the biological substrate of object recognition, we ask: can a single ventral stream neuronal linking hypothesis quantitatively account for core object recognition performance over a broad range of tasks? We measured human performance in 64 object recognition tests using thousands of challenging images that explore shape similarity and identity preserving object variation. We then used multielectrode arrays to measure neuronal population responses to those same images in visual areas V4 and inferior temporal (IT) cortex of monkeys and simulated V1 population responses. We tested leading candidate linking hypotheses and control hypotheses, each postulating how ventral stream neuronal responses underlie object recognition behavior. Specifically, for each hypothesis, we computed the predicted performance on the 64 tests and compared it with the measured pattern of human performance. All tested hypotheses based on low- and mid-level visually evoked activity (pixels, V1, and V4) were very poor predictors of the human behavioral pattern. However, simple learned weighted sums of distributed average IT firing rates exactly predicted the behavioral pattern. More elaborate linking hypotheses relying on IT trial-by-trial correlational structure, finer IT temporal codes, or ones that strictly respect the known spatial substructures of IT ("face patches") did not improve predictive power. Although these results do not reject those more elaborate hypotheses, they suggest a simple, sufficient quantitative model: each object recognition task is learned from the spatially distributed mean firing rates (100 ms) of ∼60,000 IT neurons and is executed as a simple weighted sum of those firing rates. Significance statement: We sought to go beyond qualitative models of visual object recognition and determine whether a single neuronal linking hypothesis can quantitatively account for core object recognition behavior. To achieve this, we designed a

  1. 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

  2. GERMINAL — A computer code for predicting fuel pin behaviour

    NASA Astrophysics Data System (ADS)

    Melis, J. C.; Roche, L.; Piron, J. P.; Truffert, J.

    1992-06-01

    In the frame of the R and D on FBR fuels, CEA/DEC is developing the computer code GERMINAL to study the fuel pin thermal-mechanical behaviour during steady-state and incidental conditions. The development of GERMINAL is foreseen in two steps: (1) The GERMINAL 1 code designed as a "working horse" for immediate applications. The version 1 of GERMINAL 1 is presently delivered fully documented with a physical qualification guaranteed up to 8 at%. (2) The version 2 of GERMINAL 1, in addition to what is presently treated in GERMINAL 1 includes the treatment of high burnup effects on the fission gas release and the fuel-clad joint. This version, GERMINAL 1.2, is presently under testing and will be completed up to the end of 1991. The GERMINAL 2 code designed as a reference code for future applications will cover all the aspects of GERMINAL 1 (including high burnup effects) with a more general mechanical treatment, and a completely revised and advanced informatical structure.

  3. Prediction accuracy in estimating joint angle trajectories using a video posture coding method for sagittal lifting tasks.

    PubMed

    Chang, Chien-Chi; McGorry, Raymond W; Lin, Jia-Hua; Xu, Xu; Hsiang, Simon M

    2010-08-01

    This study investigated prediction accuracy of a video posture coding method for lifting joint trajectory estimation. From three filming angles, the coder selected four key snapshots, identified joint angles and then a prediction program estimated the joint trajectories over the course of a lift. Results revealed a limited range of differences of joint angles (elbow, shoulder, hip, knee, ankle) between the manual coding method and the electromagnetic motion tracking system approach. Lifting range significantly affected estimate accuracy for all joints and camcorder filming angle had a significant effect on all joints but the hip. Joint trajectory predictions were more accurate for knuckle-to-shoulder lifts than for floor-to-shoulder or floor-to-knuckle lifts with average root mean square errors (RMSE) of 8.65 degrees , 11.15 degrees and 11.93 degrees , respectively. Accuracy was also greater for the filming angles orthogonal to the participant's sagittal plane (RMSE = 9.97 degrees ) as compared to filming angles of 45 degrees (RMSE = 11.01 degrees ) or 135 degrees (10.71 degrees ). The effects of lifting speed and loading conditions were minimal. To further increase prediction accuracy, improved prediction algorithms and/or better posture matching methods should be investigated. STATEMENT OF RELEVANCE: Observation and classification of postures are common steps in risk assessment of manual materials handling tasks. The ability to accurately predict lifting patterns through video coding can provide ergonomists with greater resolution in characterising or assessing the lifting tasks than evaluation based solely on sampling with a single lifting posture event.

  4. 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

  5. Assessment of 3D Codes for Predicting Liner Attenuation in Flow Ducts

    NASA Technical Reports Server (NTRS)

    Watson, W. R.; Nark, D. M.; Jones, M. G.

    2008-01-01

    This paper presents comparisons of seven propagation codes for predicting liner attenuation in ducts with flow. The selected codes span the spectrum of methods available (finite element, parabolic approximation, and pseudo-time domain) and are collectively representative of the state-of-art in the liner industry. These codes are included because they have two-dimensional and three-dimensional versions and can be exported to NASA's Columbia Supercomputer. The basic assumptions, governing differential equations, boundary conditions, and numerical methods underlying each code are briefly reviewed and an assessment is performed based on two predefined metrics. The two metrics used in the assessment are the accuracy of the predicted attenuation and the amount of wall clock time to predict the attenuation. The assessment is performed over a range of frequencies, mean flow rates, and grazing flow liner impedances commonly used in the liner industry. The primary conclusions of the study are (1) predicted attenuations are in good agreement for rigid wall ducts, (2) the majority of codes compare well to each other and to approximate results from mode theory for soft wall ducts, (3) most codes compare well to measured data on a statistical basis, (4) only the finite element codes with cubic Hermite polynomials capture extremely large attenuations, and (5) wall clock time increases by an order of magnitude or more are observed for a three-dimensional code relative to the corresponding two-dimensional version of the same code.

  6. A predictive transport modeling code for ICRF-heated tokamaks

    SciTech Connect

    Phillips, C.K.; Hwang, D.Q. . Plasma Physics Lab.); Houlberg, W.; Attenberger, S.; Tolliver, J.; Hively, L. )

    1992-02-01

    In this report, a detailed description of the physic included in the WHIST/RAZE package as well as a few illustrative examples of the capabilities of the package will be presented. An in depth analysis of ICRF heating experiments using WHIST/RAZE will be discussed in a forthcoming report. A general overview of philosophy behind the structure of the WHIST/RAZE package, a summary of the features of the WHIST code, and a description of the interface to the RAZE subroutines are presented in section 2 of this report. Details of the physics contained in the RAZE code are examined in section 3. Sample results from the package follow in section 4, with concluding remarks and a discussion of possible improvements to the package discussed in section 5.

  7. Curved Duct Noise Prediction Using the Fast Scattering Code

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.; Tinetti, Ana F.; Farassat, F.

    2007-01-01

    Results of a study to validate the Fast Scattering Code (FSC) as a duct noise predictor, including the effects of curvature, finite impedance on the walls, and uniform background flow, are presented in this paper. Infinite duct theory was used to generate the modal content of the sound propagating within the duct. Liner effects were incorporated via a sound absorbing boundary condition on the scattering surfaces. Simulations for a rectangular duct of constant cross-sectional area have been compared to analytical solutions and experimental data. Comparisons with analytical results indicate that the code can properly calculate a given dominant mode for hardwall surfaces. Simulated acoustic behavior in the presence of lined walls (using hardwall duct modes as incident sound) is consistent with expected trends. Duct curvature was found to enhance weaker modes and reduce pressure amplitude. Agreement between simulated and experimental results for a straight duct with hard walls (no flow) was excellent.

  8. 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

  9. 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.

  10. Operation of the helicopter antenna radiation prediction code

    NASA Technical Reports Server (NTRS)

    Braeden, E. W.; Klevenow, F. T.; Newman, E. H.; Rojas, R. G.; Sampath, K. S.; Scheik, J. T.; Shamansky, H. T.

    1993-01-01

    HARP is a front end as well as a back end for the AMC and NEWAIR computer codes. These codes use the Method of Moments (MM) and the Uniform Geometrical Theory of Diffraction (UTD), respectively, to calculate the electromagnetic radiation patterns for antennas on aircraft. The major difficulty in using these codes is in the creation of proper input files for particular aircraft and in verifying that these files are, in fact, what is intended. HARP creates these input files in a consistent manner and allows the user to verify them for correctness using sophisticated 2 and 3D graphics. After antenna field patterns are calculated using either MM or UTD, HARP can display the results on the user's screen or provide hardcopy output. Because the process of collecting data, building the 3D models, and obtaining the calculated field patterns was completely automated by HARP, the researcher's productivity can be many times what it could be if these operations had to be done by hand. A complete, step by step, guide is provided so that the researcher can quickly learn to make use of all the capabilities of HARP.

  11. ICAN: A versatile code for predicting composite properties

    NASA Technical Reports Server (NTRS)

    Ginty, C. A.; Chamis, C. C.

    1986-01-01

    The Integrated Composites ANalyzer (ICAN), a stand-alone computer code, incorporates micromechanics equations and laminate theory to analyze/design multilayered fiber composite structures. Procedures for both the implementation of new data in ICAN and the selection of appropriate measured data are summarized for: (1) composite systems subject to severe thermal environments; (2) woven fabric/cloth composites; and (3) the selection of new composite systems including those made from high strain-to-fracture fibers. The comparisons demonstrate the versatility of ICAN as a reliable method for determining composite properties suitable for preliminary design.

  12. Predictive codes of familiarity and context during the perceptual learning of facial identities.

    PubMed

    Apps, Matthew A J; Tsakiris, Manos

    2013-01-01

    Face recognition is a key component of successful social behaviour. However, the computational processes that underpin perceptual learning and recognition as faces transition from unfamiliar to familiar are poorly understood. In predictive coding, learning occurs through prediction errors that update stimulus familiarity, but recognition is a function of both stimulus and contextual familiarity. Here we show that behavioural responses on a two-option face recognition task can be predicted by the level of contextual and facial familiarity in a computational model derived from predictive-coding principles. Using fMRI, we show that activity in the superior temporal sulcus varies with the contextual familiarity in the model, whereas activity in the fusiform face area covaries with the prediction error parameter that updated facial familiarity. Our results characterize the key computations underpinning the perceptual learning of faces, highlighting that the functional properties of face-processing areas conform to the principles of predictive coding.

  13. Monte Carlo Predictions of Prompt Fission Neutrons and Photons: a Code Comparison

    NASA Astrophysics Data System (ADS)

    Talou, P.; Kawano, T.; Stetcu, I.; Vogt, R.; Randrup, J.

    2014-04-01

    This paper reports on initial comparisons between the LANL CGMF and LBNL/LLNL FREYA codes, which both aim at computing prompt fission neutrons and gammas. While the methodologies used in both codes are somewhat similar, the detailed implementations and physical assumptions are different. We are investigating how some of these differences impact predictions.

  14. Fan Noise Prediction System Development: Source/Radiation Field Coupling and Workstation Conversion for the Acoustic Radiation Code

    NASA Technical Reports Server (NTRS)

    Meyer, H. D.

    1993-01-01

    The Acoustic Radiation Code (ARC) is a finite element program used on the IBM mainframe to predict far-field acoustic radiation from a turbofan engine inlet. In this report, requirements for developers of internal aerodynamic codes regarding use of their program output an input for the ARC are discussed. More specifically, the particular input needed from the Bolt, Beranek and Newman/Pratt and Whitney (turbofan source noise generation) Code (BBN/PWC) is described. In a separate analysis, a method of coupling the source and radiation models, that recognizes waves crossing the interface in both directions, has been derived. A preliminary version of the coupled code has been developed and used for initial evaluation of coupling issues. Results thus far have shown that reflection from the inlet is sufficient to indicate that full coupling of the source and radiation fields is needed for accurate noise predictions ' Also, for this contract, the ARC has been modified for use on the Sun and Silicon Graphics Iris UNIX workstations. Changes and additions involved in this effort are described in an appendix.

  15. The HART II International Workshop: An Assessment of the State-of-the-Art in Comprehensive Code Prediction

    NASA Technical Reports Server (NTRS)

    vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

    2013-01-01

    Significant advancements in computational fluid dynamics (CFD) and their coupling with computational structural dynamics (CSD, or comprehensive codes) for rotorcraft applications have been achieved recently. Despite this, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this article, the capabilities of such codes are evaluated using the HART II International Workshop database, focusing on a typical descent operating condition which includes strong blade-vortex interactions. A companion article addresses the CFD/CSD coupled approach. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics-especially for the cases with HHC-and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

  16. An Assessment of Comprehensive Code Prediction State-of-the-Art Using the HART II International Workshop Data

    NASA Technical Reports Server (NTRS)

    vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

    2012-01-01

    Despite significant advancements in computational fluid dynamics and their coupling with computational structural dynamics (= CSD, or comprehensive codes) for rotorcraft applications, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this paper, the capabilities of such codes are evaluated using the HART II Inter- national Workshop data base, focusing on a typical descent operating condition which includes strong blade-vortex interactions. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics - especially for the cases with HHC - and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

  17. Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

    PubMed

    Bradley, Robert K; Uzilov, Andrew V; Skinner, Mitchell E; Bendaña, Yuri R; Barquist, Lars; Holmes, Ian

    2009-08-11

    We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3' end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.

  18. PARC Navier-Stokes code upgrade and validation for high speed aeroheating predictions

    NASA Technical Reports Server (NTRS)

    Liver, Peter A.; Praharaj, Sarat C.; Seaford, C. Mark

    1990-01-01

    Applications of the PARC full Navier-Stokes code for hypersonic flowfield and aeroheating predictions around blunt bodies such as the Aeroassist Flight Experiment (AFE) and Aeroassisted Orbital Transfer Vehicle (AOTV) are evaluated. Two-dimensional/axisymmetric and three-dimensional perfect gas versions of the code were upgraded and tested against benchmark wind tunnel cases of hemisphere-cylinder, three-dimensional AFE forebody, and axisymmetric AFE and AOTV aerobrake/wake flowfields. PARC calculations are in good agreement with experimental data and results of similar computer codes. Difficulties encountered in flowfield and heat transfer predictions due to effects of grid density, boundary conditions such as singular stagnation line axis and artificial dissipation terms are presented together with subsequent improvements made to the code. The experience gained with the perfect gas code is being currently utilized in applications of an equilibrium air real gas PARC version developed at REMTECH.

  19. Ducted-Fan Engine Acoustic Predictions Using a Navier-Stokes Code

    NASA Technical Reports Server (NTRS)

    Rumsey, C. L.; Biedron, R. T.; Farassat, F.; Spence, P. L.

    1998-01-01

    A Navier-Stokes computer code is used to predict one of the ducted-fan engine acoustic modes that results from rotor-wake/stator-blade interaction. A patched sliding-zone interface is employed to pass information between the moving rotor row and the stationary stator row. The code produces averaged aerodynamic results downstream of the rotor that agree well with a widely used average-passage code. The acoustic mode of interest is generated successfully by the code and is propagated well upstream of the rotor, temporal and spatial numerical resolution are fine enough such that attenuation of the signal is small. Two acoustic codes are used to find the far-field noise. Near-field propagation is computed by using Eversman's wave envelope code, which is based on a finite-element model. Propagation to the far field is accomplished by using the Kirchhoff formula for moving surfaces with the results of the wave envelope code as input data. Comparison of measured and computed far-field noise levels show fair agreement in the range of directivity angles where the peak radiation lobes from the inlet are observed. Although only a single acoustic mode is targeted in this study, the main conclusion is a proof-of-concept: Navier Stokes codes can be used both to generate and propagate rotor-stator acoustic modes forward through an engine, where the results can be coupled to other far-field noise prediction codes.

  20. Ducted-Fan Engine Acoustic Predictions using a Navier-Stokes Code

    NASA Technical Reports Server (NTRS)

    Rumsey, C. L.; Biedron, R. T.; Farassat, F.; Spence, P. L.

    1998-01-01

    A Navier-Stokes computer code is used to predict one of the ducted-fan engine acoustic modes that results from rotor-wake/stator-blade interaction. A patched sliding-zone interface is employed to pass information between the moving rotor row and the stationary stator row. The code produces averaged aerodynamic results downstream of the rotor that agree well with a widely used average-passage code. The acoustic mode of interest is generated successfully by the code and is propagated well upstream of the rotor; temporal and spatial numerical resolution are fine enough such that attenuation of the signal is small. Two acoustic codes are used to find the far-field noise. Near-field propagation is computed by using Eversman's wave envelope code, which is based on a finite-element model. Propagation to the far field is accomplished by using the Kirchhoff formula for moving surfaces with the results of the wave envelope code as input data. Comparison of measured and computed far-field noise levels show fair agreement in the range of directivity angles where the peak radiation lobes from the inlet are observed. Although only a single acoustic mode is targeted in this study, the main conclusion is a proof-of-concept: Navier-Stokes codes can be used both to generate and propagate rotor/stator acoustic modes forward through an engine, where the results can be coupled to other far-field noise prediction codes.

  1. Tiltrotor Aeroacoustic Code (TRAC) Prediction Assessment and Initial Comparisons with Tram Test Data

    NASA Technical Reports Server (NTRS)

    Burley, Casey L.; Brooks, Thomas F.; Charles, Bruce D.; McCluer, Megan

    1999-01-01

    A prediction sensitivity assessment to inputs and blade modeling is presented for the TiltRotor Aeroacoustic Code (TRAC). For this study, the non-CFD prediction system option in TRAC is used. Here, the comprehensive rotorcraft code, CAMRAD.Mod1, coupled with the high-resolution sectional loads code HIRES, predicts unsteady blade loads to be used in the noise prediction code WOPWOP. The sensitivity of the predicted blade motions, blade airloads, wake geometry, and acoustics is examined with respect to rotor rpm, blade twist and chord, and to blade dynamic modeling. To accomplish this assessment, an interim input-deck for the TRAM test model and an input-deck for a reference test model are utilized in both rigid and elastic modes. Both of these test models are regarded as near scale models of the V-22 proprotor (tiltrotor). With basic TRAC sensitivities established, initial TRAC predictions are compared to results of an extensive test of an isolated model proprotor. The test was that of the TiltRotor Aeroacoustic Model (TRAM) conducted in the Duits-Nederlandse Windtunnel (DNW). Predictions are compared to measured noise for the proprotor operating over an extensive range of conditions. The variation of predictions demonstrates the great care that must be taken in defining the blade motion. However, even with this variability, the predictions using the different blade modeling successfully capture (bracket) the levels and trends of the noise for conditions ranging from descent to ascent.

  2. A new hybrid coding for protein secondary structure prediction based on primary structure similarity.

    PubMed

    Li, Zhong; Wang, Jing; Zhang, Shunpu; Zhang, Qifeng; Wu, Wuming

    2017-03-16

    The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the physicochemical properties of amino acids to construct a 3-bit-code, and then the 3 tendency factors of amino acids are calculated to generate another 3-bit-code. Two 3-bit-codes are fused to form a novel hybrid 6-bit-code. Furthermore, we make a geometry-based similarity comparison of the protein primary structure between the reference set and the test set before the secondary structure prediction. We finally use the support vector machine (SVM) to predict those amino acids which are not detected by the primary structure similarity comparison. Experimental results show that our method achieves a satisfactory improvement in accuracy in the prediction of protein secondary structure.

  3. High Speed Research Noise Prediction Code (HSRNOISE) User's and Theoretical Manual

    NASA Technical Reports Server (NTRS)

    Golub, Robert (Technical Monitor); Rawls, John W., Jr.; Yeager, Jessie C.

    2004-01-01

    This report describes a computer program, HSRNOISE, that predicts noise levels for a supersonic aircraft powered by mixed flow turbofan engines with rectangular mixer-ejector nozzles. It fully documents the noise prediction algorithms, provides instructions for executing the HSRNOISE code, and provides predicted noise levels for the High Speed Research (HSR) program Technology Concept (TC) aircraft. The component source noise prediction algorithms were developed jointly by Boeing, General Electric Aircraft Engines (GEAE), NASA and Pratt & Whitney during the course of the NASA HSR program. Modern Technologies Corporation developed an alternative mixer ejector jet noise prediction method under contract to GEAE that has also been incorporated into the HSRNOISE prediction code. Algorithms for determining propagation effects and calculating noise metrics were taken from the NASA Aircraft Noise Prediction Program.

  4. 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

  5. Predictive coding under the free-energy principle.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-05-12

    This paper considers prediction and perceptual categorization as an inference problem that is solved by the brain. We assume that the brain models the world as a hierarchy or cascade of dynamical systems that encode causal structure in the sensorium. Perception is equated with the optimization or inversion of these internal models, to explain sensory data. Given a model of how sensory data are generated, we can invoke a generic approach to model inversion, based on a free energy bound on the model's evidence. The ensuing free-energy formulation furnishes equations that prescribe the process of recognition, i.e. the dynamics of neuronal activity that represent the causes of sensory input. Here, we focus on a very general model, whose hierarchical and dynamical structure enables simulated brains to recognize and predict trajectories or sequences of sensory states. We first review hierarchical dynamical models and their inversion. We then show that the brain has the necessary infrastructure to implement this inversion and illustrate this point using synthetic birds that can recognize and categorize birdsongs.

  6. Validation of finite-element codes for prediction of machining distortions in forgings

    NASA Astrophysics Data System (ADS)

    Chandra, U.

    1993-06-01

    When a forging is machined to its net shape, unacceptably large distortions can occur if the final part shape is complex. Such distortions can be predicted with the application of the finite-element method. However, numerical errors associated with the finite element technique can render such predictions unreliable. This paper presents benchmark problems for verifying the accuracy of machining distortions predicted by any prospective finite-element code. Also, a comparison between two industry-standard general-purpose codes, ANSYS and ABAQUS, is presented.

  7. Inlet Spillage Drag Predictions Using the AIRPLANE Code

    NASA Technical Reports Server (NTRS)

    Thomas, Scott D.; Won, Mark A.; Cliff, Susan E.

    1999-01-01

    AIRPLANE (Jameson/Baker) is a steady inviscid unstructured Euler flow solver. It has been validated on many HSR geometries. It is implemented as MESHPLANE, an unstructured mesh generator, and FLOPLANE, an iterative flow solver. The surface description from an Intergraph CAD system goes into MESHPLANE as collections of polygonal curves to generate the 3D mesh. The flow solver uses a multistage time stepping scheme with residual averaging to approach steady state, but R is not time accurate. The flow solver was ported from Cray to IBM SP2 by Wu-Sun Cheng (IBM); it could only be run on 4 CPUs at a time because of memory limitations. Meshes for the four cases had about 655,000 points in the flow field, about 3.9 million tetrahedra, about 77,500 points on the surface. The flow solver took about 23 wall seconds per iteration when using 4 CPUs. It took about eight and a half wall hours to run 1,300 iterations at a time (the queue limit is 10 hours). A revised version of FLOPLANE (Thomas) was used on up to 64 CPUs to finish up some calculations at the end. We had to turn on more communication when using more processors to eliminate noise that was contaminating the flow field; this added about 50% to the elapsed wall time per iteration when using 64 CPUs. This study involved computing lift and drag for a wing/body/nacelle configuration at Mach 0.9 and 4 degrees pitch. Four cases were considered, corresponding to four nacelle mass flow conditions.

  8. Maneuvering Rotorcraft Noise Prediction: A New Code for a New Problem

    NASA Technical Reports Server (NTRS)

    Brentner, Kenneth S.; Bres, Guillaume A.; Perez, Guillaume; Jones, Henry E.

    2002-01-01

    This paper presents the unique aspects of the development of an entirely new maneuver noise prediction code called PSU-WOPWOP. The main focus of the code is the aeroacoustic aspects of the maneuver noise problem, when the aeromechanical input data are provided (namely aircraft and blade motion, blade airloads). The PSU-WOPWOP noise prediction capability was developed for rotors in steady and transient maneuvering flight. Featuring an object-oriented design, the code allows great flexibility for complex rotor configuration and motion (including multiple rotors and full aircraft motion). The relative locations and number of hinges, flexures, and body motions can be arbitrarily specified to match the any specific rotorcraft. An analysis of algorithm efficiency is performed for maneuver noise prediction along with a description of the tradeoffs made specifically for the maneuvering noise problem. Noise predictions for the main rotor of a rotorcraft in steady descent, transient (arrested) descent, hover and a mild "pop-up" maneuver are demonstrated.

  9. lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine.

    PubMed

    Sun, Lei; Liu, Hui; Zhang, Lin; Meng, Jia

    2015-01-01

    Functional long non-coding RNAs (lncRNAs) have been bringing novel insight into biological study, however it is still not trivial to accurately distinguish the lncRNA transcripts (LNCTs) from the protein coding ones (PCTs). As various information and data about lncRNAs are preserved by previous studies, it is appealing to develop novel methods to identify the lncRNAs more accurately. Our method lncRScan-SVM aims at classifying PCTs and LNCTs using support vector machine (SVM). The gold-standard datasets for lncRScan-SVM model training, lncRNA prediction and method comparison were constructed according to the GENCODE gene annotations of human and mouse respectively. By integrating features derived from gene structure, transcript sequence, potential codon sequence and conservation, lncRScan-SVM outperforms other approaches, which is evaluated by several criteria such as sensitivity, specificity, accuracy, Matthews correlation coefficient (MCC) and area under curve (AUC). In addition, several known human lncRNA datasets were assessed using lncRScan-SVM. LncRScan-SVM is an efficient tool for predicting the lncRNAs, and it is quite useful for current lncRNA study.

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

    DTIC Science & Technology

    2010-01-01

    photosynthetically available radiation) in terms of the chlorophyll concentration and a few parameters such as the solar zenith angle. Such simple light models...and to account for all inherent optical property (IOP, namely the absorption , scatter, and backscatter coefficients) effects. However, once an...and upwelling radiance. The EcoLight-S code is also being incorporated into the final version of the spectrum -matching and look-up-table software

  11. 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

  12. 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.

  13. 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.

  14. A Predictive Approach to Eliminating Errors in Software Code

    NASA Technical Reports Server (NTRS)

    2006-01-01

    NASA s Metrics Data Program Data Repository is a database that stores problem, product, and metrics data. The primary goal of this data repository is to provide project data to the software community. In doing so, the Metrics Data Program collects artifacts from a large NASA dataset, generates metrics on the artifacts, and then generates reports that are made available to the public at no cost. The data that are made available to general users have been sanitized and authorized for publication through the Metrics Data Program Web site by officials representing the projects from which the data originated. The data repository is operated by NASA s Independent Verification and Validation (IV&V) Facility, which is located in Fairmont, West Virginia, a high-tech hub for emerging innovation in the Mountain State. The IV&V Facility was founded in 1993, under the NASA Office of Safety and Mission Assurance, as a direct result of recommendations made by the National Research Council and the Report of the Presidential Commission on the Space Shuttle Challenger Accident. Today, under the direction of Goddard Space Flight Center, the IV&V Facility continues its mission to provide the highest achievable levels of safety and cost-effectiveness for mission-critical software. By extending its data to public users, the facility has helped improve the safety, reliability, and quality of complex software systems throughout private industry and other government agencies. Integrated Software Metrics, Inc., is one of the organizations that has benefited from studying the metrics data. As a result, the company has evolved into a leading developer of innovative software-error prediction tools that help organizations deliver better software, on time and on budget.

  15. Fast bi-directional prediction selection in H.264/MPEG-4 AVC temporal scalable video coding.

    PubMed

    Lin, Hung-Chih; Hang, Hsueh-Ming; Peng, Wen-Hsiao

    2011-12-01

    In this paper, we propose a fast algorithm that efficiently selects the temporal prediction type for the dyadic hierarchical-B prediction structure in the H.264/MPEG-4 temporal scalable video coding (SVC). We make use of the strong correlations in prediction type inheritance to eliminate the superfluous computations for the bi-directional (BI) prediction in the finer partitions, 16×8/8×16/8×8 , by referring to the best temporal prediction type of 16 × 16. In addition, we carefully examine the relationship in motion bit-rate costs and distortions between the BI and the uni-directional temporal prediction types. As a result, we construct a set of adaptive thresholds to remove the unnecessary BI calculations. Moreover, for the block partitions smaller than 8 × 8, either the forward prediction (FW) or the backward prediction (BW) is skipped based upon the information of their 8 × 8 partitions. Hence, the proposed schemes can efficiently reduce the extensive computational burden in calculating the BI prediction. As compared to the JSVM 9.11 software, our method saves the encoding time from 48% to 67% for a large variety of test videos over a wide range of coding bit-rates and has only a minor coding performance loss.

  16. Use of an Accurate DNS Particulate Flow Method to Supply and Validate Boundary Conditions for the MFIX Code

    SciTech Connect

    Zhi-Gang Feng

    2012-05-31

    The simulation of particulate flows for industrial applications often requires the use of two-fluid models, where the solid particles are considered as a separate continuous phase. One of the underlining uncertainties in the use of the two-fluid models in multiphase computations comes from the boundary condition of the solid phase. Typically, the gas or liquid fluid boundary condition at a solid wall is the so called no-slip condition, which has been widely accepted to be valid for single-phase fluid dynamics provided that the Knudsen number is low. However, the boundary condition for the solid phase is not well understood. The no-slip condition at a solid boundary is not a valid assumption for the solid phase. Instead, several researchers advocate a slip condition as a more appropriate boundary condition. However, the question on the selection of an exact slip length or a slip velocity coefficient is still unanswered. Experimental or numerical simulation data are needed in order to determinate the slip boundary condition that is applicable to a two-fluid model. The goal of this project is to improve the performance and accuracy of the boundary conditions used in two-fluid models such as the MFIX code, which is frequently used in multiphase flow simulations. The specific objectives of the project are to use first principles embedded in a validated Direct Numerical Simulation particulate flow numerical program, which uses the Immersed Boundary method (DNS-IB) and the Direct Forcing scheme in order to establish, modify and validate needed energy and momentum boundary conditions for the MFIX code. To achieve these objectives, we have developed a highly efficient DNS code and conducted numerical simulations to investigate the particle-wall and particle-particle interactions in particulate flows. Most of our research findings have been reported in major conferences and archived journals, which are listed in Section 7 of this report. In this report, we will present a

  17. Sample-adaptive-prediction for HEVC SCC intra coding with ridge estimation from spatially neighboring samples

    NASA Astrophysics Data System (ADS)

    Kang, Je-Won; Ryu, Soo-Kyung

    2017-02-01

    In this paper a sample-adaptive prediction technique is proposed to yield efficient coding performance in an intracoding for screen content video coding. The sample-based prediction is to reduce spatial redundancies in neighboring samples. To this aim, the proposed technique uses a weighted linear combination of neighboring samples and applies the robust optimization technique, namely, ridge estimation to derive the weights in a decoder side. The ridge estimation uses L2 norm based regularization term, and, thus the solution is more robust to high variance samples such as in sharp edges and high color contrasts exhibited in screen content videos. It is demonstrated with the experimental results that the proposed technique provides an improved coding gain as compared to the HEVC screen content video coding reference software.

  18. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming.

    PubMed

    Saetrom, Pål; Sneve, Ragnhild; Kristiansen, Knut I; Snøve, Ola; Grünfeld, Thomas; Rognes, Torbjørn; Seeberg, Erling

    2005-01-01

    Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.

  19. 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.

  20. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    PubMed Central

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  1. 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.

  2. 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

  3. Predicting the influence of the electronic health record on clinical coding practice in hospitals.

    PubMed

    Robinson, Kerin; Shepheard, Jennie

    2004-01-01

    The key drivers of change to clinical coding practice are identified and examined, and a major shift is predicted. The traditional purposes of the coding function have been the provision of data for research and epidemiology, in morbidity data reporting and, latterly, for casemix-based funding. It is contended that, as the development of electronic health records progresses, the need for an embedded nomenclature will force major change in clinical coding practice. Clinical coders must become expert in information technology and analysis, change their work practices, and become an integral part of the clinical team.

  4. 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?

  5. 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

  6. 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

  7. EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes

    PubMed Central

    Santoni, Federico Andrea

    2013-01-01

    Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes are supporting this postulation. EMdeCODE is an original algorithm that approximate the genomic distribution of given DNA features (e.g. promoter, enhancer, viral integration) by identifying relevant ChIPSeq profiles of post-translational histone marks or DNA binding proteins and combining them in a supermark. EMdeCODE kernel is essentially a two-step procedure: (i) an expectation-maximization process calculates the mixture of epigenetic factors that maximize the Sensitivity (recall) of the association with the feature under study; (ii) the approximated density is then recursively trimmed with respect to a control dataset to increase the precision by reducing the number of false positives. EMdeCODE densities improve significantly the prediction of enhancer loci and retroviral integration sites with respect to previous methods. Importantly, it can also be used to extract distinctive factors between two arbitrary conditions. Indeed EMdeCODE identifies unexpected epigenetic profiles specific for coding versus non-coding RNA, pointing towards a new role for H3R2me1 in coding regions. PMID:23234700

  8. Neural markers of predictive coding under perceptual uncertainty revealed with Hierarchical Frequency Tagging

    PubMed Central

    Gordon, Noam; Koenig-Robert, Roger; Tsuchiya, Naotsugu; van Boxtel, Jeroen JA; Hohwy, Jakob

    2017-01-01

    There is a growing understanding that both top-down and bottom-up signals underlie perception. But it is not known how these signals integrate with each other and how this depends on the perceived stimuli’s predictability. ‘Predictive coding’ theories describe this integration in terms of how well top-down predictions fit with bottom-up sensory input. Identifying neural markers for such signal integration is therefore essential for the study of perception and predictive coding theories. To achieve this, we combined EEG methods that preferentially tag different levels in the visual hierarchy. Importantly, we examined intermodulation components as a measure of integration between these signals. Our results link the different signals to core aspects of predictive coding, and suggest that top-down predictions indeed integrate with bottom-up signals in a manner that is modulated by the predictability of the sensory input, providing evidence for predictive coding and opening new avenues to studying such interactions in perception. DOI: http://dx.doi.org/10.7554/eLife.22749.001 PMID:28244874

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. TFaNS Tone Fan Noise Design/Prediction System. Volume 3; Evaluation of System Codes

    NASA Technical Reports Server (NTRS)

    Topol, David A.

    1999-01-01

    TFANS is the Tone Fan Noise Design/Prediction System developed by Pratt & Whitney under contract to NASA Lewis (presently NASA Glenn). The purpose of this system is to predict tone noise emanating from a fan stage including the effects of reflection and transmission by the rotor and stator and by the duct inlet and nozzle. These effects have been added to an existing annular duct/isolated stator noise prediction capability. TFANS consists of: The codes that compute the acoustic properties (reflection and transmission coefficients) of the various elements and write them to files. Cup3D: Fan Noise Coupling Code that reads these files, solves the coupling problem, and outputs the desired noise predictions. AWAKEN: CFD/Measured Wake Postprocessor which reformats CFD wake predictions and/or measured wake data so it can be used by the system. This volume of the report evaluates TFANS versus full-scale and ADP 22" fig data using the semi-empirical wake modelling in the system. This report is divided into three volumes: Volume 1: System Description, CUP3D Technical Documentation, and Manual for Code Developers; Volume II: User's Manual, TFANS Version 1.4; Volume III: Evaluation of System Codes.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Application of TURBO-AE to Flutter Prediction: Aeroelastic Code Development

    NASA Technical Reports Server (NTRS)

    Hoyniak, Daniel; Simons, Todd A.; Stefko, George (Technical Monitor)

    2001-01-01

    The TURBO-AE program has been evaluated by comparing the obtained results to cascade rig data and to prediction made from various in-house programs. A high-speed fan cascade, a turbine cascade, a turbine cascade and a fan geometry that shower flutter in torsion mode were analyzed. The steady predictions for the high-speed fan cascade showed the TURBO-AE predictions to match in-house codes. However, the predictions did not match the measured blade surface data. Other researchers also reported similar disagreement with these data set. Unsteady runs for the fan configuration were not successful using TURBO-AE .

  2. Object-adaptive depth compensated inter prediction for depth video coding in 3D video system

    NASA Astrophysics Data System (ADS)

    Kang, Min-Koo; Lee, Jaejoon; Lim, Ilsoon; Ho, Yo-Sung

    2011-01-01

    Nowadays, the 3D video system using the MVD (multi-view video plus depth) data format is being actively studied. The system has many advantages with respect to virtual view synthesis such as an auto-stereoscopic functionality, but compression of huge input data remains a problem. Therefore, efficient 3D data compression is extremely important in the system, and problems of low temporal consistency and viewpoint correlation should be resolved for efficient depth video coding. In this paper, we propose an object-adaptive depth compensated inter prediction method to resolve the problems where object-adaptive mean-depth difference between a current block, to be coded, and a reference block are compensated during inter prediction. In addition, unique properties of depth video are exploited to reduce side information required for signaling decoder to conduct the same process. To evaluate the coding performance, we have implemented the proposed method into MVC (multiview video coding) reference software, JMVC 8.2. Experimental results have demonstrated that our proposed method is especially efficient for depth videos estimated by DERS (depth estimation reference software) discussed in the MPEG 3DV coding group. The coding gain was up to 11.69% bit-saving, and it was even increased when we evaluated it on synthesized views of virtual viewpoints.

  3. The Cortical Organization of Speech Processing: Feedback Control and Predictive Coding the Context of a Dual-Stream Model

    ERIC Educational Resources Information Center

    Hickok, Gregory

    2012-01-01

    Speech recognition is an active process that involves some form of predictive coding. This statement is relatively uncontroversial. What is less clear is the source of the prediction. The dual-stream model of speech processing suggests that there are two possible sources of predictive coding in speech perception: the motor speech system and the…

  4. 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.

  5. 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.

  6. Thermal treatments of foods: a predictive general-purpose code for heat and mass transfer

    NASA Astrophysics Data System (ADS)

    Barba, Anna Angela

    2005-05-01

    Thermal treatments of foods required accurate processing protocols. In this context, mathematical modeling of heat and mass transfer can play an important role in the control and definition of the process parameters as well as to design processing systems. In this work a code able to simulate heat and mass transfer phenomena within solid bodies has been developed. The code has been written with the ability of describing different geometries and it can account for any kind of different initial/boundary conditions. Transport phenomena within multi-layer bodies can be described, and time/position dependent material parameters can be implemented. Finally, the code has been validated by comparison with a problem for which the analytical solution is known, and by comparison with a differential scanning calorimetry signal that described the heating treatment of a raw potato (Solanum tuberosum).

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. TRAP/SEE Code Users Manual for Predicting Trapped Radiation Environments

    NASA Astrophysics Data System (ADS)

    Armstrong, T. W.; Colborn, B. L.

    2000-01-01

    TRAP/SEE is a PC-based computer code with a user-friendly interface which predicts the ionizing radiation exposure of spacecraft having orbits in the Earth's trapped radiation belts. The code incorporates the standard AP8 and AE8 trapped proton and electron models but also allows application of an improved database interpolation method. The code treats low-Earth as well as highly-elliptical Earth orbits, taking into account trajectory perturbations due to gravitational forces from the Moon and Sun, atmospheric drag, and solar radiation pressure. Orbit-average spectra, peak spectra per orbit, and instantaneous spectra at points along the orbit trajectory are calculated. Described in this report are the features, models, model limitations and uncertainties, input and output descriptions, and example calculations and applications for the TRAP/SEE code.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. A NEW SEMI-EMPIRICAL AMBIENT TO EFFECTIVE DOSE CONVERSION MODEL FOR THE PREDICTIVE CODE FOR AIRCREW RADIATION EXPOSURE (PCAIRE).

    PubMed

    Dumouchel, T; McCall, M; Lemay, F; Bennett, L; Lewis, B; Bean, M

    2016-12-01

    The Predictive Code for Aircrew Radiation Exposure (PCAIRE) is a semi-empirical code that estimates both ambient dose equivalent, based on years of on-board measurements, and effective dose to aircrew. Currently, PCAIRE estimates effective dose by converting the ambient dose equivalent to effective dose (E/H) using a model that is based on radiation transport calculations and on the radiation weighting factors recommended in International Commission on Radiological Protection (ICRP) 60. In this study, a new semi-empirical E/H model is proposed to replace the existing transport calculation models. The new model is based on flight data measured using a tissue-equivalent proportional counter (TEPC). The measured flight TEPC data are separated into a low- and a high-lineal-energy spectrum using an amplitude-weighted (137)Cs TEPC spectrum. The high-lineal-energy spectrum is determined by subtracting the low-lineal-energy spectrum from the measured flight TEPC spectrum. With knowledge of E/H for the low- and high-lineal-energy spectra, the total E/H is estimated for a given flight altitude and geographic location. The semi-empirical E/H model also uses new radiation weighting factors to align the model with the most recent ICRP 103 recommendations. The ICRP 103-based semi-empirical effective dose model predicts that there is a ∼30 % reduction in dose in comparison with the ICRP 60-based model. Furthermore, the ambient dose equivalent is now a more conservative dose estimate for jet aircraft altitudes in the range of 7-13 km (FL230-430). This new semi-empirical E/H model is validated against E/H predicted from a Monte Carlo N-Particle transport code simulation of cosmic ray propagation through the Earth's atmosphere. Its implementation allows PCAIRE to provide an accurate semi-empirical estimate of the effective dose.

  3. NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems.

    PubMed

    Schmidt, Matthew C; Rocha, Andrea M; Padmanabhan, Kanchana; Shpanskaya, Yekaterina; Banfield, Jill; Scott, Kathleen; Mihelcic, James R; Samatova, Nagiza F

    2012-01-01

    the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Dopamine Modulates Adaptive Prediction Error Coding in the Human Midbrain and Striatum

    PubMed Central

    Ziauddeen, Hisham; Vestergaard, Martin D.; Spencer, Tom

    2017-01-01

    Learning to optimally predict rewards requires agents to account for fluctuations in reward value. Recent work suggests that individuals can efficiently learn about variable rewards through adaptation of the learning rate, and coding of prediction errors relative to reward variability. Such adaptive coding has been linked to midbrain dopamine neurons in nonhuman primates, and evidence in support for a similar role of the dopaminergic system in humans is emerging from fMRI data. Here, we sought to investigate the effect of dopaminergic perturbations on adaptive prediction error coding in humans, using a between-subject, placebo-controlled pharmacological fMRI study with a dopaminergic agonist (bromocriptine) and antagonist (sulpiride). Participants performed a previously validated task in which they predicted the magnitude of upcoming rewards drawn from distributions with varying SDs. After each prediction, participants received a reward, yielding trial-by-trial prediction errors. Under placebo, we replicated previous observations of adaptive coding in the midbrain and ventral striatum. Treatment with sulpiride attenuated adaptive coding in both midbrain and ventral striatum, and was associated with a decrease in performance, whereas bromocriptine did not have a significant impact. Although we observed no differential effect of SD on performance between the groups, computational modeling suggested decreased behavioral adaptation in the sulpiride group. These results suggest that normal dopaminergic function is critical for adaptive prediction error coding, a key property of the brain thought to facilitate efficient learning in variable environments. Crucially, these results also offer potential insights for understanding the impact of disrupted dopamine function in mental illness. SIGNIFICANCE STATEMENT To choose optimally, we have to learn what to expect. Humans dampen learning when there is a great deal of variability in reward outcome, and two brain regions that

  11. Dopamine Modulates Adaptive Prediction Error Coding in the Human Midbrain and Striatum.

    PubMed

    Diederen, Kelly M J; Ziauddeen, Hisham; Vestergaard, Martin D; Spencer, Tom; Schultz, Wolfram; Fletcher, Paul C

    2017-02-15

    Learning to optimally predict rewards requires agents to account for fluctuations in reward value. Recent work suggests that individuals can efficiently learn about variable rewards through adaptation of the learning rate, and coding of prediction errors relative to reward variability. Such adaptive coding has been linked to midbrain dopamine neurons in nonhuman primates, and evidence in support for a similar role of the dopaminergic system in humans is emerging from fMRI data. Here, we sought to investigate the effect of dopaminergic perturbations on adaptive prediction error coding in humans, using a between-subject, placebo-controlled pharmacological fMRI study with a dopaminergic agonist (bromocriptine) and antagonist (sulpiride). Participants performed a previously validated task in which they predicted the magnitude of upcoming rewards drawn from distributions with varying SDs. After each prediction, participants received a reward, yielding trial-by-trial prediction errors. Under placebo, we replicated previous observations of adaptive coding in the midbrain and ventral striatum. Treatment with sulpiride attenuated adaptive coding in both midbrain and ventral striatum, and was associated with a decrease in performance, whereas bromocriptine did not have a significant impact. Although we observed no differential effect of SD on performance between the groups, computational modeling suggested decreased behavioral adaptation in the sulpiride group. These results suggest that normal dopaminergic function is critical for adaptive prediction error coding, a key property of the brain thought to facilitate efficient learning in variable environments. Crucially, these results also offer potential insights for understanding the impact of disrupted dopamine function in mental illness.SIGNIFICANCE STATEMENT To choose optimally, we have to learn what to expect. Humans dampen learning when there is a great deal of variability in reward outcome, and two brain regions that

  12. Validation of Framework Code Approach to a Life Prediction System for Fiber Reinforced Composites

    NASA Technical Reports Server (NTRS)

    Gravett, Phillip

    1997-01-01

    The grant was conducted by the MMC Life Prediction Cooperative, an industry/government collaborative team, Ohio Aerospace Institute (OAI) acted as the prime contractor on behalf of the Cooperative for this grant effort. See Figure I for the organization and responsibilities of team members. The technical effort was conducted during the period August 7, 1995 to June 30, 1996 in cooperation with Erwin Zaretsky, the LERC Program Monitor. Phil Gravett of Pratt & Whitney was the principal technical investigator. Table I documents all meeting-related coordination memos during this period. The effort under this grant was closely coordinated with an existing USAF sponsored program focused on putting into practice a life prediction system for turbine engine components made of metal matrix composites (MMC). The overall architecture of the NMC life prediction system was defined in the USAF sponsored program (prior to this grant). The efforts of this grant were focussed on implementing and tailoring of the life prediction system, the framework code within it and the damage modules within it to meet the specific requirements of the Cooperative. T'he tailoring of the life prediction system provides the basis for pervasive and continued use of this capability by the industry/government cooperative. The outputs of this grant are: 1. Definition of the framework code to analysis modules interfaces, 2. Definition of the interface between the materials database and the finite element model, and 3. Definition of the integration of the framework code into an FEM design tool.

  13. 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.

  14. 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

  15. 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

  16. Efficient Prediction Structures for H.264 Multi View Coding Using Temporal Scalability

    NASA Astrophysics Data System (ADS)

    Guruvareddiar, Palanivel; Joseph, Biju K.

    2014-03-01

    Prediction structures with "disposable view components based" hierarchical coding have been proven to be efficient for H.264 multi view coding. Though these prediction structures along with the QP cascading schemes provide superior compression efficiency when compared to the traditional IBBP coding scheme, the temporal scalability requirements of the bit stream could not be met to the fullest. On the other hand, a fully scalable bit stream, obtained by "temporal identifier based" hierarchical coding, provides a number of advantages including bit rate adaptations and improved error resilience, but lacks in compression efficiency when compared to the former scheme. In this paper it is proposed to combine the two approaches such that a fully scalable bit stream could be realized with minimal reduction in compression efficiency when compared to state-of-the-art "disposable view components based" hierarchical coding. Simulation results shows that the proposed method enables full temporal scalability with maximum BDPSNR reduction of only 0.34 dB. A novel method also has been proposed for the identification of temporal identifier for the legacy H.264/AVC base layer packets. Simulation results also show that this enables the scenario where the enhancement views could be extracted at a lower frame rate (1/2nd or 1/4th of base view) with average extraction time for a view component of only 0.38 ms.

  17. Predictive Coding: A Possible Explanation of Filling-In at the Blind Spot

    PubMed Central

    Raman, Rajani; Sarkar, Sandip

    2016-01-01

    Filling-in at the blind spot is a perceptual phenomenon in which the visual system fills the informational void, which arises due to the absence of retinal input corresponding to the optic disc, with surrounding visual attributes. It is known that during filling-in, nonlinear neural responses are observed in the early visual area that correlates with the perception, but the knowledge of underlying neural mechanism for filling-in at the blind spot is far from complete. In this work, we attempted to present a fresh perspective on the computational mechanism of filling-in process in the framework of hierarchical predictive coding, which provides a functional explanation for a range of neural responses in the cortex. We simulated a three-level hierarchical network and observe its response while stimulating the network with different bar stimulus across the blind spot. We find that the predictive-estimator neurons that represent blind spot in primary visual cortex exhibit elevated non-linear response when the bar stimulated both sides of the blind spot. Using generative model, we also show that these responses represent the filling-in completion. All these results are consistent with the finding of psychophysical and physiological studies. In this study, we also demonstrate that the tolerance in filling-in qualitatively matches with the experimental findings related to non-aligned bars. We discuss this phenomenon in the predictive coding paradigm and show that all our results could be explained by taking into account the efficient coding of natural images along with feedback and feed-forward connections that allow priors and predictions to co-evolve to arrive at the best prediction. These results suggest that the filling-in process could be a manifestation of the general computational principle of hierarchical predictive coding of natural images. PMID:26959812

  18. Prediction error as a linear function of reward probability is coded in human nucleus accumbens.

    PubMed

    Abler, Birgit; Walter, Henrik; Erk, Susanne; Kammerer, Hannes; Spitzer, Manfred

    2006-06-01

    Reward probability has been shown to be coded by dopamine neurons in monkeys. Phasic neuronal activation not only increased linearly with reward probability upon expectation of reward, but also varied monotonically across the range of probabilities upon omission or receipt of rewards, therefore modeling discrepancies between expected and received rewards. Such a discrete coding of prediction error has been suggested to be one of the basic principles of learning. We used functional magnetic resonance imaging (fMRI) to show that the human dopamine system codes reward probability and prediction error in a similar way. We used a simple delayed incentive task with a discrete range of reward probabilities from 0%-100%. Activity in the nucleus accumbens of human subjects strongly resembled the phasic responses found in monkey neurons. First, during the expectation period of the task, the fMRI signal in the human nucleus accumbens (NAc) increased linearly with the probability of the reward. Second, during the outcome phase, activity in the NAc coded the prediction error as a linear function of reward probabilities. Third, we found that the Nac signal was correlated with individual differences in sensation seeking and novelty seeking, indicating a link between individual fMRI activation of the dopamine system in a probabilistic paradigm and personality traits previously suggested to be linked with reward processing. We therefore identify two different covariates that model activity in the Nac: specific properties of a psychological task and individual character traits.

  19. 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.

  20. A comparison of shuttle vernier engine plume contamination with CONTAM 3.4 code predictions

    NASA Technical Reports Server (NTRS)

    Maag, Carl R.; Jones, Thomas M.; Rao, Shankar M.; Linder, W. Kelly

    1992-01-01

    In 1985, using the CONTAM 3.2 code, it was predicted that the shuttle Primary Reaction Control System (PRCS) and Vernier Reaction Control System (VRCS) engines could be potential contamination sources to sensitive surfaces located within the shuttle payload bay. Spaceflight test data on these engines is quite limited. Shuttle mission STS-32, the Long Duration Exposure Facility retrieval mission, was instrumented with an experiment that provided the design engineer with evidence that contaminant species from the VRCS engines can enter the payload bay. More recently, the most recent version of the analysis code, CONTAM 3.4, has re-examined the contamination potential of these engines.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. The basal ganglia select the expected sensory input used for predictive coding.

    PubMed

    Colder, Brian

    2015-01-01

    While considerable evidence supports the notion that lower-level interpretation of incoming sensory information is guided by top-down sensory expectations, less is known about the source of the sensory expectations or the mechanisms by which they are spread. Predictive coding theory proposes that sensory expectations flow down from higher-level association areas to lower-level sensory cortex. A separate theory of the role of prediction in cognition describes "emulations" as linked representations of potential actions and their associated expected sensation that are hypothesized to play an important role in many aspects of cognition. The expected sensations in active emulations are proposed to be the top-down expectation used in predictive coding. Representations of the potential action and expected sensation in emulations are claimed to be instantiated in distributed cortical networks. Combining predictive coding with emulations thus provides a theoretical link between the top-down expectations that guide sensory expectations and the cortical networks representing potential actions. Now moving to theories of action selection, the basal ganglia has long been proposed to select between potential actions by reducing inhibition to the cortical network instantiating the desired action plan. Integration of these isolated theories leads to the novel hypothesis that reduction in inhibition from the basal ganglia selects not just action plans, but entire emulations, including the sensory input expected to result from the action. Basal ganglia disinhibition is hypothesized to both initiate an action and also allow propagation of the action's associated sensory expectation down towards primary sensory cortex. This is a novel proposal for the role of the basal ganglia in biasing perception by selecting the expected sensation, and initiating the top-down transmission of those expectations in predictive coding.

  6. GeneValidator: identify problems with protein-coding gene predictions

    PubMed Central

    Drăgan, Monica-Andreea; Moghul, Ismail; Priyam, Anurag; Bustos, Claudio; Wurm, Yannick

    2016-01-01

    Summary: Genomes of emerging model organisms are now being sequenced at very low cost. However, obtaining accurate gene predictions remains challenging: even the best gene prediction algorithms make substantial errors and can jeopardize subsequent analyses. Therefore, many predicted genes must be time-consumingly visually inspected and manually curated. We developed GeneValidator (GV) to automatically identify problematic gene predictions and to aid manual curation. For each gene, GV performs multiple analyses based on comparisons to gene sequences from large databases. The resulting report identifies problematic gene predictions and includes extensive statistics and graphs for each prediction to guide manual curation efforts. GV thus accelerates and enhances the work of biocurators and researchers who need accurate gene predictions from newly sequenced genomes. Availability and implementation: GV can be used through a web interface or in the command-line. GV is open-source (AGPL), available at https://wurmlab.github.io/tools/genevalidator. Contact: y.wurm@qmul.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26787666

  7. 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

  8. APPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE

    PubMed Central

    Zhang, Jie; Stonnington, Cynthia; Li, Qingyang; Shi, Jie; Bauer, Robert J.; Gutman, Boris A.; Chen, Kewei; Reiman, Eric M.; Thompson, Paul M.; Ye, Jieping; Wang, Yalin

    2016-01-01

    Alzheimer’s disease (AD) is a progressive brain disease. Accurate diagnosis of AD and its prodromal stage, mild cognitive impairment, is crucial for clinical trial design. There is also growing interests in identifying brain imaging biomarkers that help evaluate AD risk presymptomatically. Here, we applied a recently developed multivariate tensor-based morphometry (mTBM) method to extract features from hippocampal surfaces, derived from anatomical brain MRI. For such surface-based features, the feature dimension is usually much larger than the number of subjects. We used dictionary learning and sparse coding to effectively reduce the feature dimensions. With the new features, an Adaboost classifier was employed for binary group classification. In tests on publicly available data from the Alzheimers Disease Neuroimaging Initiative, the new framework outperformed several standard imaging measures in classifying different stages of AD. The new approach combines the efficiency of sparse coding with the sensitivity of surface mTBM, and boosts classification performance. PMID:27499829

  9. 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.

  10. Hyperbolic Space Sparse Coding with Its Application on Prediction of Alzheimer's Disease in Mild Cognitive Impairment.

    PubMed

    Zhang, Jie; Shi, Jie; Stonnington, Cynthia; Li, Qingyang; Gutman, Boris A; Chen, Kewei; Reiman, Eric M; Caselli, Richard J; Thompson, Paul M; Ye, Jieping; Wang, Yalin

    2016-10-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal age-related cognitive decline and Alzheimer's disease (AD). Here we introduce a hyperbolic space sparse coding method to predict impending decline of MCI patients to dementia using surface measures of ventricular enlargement. First, we compute diffeomorphic mappings between ventricular surfaces using a canonical hyperbolic parameter space with consistent boundary conditions and surface tensor-based morphometry is computed to measure local surface deformations. Second, ring-shaped patches of TBM features are selected according to the geometric structure of the hyperbolic parameter space to initialize a dictionary. Sparse coding is then applied on the patch features to learn sparse codes and update the dictionary. Finally, we adopt max-pooling to reduce the feature dimensions and apply Adaboost to predict AD in MCI patients (N = 133) from the Alzheimer's Disease Neuroimaging Initiative baseline dataset. Our work achieved an accuracy rate of 96.7% and outperformed some other morphometry measures. The hyperbolic space sparse coding method may offer a more sensitive tool to study AD and its early symptom.

  11. Structural Life and Reliability Metrics: Benchmarking and Verification of Probabilistic Life Prediction Codes

    NASA Technical Reports Server (NTRS)

    Litt, Jonathan S.; Soditus, Sherry; Hendricks, Robert C.; Zaretsky, Erwin V.

    2002-01-01

    Over the past two decades there has been considerable effort by NASA Glenn and others to develop probabilistic codes to predict with reasonable engineering certainty the life and reliability of critical components in rotating machinery and, more specifically, in the rotating sections of airbreathing and rocket engines. These codes have, to a very limited extent, been verified with relatively small bench rig type specimens under uniaxial loading. Because of the small and very narrow database the acceptance of these codes within the aerospace community has been limited. An alternate approach to generating statistically significant data under complex loading and environments simulating aircraft and rocket engine conditions is to obtain, catalog and statistically analyze actual field data. End users of the engines, such as commercial airlines and the military, record and store operational and maintenance information. This presentation describes a cooperative program between the NASA GRC, United Airlines, USAF Wright Laboratory, U.S. Army Research Laboratory and Australian Aeronautical & Maritime Research Laboratory to obtain and analyze these airline data for selected components such as blades, disks and combustors. These airline data will be used to benchmark and compare existing life prediction codes.

  12. Prediction of material strength and fracture of glass using the SPHINX smooth particle hydrodynamics code

    SciTech Connect

    Mandell, D.A.; Wingate, C.A.

    1994-08-01

    The design of many military devices involves numerical predictions of the material strength and fracture of brittle materials. The materials of interest include ceramics, that are used in armor packages; glass that is used in truck and jeep windshields and in helicopters; and rock and concrete that are used in underground bunkers. As part of a program to develop advanced hydrocode design tools, the authors have implemented a brittle fracture model for glass into the SPHINX smooth particle hydrodynamics code. The authors have evaluated this model and the code by predicting data from one-dimensional flyer plate impacts into glass, and data from tungsten rods impacting glass. Since fractured glass properties, which are needed in the model, are not available, the authors did sensitivity studies of these properties, as well as sensitivity studies to determine the number of particles needed in the calculations. The numerical results are in good agreement with the data.

  13. A Cerebellar Framework for Predictive Coding and Homeostatic Regulation in Depressive Disorder.

    PubMed

    Schutter, Dennis J L G

    2016-02-01

    Depressive disorder is associated with abnormalities in the processing of reward and punishment signals and disturbances in homeostatic regulation. These abnormalities are proposed to impair error minimization routines for reducing uncertainty. Several lines of research point towards a role of the cerebellum in reward- and punishment-related predictive coding and homeostatic regulatory function in depressive disorder. Available functional and anatomical evidence suggests that in addition to the cortico-limbic networks, the cerebellum is part of the dysfunctional brain circuit in depressive disorder as well. It is proposed that impaired cerebellar function contributes to abnormalities in predictive coding and homeostatic dysregulation in depressive disorder. Further research on the role of the cerebellum in depressive disorder may further extend our knowledge on the functional and neural mechanisms of depressive disorder and development of novel antidepressant treatments strategies targeting the cerebellum.

  14. Severe accident source term characteristics for selected Peach Bottom sequences predicted by the MELCOR Code

    SciTech Connect

    Carbajo, J.J.

    1993-09-01

    The purpose of this report is to compare in-containment source terms developed for NUREG-1159, which used the Source Term Code Package (STCP), with those generated by MELCOR to identify significant differences. For this comparison, two short-term depressurized station blackout sequences (with a dry cavity and with a flooded cavity) and a Loss-of-Coolant Accident (LOCA) concurrent with complete loss of the Emergency Core Cooling System (ECCS) were analyzed for the Peach Bottom Atomic Power Station (a BWR-4 with a Mark I containment). The results indicate that for the sequences analyzed, the two codes predict similar total in-containment release fractions for each of the element groups. However, the MELCOR/CORBH Package predicts significantly longer times for vessel failure and reduced energy of the released material for the station blackout sequences (when compared to the STCP results). MELCOR also calculated smaller releases into the environment than STCP for the station blackout sequences.

  15. 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.

  16. SIM_ADJUST -- A computer code that adjusts simulated equivalents for observations or predictions

    USGS Publications Warehouse

    Poeter, Eileen P.; Hill, Mary C.

    2008-01-01

    This report documents the SIM_ADJUST computer code. SIM_ADJUST surmounts an obstacle that is sometimes encountered when using universal model analysis computer codes such as UCODE_2005 (Poeter and others, 2005), PEST (Doherty, 2004), and OSTRICH (Matott, 2005; Fredrick and others (2007). These codes often read simulated equivalents from a list in a file produced by a process model such as MODFLOW that represents a system of interest. At times values needed by the universal code are missing or assigned default values because the process model could not produce a useful solution. SIM_ADJUST can be used to (1) read a file that lists expected observation or prediction names and possible alternatives for the simulated values; (2) read a file produced by a process model that contains space or tab delimited columns, including a column of simulated values and a column of related observation or prediction names; (3) identify observations or predictions that have been omitted or assigned a default value by the process model; and (4) produce an adjusted file that contains a column of simulated values and a column of associated observation or prediction names. The user may provide alternatives that are constant values or that are alternative simulated values. The user may also provide a sequence of alternatives. For example, the heads from a series of cells may be specified to ensure that a meaningful value is available to compare with an observation located in a cell that may become dry. SIM_ADJUST is constructed using modules from the JUPITER API, and is intended for use on any computer operating system. SIM_ADJUST consists of algorithms programmed in Fortran90, which efficiently performs numerical calculations.

  17. Results from baseline tests of the SPRE I and comparison with code model predictions

    SciTech Connect

    Cairelli, J.E.; Geng, S.M.; Skupinski, R.C.

    1994-09-01

    The Space Power Research Engine (SPRE), a free-piston Stirling engine with linear alternator, is being tested at the NASA Lewis Research Center as part of the Civil Space Technology Initiative (CSTI) as a candidate for high capacity space power. This paper presents results of base-line engine tests at design and off-design operating conditions. The test results are compared with code model predictions.

  18. Predictions of bubbly flows in vertical pipes using two-fluid models in CFDS-FLOW3D code

    SciTech Connect

    Banas, A.O.; Carver, M.B.; Unrau, D.

    1995-09-01

    This paper reports the results of a preliminary study exploring the performance of two sets of two-fluid closure relationships applied to the simulation of turbulent air-water bubbly upflows through vertical pipes. Predictions obtained with the default CFDS-FLOW3D model for dispersed flows were compared with the predictions of a new model (based on the work of Lee), and with the experimental data of Liu. The new model, implemented in the CFDS-FLOW3D code, included additional source terms in the {open_quotes}standard{close_quotes} {kappa}-{epsilon} transport equations for the liquid phase, as well as modified model coefficients and wall functions. All simulations were carried out in a 2-D axisymmetric format, collapsing the general multifluid framework of CFDS-FLOW3D to the two-fluid (air-water) case. The newly implemented model consistently improved predictions of radial-velocity profiles of both phases, but failed to accurately reproduce the experimental phase-distribution data. This shortcoming was traced to the neglect of anisotropic effects in the modelling of liquid-phase turbulence. In this sense, the present investigation should be considered as the first step toward the ultimate goal of developing a theoretically sound and universal CFD-type two-fluid model for bubbly flows in channels.

  19. 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.

  20. 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).

  1. Predicting multi-wall structural response to hypervelocity impact using the hull code

    NASA Technical Reports Server (NTRS)

    Schonberg, William P.

    1993-01-01

    Previously, multi-wall structures have been analyzed extensively, primarily through experiment, as a means of increasing the meteoroid/space debris impact protection of spacecraft. As structural configurations become more varied, the number of tests required to characterize their response increases dramatically. As an alternative to experimental testing, numerical modeling of high-speed impact phenomena is often being used to predict the response of a variety of structural systems under different impact loading conditions. The results of comparing experimental tests to Hull Hydrodynamic Computer Code predictions are reported. Also, the results of a numerical parametric study of multi-wall structural response to hypervelocity cylindrical projectile impact are presented.

  2. 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

  3. 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.

  4. A high temperature fatigue life prediction computer code based on the total strain version of StrainRange Partitioning (SRP)

    NASA Astrophysics Data System (ADS)

    McGaw, Michael A.; Saltsman, James F.

    1993-10-01

    A recently developed high-temperature fatigue life prediction computer code is presented and an example of its usage given. The code discussed is based on the Total Strain version of Strainrange Partitioning (TS-SRP). Included in this code are procedures for characterizing the creep-fatigue durability behavior of an alloy according to TS-SRP guidelines and predicting cyclic life for complex cycle types for both isothermal and thermomechanical conditions. A reasonably extensive materials properties database is included with the code.

  5. A high temperature fatigue life prediction computer code based on the total strain version of StrainRange Partitioning (SRP)

    NASA Technical Reports Server (NTRS)

    Mcgaw, Michael A.; Saltsman, James F.

    1993-01-01

    A recently developed high-temperature fatigue life prediction computer code is presented and an example of its usage given. The code discussed is based on the Total Strain version of Strainrange Partitioning (TS-SRP). Included in this code are procedures for characterizing the creep-fatigue durability behavior of an alloy according to TS-SRP guidelines and predicting cyclic life for complex cycle types for both isothermal and thermomechanical conditions. A reasonably extensive materials properties database is included with the code.

  6. 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.

  7. 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.

  8. Thought Insertion as a Self-Disturbance: An Integration of Predictive Coding and Phenomenological Approaches

    PubMed Central

    Sterzer, Philipp; Mishara, Aaron L.; Voss, Martin; Heinz, Andreas

    2016-01-01

    Current theories in the framework of hierarchical predictive coding propose that positive symptoms of schizophrenia, such as delusions and hallucinations, arise from an alteration in Bayesian inference, the term inference referring to a process by which learned predictions are used to infer probable causes of sensory data. However, for one particularly striking and frequent symptom of schizophrenia, thought insertion, no plausible account has been proposed in terms of the predictive-coding framework. Here we propose that thought insertion is due to an altered experience of thoughts as coming from “nowhere”, as is already indicated by the early 20th century phenomenological accounts by the early Heidelberg School of psychiatry. These accounts identified thought insertion as one of the self-disturbances (from German: “Ichstörungen”) of schizophrenia and used mescaline as a model-psychosis in healthy individuals to explore the possible mechanisms. The early Heidelberg School (Gruhle, Mayer-Gross, Beringer) first named and defined the self-disturbances, and proposed that thought insertion involves a disruption of the inner connectedness of thoughts and experiences, and a “becoming sensory” of those thoughts experienced as inserted. This account offers a novel way to integrate the phenomenology of thought insertion with the predictive coding framework. We argue that the altered experience of thoughts may be caused by a reduced precision of context-dependent predictions, relative to sensory precision. According to the principles of Bayesian inference, this reduced precision leads to increased prediction-error signals evoked by the neural activity that encodes thoughts. Thus, in analogy with the prediction-error related aberrant salience of external events that has been proposed previously, “internal” events such as thoughts (including volitions, emotions and memories) can also be associated with increased prediction-error signaling and are thus imbued

  9. Rotor Wake/Stator Interaction Noise Prediction Code Technical Documentation and User's Manual

    NASA Technical Reports Server (NTRS)

    Topol, David A.; Mathews, Douglas C.

    2010-01-01

    This report documents the improvements and enhancements made by Pratt & Whitney to two NASA programs which together will calculate noise from a rotor wake/stator interaction. The code is a combination of subroutines from two NASA programs with many new features added by Pratt & Whitney. To do a calculation V072 first uses a semi-empirical wake prediction to calculate the rotor wake characteristics at the stator leading edge. Results from the wake model are then automatically input into a rotor wake/stator interaction analytical noise prediction routine which calculates inlet aft sound power levels for the blade-passage-frequency tones and their harmonics, along with the complex radial mode amplitudes. The code allows for a noise calculation to be performed for a compressor rotor wake/stator interaction, a fan wake/FEGV interaction, or a fan wake/core stator interaction. This report is split into two parts, the first part discusses the technical documentation of the program as improved by Pratt & Whitney. The second part is a user's manual which describes how input files are created and how the code is run.

  10. Simulation study of HL-2A-like plasma using integrated predictive modeling code

    SciTech Connect

    Poolyarat, N.; Onjun, T.; Promping, J.

    2009-11-15

    Self-consistent simulations of HL-2A-like plasma are carried out using 1.5D BALDUR integrated predictive modeling code. In these simulations, the core transport is predicted using the combination of Multi-mode (MMM95) anomalous core transport model and NCLASS neoclassical transport model. The evolution of plasma current, temperature and density is carried out. Consequently, the plasma current, temperature and density profiles, as well as other plasma parameters, are obtained as the predictions in each simulation. It is found that temperature and density profiles in these simulations are peak near the plasma center. In addition, the sawtooth period is studied using the Porcilli model and is found that before, during, and after the electron cyclotron resonance heating (ECRH) operation the sawtooth period are approximately the same. It is also observed that the mixing radius of sawtooth crashes is reduced during the ECRH operation.

  11. A modified prediction scheme of the H.264 multiview video coding to improve the decoder performance

    NASA Astrophysics Data System (ADS)

    Hamadan, Ayman M.; Aly, Hussein A.; Fouad, Mohamed M.; Dansereau, Richard M.

    2013-02-01

    In this paper, we present a modified inter-view prediction scheme for the multiview video coding (MVC).With more inter-view prediction, the number of reference frames required to decode a single view increase. Consequently, the data size of decoding a single view increases, thus impacting the decoder performance. In this paper, we propose an MVC scheme that requires less inter-view prediction than that of the MVC standard scheme. The proposed scheme is implemented and tested on real multiview video sequences. Improvements are shown using the proposed scheme in terms of average data size required either to decode a single view, or to access any frame (i.e., random access), with comparable rate-distortion. It is compared to the MVC standard scheme and another improved techniques from the literature.

  12. Comparison of secondary flows predicted by a viscous code and an inviscid code with experimental data for a turning duct

    NASA Technical Reports Server (NTRS)

    Schwab, J. R.; Povinelli, L. A.

    1984-01-01

    A comparison of the secondary flows computed by the viscous Kreskovsky-Briley-McDonald code and the inviscid Denton code with benchmark experimental data for turning duct is presented. The viscous code is a fully parabolized space-marching Navier-Stokes solver while the inviscid code is a time-marching Euler solver. The experimental data were collected by Taylor, Whitelaw, and Yianneskis with a laser Doppler velocimeter system in a 90 deg turning duct of square cross-section. The agreement between the viscous and inviscid computations was generally very good for the streamwise primary velocity and the radial secondary velocity, except at the walls, where slip conditions were specified for the inviscid code. The agreement between both the computations and the experimental data was not as close, especially at the 60.0 deg and 77.5 deg angular positions within the duct. This disagreement was attributed to incomplete modelling of the vortex development near the suction surface.

  13. Comparison of secondary flows predicted by a viscous code and an inviscid code with experimental data for a turning duct

    NASA Technical Reports Server (NTRS)

    Schwab, J. R.; Povinelli, L. A.

    1983-01-01

    A comparison of the secondary flows computed by the viscous Kreskovsky-Briley-McDonald code and the inviscid Denton code with benchmark experimental data for turning duct is presented. The viscous code is a fully parabolized space-marching Navier-Stokes solver while the inviscid code is a time-marching Euler solver. The experimental data were collected by Taylor, Whitelaw, and Yianneskis with a laser Doppler velocimeter system in a 90 deg turning duct of square cross-section. The agreement between the viscous and inviscid computations was generally very good for the streamwise primary velocity and the radial secondary velocity, except at the walls, where slip conditions were specified for the inviscid code. The agreement between both the computations and the experimental data was not as close, especially at the 60.0 deg and 77.5 deg angular positions within the duct. This disagreement was attributed to incomplete modeling of the vortex development near the suction surface.

  14. Long-range accelerated BOTDA sensor using adaptive linear prediction and cyclic coding.

    PubMed

    Muanenda, Yonas; Taki, Mohammad; Pasquale, Fabrizio Di

    2014-09-15

    We propose and experimentally demonstrate a long-range accelerated Brillouin optical time domain analysis (BOTDA) sensor that exploits the complementary noise reduction benefits of adaptive linear prediction and optical pulse coding. The combined technique allows using orders of magnitude less the number of averages of the backscattered BOTDA traces compared to a standard single pulse BOTDA, enabling distributed strain measurement over 10 km of a standard single mode fiber with meter-scale spatial resolution and 1.8 MHz Brillouin frequency shift resolution. By optimizing the system parameters, the measurement is achieved with only 20 averages for each Brillouin gain spectrum scanned frequency, allowing for an eight times faster strain measurement compared to the use of cyclic pulse coding alone.

  15. Life Prediction for a CMC Component Using the NASALIFE Computer Code

    NASA Technical Reports Server (NTRS)

    Gyekenyesi, John Z.; Murthy, Pappu L. N.; Mital, Subodh K.

    2005-01-01

    The computer code, NASALIFE, was used to provide estimates for life of an SiC/SiC stator vane under varying thermomechanical loading conditions. The primary intention of this effort is to show how the computer code NASALIFE can be used to provide reasonable estimates of life for practical propulsion system components made of advanced ceramic matrix composites (CMC). Simple loading conditions provided readily observable and acceptable life predictions. Varying the loading conditions such that low cycle fatigue and creep were affected independently provided expected trends in the results for life due to varying loads and life due to creep. Analysis was based on idealized empirical data for the 9/99 Melt Infiltrated SiC fiber reinforced SiC.

  16. Predicted effects of sensorineural hearing loss on across-fiber envelope coding in the auditory nervea

    PubMed Central

    Swaminathan, Jayaganesh; Heinz, Michael G.

    2011-01-01

    Cross-channel envelope correlations are hypothesized to influence speech intelligibility, particularly in adverse conditions. Acoustic analyses suggest speech envelope correlations differ for syllabic and phonemic ranges of modulation frequency. The influence of cochlear filtering was examined here by predicting cross-channel envelope correlations in different speech modulation ranges for normal and impaired auditory-nerve (AN) responses. Neural cross-correlation coefficients quantified across-fiber envelope coding in syllabic (0–5 Hz), phonemic (5–64 Hz), and periodicity (64–300 Hz) modulation ranges. Spike trains were generated from a physiologically based AN model. Correlations were also computed using the model with selective hair-cell damage. Neural predictions revealed that envelope cross-correlation decreased with increased characteristic-frequency separation for all modulation ranges (with greater syllabic-envelope correlation than phonemic or periodicity). Syllabic envelope was highly correlated across many spectral channels, whereas phonemic and periodicity envelopes were correlated mainly between adjacent channels. Outer-hair-cell impairment increased the degree of cross-channel correlation for phonemic and periodicity ranges for speech in quiet and in noise, thereby reducing the number of independent neural information channels for envelope coding. In contrast, outer-hair-cell impairment was predicted to decrease cross-channel correlation for syllabic envelopes in noise, which may partially account for the reduced ability of hearing-impaired listeners to segregate speech in complex backgrounds. PMID:21682421

  17. A Predictive Coding Perspective on Beta Oscillations during Sentence-Level Language Comprehension

    PubMed Central

    Lewis, Ashley G.; Schoffelen, Jan-Mathijs; Schriefers, Herbert; Bastiaansen, Marcel

    2016-01-01

    Oscillatory neural dynamics have been steadily receiving more attention as a robust and temporally precise signature of network activity related to language processing. We have recently proposed that oscillatory dynamics in the beta and gamma frequency ranges measured during sentence-level comprehension might be best explained from a predictive coding perspective. Under our proposal we related beta oscillations to both the maintenance/change of the neural network configuration responsible for the construction and representation of sentence-level meaning, and to top–down predictions about upcoming linguistic input based on that sentence-level meaning. Here we zoom in on these particular aspects of our proposal, and discuss both old and new supporting evidence. Finally, we present some preliminary magnetoencephalography data from an experiment comparing Dutch subject- and object-relative clauses that was specifically designed to test our predictive coding framework. Initial results support the first of the two suggested roles for beta oscillations in sentence-level language comprehension. PMID:26973500

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  1. 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

  2. Vector Sum Excited Linear Prediction (VSELP) speech coding at 4.8 kbps

    NASA Technical Reports Server (NTRS)

    Gerson, Ira A.; Jasiuk, Mark A.

    1990-01-01

    Code Excited Linear Prediction (CELP) speech coders exhibit good performance at data rates as low as 4800 bps. The major drawback to CELP type coders is their larger computational requirements. The Vector Sum Excited Linear Prediction (VSELP) speech coder utilizes a codebook with a structure which allows for a very efficient search procedure. Other advantages of the VSELP codebook structure is discussed and a detailed description of a 4.8 kbps VSELP coder is given. This coder is an improved version of the VSELP algorithm, which finished first in the NSA's evaluation of the 4.8 kbps speech coders. The coder uses a subsample resolution single tap long term predictor, a single VSELP excitation codebook, a novel gain quantizer which is robust to channel errors, and a new adaptive pre/postfilter arrangement.

  3. CCFL in hot legs and steam generators and its prediction with the CATHARE code

    SciTech Connect

    Geffraye, G.; Bazin, P.; Pichon, P.

    1995-09-01

    This paper presents a study about the Counter-Current Flow Limitation (CCFL) prediction in hot legs and steam generators (SG) in both system test facilities and pressurized water reactors. Experimental data are analyzed, particularly the recent MHYRESA test data. Geometrical and scale effects on the flooding behavior are shown. The CATHARE code modelling problems concerning the CCFL prediction are discussed. A method which gives the user the possibility of controlling the flooding limit at a given location is developed. In order to minimize the user effect, a methodology is proposed to the user in case of a calculation with a counter-current flow between the upper plenum and the SF U-tubes. The following questions have to be made clear for the user: when to use the CATHARE CCFL option, which correlation to use, and where to locate the flooding limit.

  4. Improved inter-layer prediction for light field content coding with display scalability

    NASA Astrophysics Data System (ADS)

    Conti, Caroline; Ducla Soares, Luís.; Nunes, Paulo

    2016-09-01

    Light field imaging based on microlens arrays - also known as plenoptic, holoscopic and integral imaging - has recently risen up as feasible and prospective technology due to its ability to support functionalities not straightforwardly available in conventional imaging systems, such as: post-production refocusing and depth of field changing. However, to gradually reach the consumer market and to provide interoperability with current 2D and 3D representations, a display scalable coding solution is essential. In this context, this paper proposes an improved display scalable light field codec comprising a three-layer hierarchical coding architecture (previously proposed by the authors) that provides interoperability with 2D (Base Layer) and 3D stereo and multiview (First Layer) representations, while the Second Layer supports the complete light field content. For further improving the compression performance, novel exemplar-based inter-layer coding tools are proposed here for the Second Layer, namely: (i) an inter-layer reference picture construction relying on an exemplar-based optimization algorithm for texture synthesis, and (ii) a direct prediction mode based on exemplar texture samples from lower layers. Experimental results show that the proposed solution performs better than the tested benchmark solutions, including the authors' previous scalable codec.

  5. IN-MACA-MCC: Integrated Multiple Attractor Cellular Automata with Modified Clonal Classifier for Human Protein Coding and Promoter Prediction.

    PubMed

    Pokkuluri, Kiran Sree; Inampudi, Ramesh Babu; Nedunuri, S S S N Usha Devi

    2014-01-01

    Protein coding and promoter region predictions are very important challenges of bioinformatics (Attwood and Teresa, 2000). The identification of these regions plays a crucial role in understanding the genes. Many novel computational and mathematical methods are introduced as well as existing methods that are getting refined for predicting both of the regions separately; still there is a scope for improvement. We propose a classifier that is built with MACA (multiple attractor cellular automata) and MCC (modified clonal classifier) to predict both regions with a single classifier. The proposed classifier is trained and tested with Fickett and Tung (1992) datasets for protein coding region prediction for DNA sequences of lengths 54, 108, and 162. This classifier is trained and tested with MMCRI datasets for protein coding region prediction for DNA sequences of lengths 252 and 354. The proposed classifier is trained and tested with promoter sequences from DBTSS (Yamashita et al., 2006) dataset and nonpromoters from EID (Saxonov et al., 2000) and UTRdb (Pesole et al., 2002) datasets. The proposed model can predict both regions with an average accuracy of 90.5% for promoter and 89.6% for protein coding region predictions. The specificity and sensitivity values of promoter and protein coding region predictions are 0.89 and 0.92, respectively.

  6. Neural evidence for predictive coding in auditory cortex during speech production.

    PubMed

    Okada, Kayoko; Matchin, William; Hickok, Gregory

    2017-04-10

    Recent models of speech production suggest that motor commands generate forward predictions of the auditory consequences of those commands, that these forward predications can be used to monitor and correct speech output, and that this system is hierarchically organized (Hickok, Houde, & Rong, Neuron, 69(3), 407--422, 2011; Pickering & Garrod, Behavior and Brain Sciences, 36(4), 329--347, 2013). Recent psycholinguistic research has shown that internally generated speech (i.e., imagined speech) produces different types of errors than does overt speech (Oppenheim & Dell, Cognition, 106(1), 528--537, 2008; Oppenheim & Dell, Memory & Cognition, 38(8), 1147-1160, 2010). These studies suggest that articulated speech might involve predictive coding at additional levels than imagined speech. The current fMRI experiment investigates neural evidence of predictive coding in speech production. Twenty-four participants from UC Irvine were recruited for the study. Participants were scanned while they were visually presented with a sequence of words that they reproduced in sync with a visual metronome. On each trial, they were cued to either silently articulate the sequence or to imagine the sequence without overt articulation. As expected, silent articulation and imagined speech both engaged a left hemisphere network previously implicated in speech production. A contrast of silent articulation with imagined speech revealed greater activation for articulated speech in inferior frontal cortex, premotor cortex and the insula in the left hemisphere, consistent with greater articulatory load. Although both conditions were silent, this contrast also produced significantly greater activation in auditory cortex in dorsal superior temporal gyrus in both hemispheres. We suggest that these activations reflect forward predictions arising from additional levels of the perceptual/motor hierarchy that are involved in monitoring the intended speech output.

  7. 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.

  8. Structured Set Intra Prediction With Discriminative Learning in a Max-Margin Markov Network for High Efficiency Video Coding

    PubMed Central

    Dai, Wenrui; Xiong, Hongkai; Jiang, Xiaoqian; Chen, Chang Wen

    2014-01-01

    This paper proposes a novel model on intra coding for High Efficiency Video Coding (HEVC), which simultaneously predicts blocks of pixels with optimal rate distortion. It utilizes the spatial statistical correlation for the optimal prediction based on 2-D contexts, in addition to formulating the data-driven structural interdependences to make the prediction error coherent with the probability distribution, which is desirable for successful transform and coding. The structured set prediction model incorporates a max-margin Markov network (M3N) to regulate and optimize multiple block predictions. The model parameters are learned by discriminating the actual pixel value from other possible estimates to maximize the margin (i.e., decision boundary bandwidth). Compared to existing methods that focus on minimizing prediction error, the M3N-based model adaptively maintains the coherence for a set of predictions. Specifically, the proposed model concurrently optimizes a set of predictions by associating the loss for individual blocks to the joint distribution of succeeding discrete cosine transform coefficients. When the sample size grows, the prediction error is asymptotically upper bounded by the training error under the decomposable loss function. As an internal step, we optimize the underlying Markov network structure to find states that achieve the maximal energy using expectation propagation. For validation, we integrate the proposed model into HEVC for optimal mode selection on rate-distortion optimization. The proposed prediction model obtains up to 2.85% bit rate reduction and achieves better visual quality in comparison to the HEVC intra coding. PMID:25505829

  9. Predictive coding in autism spectrum disorder and attention deficit hyperactivity disorder

    PubMed Central

    Gonzalez-Gadea, Maria Luz; Chennu, Srivas; Bekinschtein, Tristan A.; Rattazzi, Alexia; Beraudi, Ana; Tripicchio, Paula; Moyano, Beatriz; Soffita, Yamila; Steinberg, Laura; Adolfi, Federico; Sigman, Mariano; Marino, Julian; Manes, Facundo

    2015-01-01

    Predictive coding has been proposed as a framework to understand neural processes in neuropsychiatric disorders. We used this approach to describe mechanisms responsible for attentional abnormalities in autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). We monitored brain dynamics of 59 children (8–15 yr old) who had ASD or ADHD or who were control participants via high-density electroencephalography. We performed analysis at the scalp and source-space levels while participants listened to standard and deviant tone sequences. Through task instructions, we manipulated top-down expectation by presenting expected and unexpected deviant sequences. Children with ASD showed reduced superior frontal cortex (FC) responses to unexpected events but increased dorsolateral prefrontal cortex (PFC) activation to expected events. In contrast, children with ADHD exhibited reduced cortical responses in superior FC to expected events but strong PFC activation to unexpected events. Moreover, neural abnormalities were associated with specific control mechanisms, namely, inhibitory control in ASD and set-shifting in ADHD. Based on the predictive coding account, top-down expectation abnormalities could be attributed to a disproportionate reliance (precision) allocated to prior beliefs in ASD and to sensory input in ADHD. PMID:26311184

  10. Predictive coding in autism spectrum disorder and attention deficit hyperactivity disorder.

    PubMed

    Gonzalez-Gadea, Maria Luz; Chennu, Srivas; Bekinschtein, Tristan A; Rattazzi, Alexia; Beraudi, Ana; Tripicchio, Paula; Moyano, Beatriz; Soffita, Yamila; Steinberg, Laura; Adolfi, Federico; Sigman, Mariano; Marino, Julian; Manes, Facundo; Ibanez, Agustin

    2015-11-01

    Predictive coding has been proposed as a framework to understand neural processes in neuropsychiatric disorders. We used this approach to describe mechanisms responsible for attentional abnormalities in autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). We monitored brain dynamics of 59 children (8-15 yr old) who had ASD or ADHD or who were control participants via high-density electroencephalography. We performed analysis at the scalp and source-space levels while participants listened to standard and deviant tone sequences. Through task instructions, we manipulated top-down expectation by presenting expected and unexpected deviant sequences. Children with ASD showed reduced superior frontal cortex (FC) responses to unexpected events but increased dorsolateral prefrontal cortex (PFC) activation to expected events. In contrast, children with ADHD exhibited reduced cortical responses in superior FC to expected events but strong PFC activation to unexpected events. Moreover, neural abnormalities were associated with specific control mechanisms, namely, inhibitory control in ASD and set-shifting in ADHD. Based on the predictive coding account, top-down expectation abnormalities could be attributed to a disproportionate reliance (precision) allocated to prior beliefs in ASD and to sensory input in ADHD.

  11. 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.)

  12. Computer code to predict the heat of explosion of high energy materials.

    PubMed

    Muthurajan, H; Sivabalan, R; Pon Saravanan, N; Talawar, M B

    2009-01-30

    The computational approach to the thermochemical changes involved in the process of explosion of a high energy materials (HEMs) vis-à-vis its molecular structure aids a HEMs chemist/engineers to predict the important thermodynamic parameters such as heat of explosion of the HEMs. Such a computer-aided design will be useful in predicting the performance of a given HEM as well as in conceiving futuristic high energy molecules that have significant potential in the field of explosives and propellants. The software code viz., LOTUSES developed by authors predicts various characteristics of HEMs such as explosion products including balanced explosion reactions, density of HEMs, velocity of detonation, CJ pressure, etc. The new computational approach described in this paper allows the prediction of heat of explosion (DeltaH(e)) without any experimental data for different HEMs, which are comparable with experimental results reported in literature. The new algorithm which does not require any complex input parameter is incorporated in LOTUSES (version 1.5) and the results are presented in this paper. The linear regression analysis of all data point yields the correlation coefficient R(2)=0.9721 with a linear equation y=0.9262x+101.45. The correlation coefficient value 0.9721 reveals that the computed values are in good agreement with experimental values and useful for rapid hazard assessment of energetic materials.

  13. 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…

  14. Rhythmic complexity and predictive coding: a novel approach to modeling rhythm and meter perception in music.

    PubMed

    Vuust, Peter; Witek, Maria A G

    2014-01-01

    Musical rhythm, consisting of apparently abstract intervals of accented temporal events, has a remarkable capacity to move our minds and bodies. How does the cognitive system enable our experiences of rhythmically complex music? In this paper, we describe some common forms of rhythmic complexity in music and propose the theory of predictive coding (PC) as a framework for understanding how rhythm and rhythmic complexity are processed in the brain. We also consider why we feel so compelled by rhythmic tension in music. First, we consider theories of rhythm and meter perception, which provide hierarchical and computational approaches to modeling. Second, we present the theory of PC, which posits a hierarchical organization of brain responses reflecting fundamental, survival-related mechanisms associated with predicting future events. According to this theory, perception and learning is manifested through the brain's Bayesian minimization of the error between the input to the brain and the brain's prior expectations. Third, we develop a PC model of musical rhythm, in which rhythm perception is conceptualized as an interaction between what is heard ("rhythm") and the brain's anticipatory structuring of music ("meter"). Finally, we review empirical studies of the neural and behavioral effects of syncopation, polyrhythm and groove, and propose how these studies can be seen as special cases of the PC theory. We argue that musical rhythm exploits the brain's general principles of prediction and propose that pleasure and desire for sensorimotor synchronization from musical rhythm may be a result of such mechanisms.

  15. Brain responses to regular and octave-scrambled melodies: A case of predictive-coding?

    PubMed

    Globerson, Eitan; Granot, Roni; Tal, Idan; Harpaz, Yuval; Zeev-Wolf, Maor; Golstein, Abraham

    2017-03-01

    Melody recognition is an online process of evaluating incoming information and comparing this information to an existing internal corpus, thereby reducing prediction error. The predictive-coding model postulates top-down control on sensory processing accompanying reduction in prediction error. To investigate the relevancy of this model to melody processing, the current study examined early magnetoencephalogram (MEG) auditory responses to familiar and unfamiliar melodies in 25 participants. The familiar melodies followed and primed an octave-scrambled version of the same melody. The retrograde version of theses melodies served as the unfamiliar control condition. Octave-transposed melodies were included to examine the influence of pitch representation (pitch-height/pitch-chroma representation) on brain responses to melody recognition. Results demonstrate a reduction of the M100 auditory response to familiar, as compared with unfamiliar, melodies regardless of their form of presentation (condensed vs. octave-scrambled). This trend appeared to begin after the third tone of the melody. An additional behavioral study with the same melody corpus showed a similar trend-namely, a significant difference between familiarity rating for familiar and unfamiliar melodies, beginning with the third tone of the melody. These results may indicate a top-down inhibition of early auditory responses to melodies that is influenced by pitch representation. (PsycINFO Database Record

  16. Circulating long non-coding RNAs NRON and MHRT as novel predictive biomarkers of heart failure.

    PubMed

    Xuan, Lina; Sun, Lihua; Zhang, Ying; Huang, Yuechao; Hou, Yan; Li, Qingqi; Guo, Ying; Feng, Bingbing; Cui, Lina; Wang, Xiaoxue; Wang, Zhiguo; Tian, Ye; Yu, Bo; Wang, Shu; Xu, Chaoqian; Zhang, Mingyu; Du, Zhimin; Lu, Yanjie; Yang, Bao Feng

    2017-03-14

    This study sought to evaluate the potential of circulating long non-coding RNAs (lncRNAs) as biomarkers for heart failure (HF). We measured the circulating levels of 13 individual lncRNAs which are known to be relevant to cardiovascular disease in the plasma samples from 72 HF patients and 60 non-HF control participants using real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) methods. We found that out of the 13 lncRNAs tested, non-coding repressor of NFAT (NRON) and myosin heavy-chain-associated RNA transcripts (MHRT) had significantly higher plasma levels in HF than in non-HF subjects: 3.17 ± 0.30 versus 1.0 ± 0.07 for NRON (P < 0.0001) and 1.66 ± 0.14 versus 1.0 ± 0.12 for MHRT (P < 0.0001). The area under the ROC curve was 0.865 for NRON and 0.702 for MHRT. Univariate and multivariate analyses identified NRON and MHRT as independent predictors for HF. Spearman's rank correlation analysis showed that NRON was negatively correlated with HDL and positively correlated with LDH, whereas MHRT was positively correlated with AST and LDH. Hence, elevation of circulating NRON and MHRT predicts HF and may be considered as novel biomarkers of HF.

  17. Computational Account of Spontaneous Activity as a Signature of Predictive Coding

    PubMed Central

    Koren, Veronika

    2017-01-01

    Spontaneous activity is commonly observed in a variety of cortical states. Experimental evidence suggested that neural assemblies undergo slow oscillations with Up ad Down states even when the network is isolated from the rest of the brain. Here we show that these spontaneous events can be generated by the recurrent connections within the network and understood as signatures of neural circuits that are correcting their internal representation. A noiseless spiking neural network can represent its input signals most accurately when excitatory and inhibitory currents are as strong and as tightly balanced as possible. However, in the presence of realistic neural noise and synaptic delays, this may result in prohibitively large spike counts. An optimal working regime can be found by considering terms that control firing rates in the objective function from which the network is derived and then minimizing simultaneously the coding error and the cost of neural activity. In biological terms, this is equivalent to tuning neural thresholds and after-spike hyperpolarization. In suboptimal working regimes, we observe spontaneous activity even in the absence of feed-forward inputs. In an all-to-all randomly connected network, the entire population is involved in Up states. In spatially organized networks with local connectivity, Up states spread through local connections between neurons of similar selectivity and take the form of a traveling wave. Up states are observed for a wide range of parameters and have similar statistical properties in both active and quiescent state. In the optimal working regime, Up states are vanishing, leaving place to asynchronous activity, suggesting that this working regime is a signature of maximally efficient coding. Although they result in a massive increase in the firing activity, the read-out of spontaneous Up states is in fact orthogonal to the stimulus representation, therefore interfering minimally with the network function. PMID:28114353

  18. A computer code (SKINTEMP) for predicting transient missile and aircraft heat transfer characteristics

    NASA Astrophysics Data System (ADS)

    Cummings, Mary L.

    1994-09-01

    A FORTRAN computer code (SKINTEMP) has been developed to calculate transient missile/aircraft aerodynamic heating parameters utilizing basic flight parameters such as altitude, Mach number, and angle of attack. The insulated skin temperature of a vehicle surface on either the fuselage (axisymmetric body) or wing (two-dimensional body) is computed from a basic heat balance relationship throughout the entire spectrum (subsonic, transonic, supersonic, hypersonic) of flight. This calculation method employs a simple finite difference procedure which considers radiation, forced convection, and non-reactive chemistry. Surface pressure estimates are based on a modified Newtonian flow model. Eckert's reference temperature method is used as the forced convection heat transfer model. SKINTEMP predictions are compared with a limited number of test cases. SKINTEMP was developed as a tool to enhance the conceptual design process of high speed missiles and aircraft. Recommendations are made for possible future development of SKINTEMP to further support the design process.

  19. Prediction of explosive cylinder tests using equations of state from the PANDA code

    SciTech Connect

    Kerley, G.I.; Christian-Frear, T.L.

    1993-09-28

    The PANDA code is used to construct tabular equations of state (EOS) for the detonation products of 24 explosives having CHNO compositions. These EOS, together with a reactive burn model, are used in numerical hydrocode calculations of cylinder tests. The predicted detonation properties and cylinder wall velocities are found to give very good agreement with experimental data. Calculations of flat plate acceleration tests for the HMX-based explosive LX14 are also made and shown to agree well with the measurements. The effects of the reaction zone on both the cylinder and flat plate tests are discussed. For TATB-based explosives, the differences between experiment and theory are consistently larger than for other compositions and may be due to nonideal (finite dimameter) behavior.

  20. Contribution to the Prediction of the Fold Code: Application to Immunoglobulin and Flavodoxin Cases

    PubMed Central

    Banach, Mateusz; Prudhomme, Nicolas; Carpentier, Mathilde; Duprat, Elodie; Papandreou, Nikolaos; Kalinowska, Barbara; Chomilier, Jacques; Roterman, Irena

    2015-01-01

    Background Folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3D structure. These early steps can be predicted by simulation of the folding process through a Monte Carlo (MC) coarse grain model in a discrete space. We previously defined MIRs (Most Interacting Residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simulation. MIRs are good candidates to define the minimal number of residues giving rise to a given fold instead of another one, although their proportion is rather high, typically [15-20]% of the sequences. Having in mind experiments with two sequences of very high levels of sequence identity (up to 90%) but different folds, we combined the MIR method, which takes sequence as single input, with the “fuzzy oil drop” (FOD) model that requires a 3D structure, in order to estimate the residues coding for the fold. FOD assumes that a globular protein follows an idealised 3D Gaussian distribution of hydrophobicity density, with the maximum in the centre and minima at the surface of the “drop”. If the actual local density of hydrophobicity around a given amino acid is as high as the ideal one, then this amino acid is assigned to the core of the globular protein, and it is assumed to follow the FOD model. Therefore one obtains a distribution of the amino acids of a protein according to their agreement or rejection with the FOD model. Results We compared and combined MIR and FOD methods to define the minimal nucleus, or keystone, of two populated folds: immunoglobulin-like (Ig) and flavodoxins (Flav). The combination of these two approaches defines some positions both predicted as a MIR and assigned as accordant with the FOD model. It is shown here that for these two folds, the intersection of the predicted sets of residues significantly differs from random selection

  1. On the efficiency of image completion methods for intra prediction in video coding with large block structures

    NASA Astrophysics Data System (ADS)

    Doshkov, Dimitar; Jottrand, Oscar; Wiegand, Thomas; Ndjiki-Nya, Patrick

    2013-02-01

    Intra prediction is a fundamental tool in video coding with hybrid block-based architecture. Recent investigations have shown that one of the most beneficial elements for a higher compression performance in high-resolution videos is the incorporation of larger block structures. Thus in this work, we investigate the performance of novel intra prediction modes based on different image completion techniques in a new video coding scheme with large block structures. Image completion methods exploit the fact that high frequency image regions yield high coding costs when using classical H.264/AVC prediction modes. This problem is tackled by investigating the incorporation of several intra predictors using the concept of Laplace partial differential equation (PDE), Least Square (LS) based linear prediction and the Auto Regressive model. A major aspect of this article is the evaluation of the coding performance in a qualitative (i.e. coding efficiency) manner. Experimental results show significant improvements in compression (up to 7.41 %) by integrating the LS-based linear intra prediction.

  2. 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

  3. Phase-coded microwave signal generation based on a single electro-optical modulator and its application in accurate distance measurement.

    PubMed

    Zhang, Fangzheng; Ge, Xiaozhong; Gao, Bindong; Pan, Shilong

    2015-08-24

    A novel scheme for photonic generation of a phase-coded microwave signal is proposed and its application in one-dimension distance measurement is demonstrated. The proposed signal generator has a simple and compact structure based on a single dual-polarization modulator. Besides, the generated phase-coded signal is stable and free from the DC and low-frequency backgrounds. An experiment is carried out. A 2 Gb/s phase-coded signal at 20 GHz is successfully generated, and the recovered phase information agrees well with the input 13-bit Barker code. To further investigate the performance of the proposed signal generator, its application in one-dimension distance measurement is demonstrated. The measurement accuracy is less than 1.7 centimeters within a measurement range of ~2 meters. The experimental results can verify the feasibility of the proposed phase-coded microwave signal generator and also provide strong evidence to support its practical applications.

  4. The WISGSK: A computer code for the prediction of a multistage axial compressor performance with water ingestion

    NASA Technical Reports Server (NTRS)

    Tsuchiya, T.; Murthy, S. N. B.

    1982-01-01

    A computer code is presented for the prediction of off-design axial flow compressor performance with water ingestion. Four processes were considered to account for the aero-thermo-mechanical interactions during operation with air-water droplet mixture flow: (1) blade performance change, (2) centrifuging of water droplets, (3) heat and mass transfer process between the gaseous and the liquid phases and (4) droplet size redistribution due to break-up. Stage and compressor performance are obtained by a stage stacking procedure using representative veocity diagrams at a rotor inlet and outlet mean radii. The Code has options for performance estimation with (1) mixtures of gas and (2) gas-water droplet mixtures, and therefore can take into account the humidity present in ambient conditions. A test case illustrates the method of using the Code. The Code follows closely the methodology and architecture of the NASA-STGSTK Code for the estimation of axial-flow compressor performance with air flow.

  5. Potential prognostic long non-coding RNA identification and their validation in predicting survival of patients with multiple myeloma.

    PubMed

    Hu, Ai-Xin; Huang, Zhi-Yong; Zhang, Lin; Shen, Jian

    2017-04-01

    Multiple myeloma, a typical hematological malignancy, is characterized by malignant proliferation of plasma cells. This study was to identify differently expressed long non-coding RNAs to predict the survival of patients with multiple myeloma efficiently. Gene expressing profiles of diagnosed patients with multiple myeloma, GSE24080 (559 samples) and GSE57317 (55 samples), were downloaded from Gene Expression Omnibus database. After processing, survival-related long non-coding RNAs were identified by Cox regression analysis. The prognosis of multiple myeloma patients with differently expressed long non-coding RNAs was predicted by Kaplan-Meier analysis. Meanwhile, stratified analysis was performed based on the concentrations of serum beta 2-microglobulin (S-beta 2m), albumin, and lactate dehydrogenase of multiple myeloma patients. Gene set enrichment analysis was performed to further explore the functions of identified long non-coding RNAs. A total of 176 long non-coding RNAs significantly related to the survival of multiple myeloma patients (p < 0.05) were identified. In dataset GSE24080 and GSE57317, there were 558 and 55 patients being clustered into two groups with significant differences, respectively. Stratified analysis indicated that prediction of the prognoses with these long non-coding RNAs was independent from other clinical phenotype of multiple myeloma. Gene set enrichment analysis-identified pathways of cell cycle, focal adhesion, and G2-M checkpoint were associated with these long non-coding RNAs. A total of 176 long non-coding RNAs, especially RP1-286D6.1, AC008875.2, MTMR9L, AC069360.2, and AL512791.1, were potential biomarkers to evaluate the prognosis of multiple myeloma patients. These long non-coding RNAs participated indispensably in many pathways associated to the development of multiple myeloma; however, the molecular mechanisms need to be further studied.

  6. 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…

  7. Near-fault earthquake ground motion prediction by a high-performance spectral element numerical code

    NASA Astrophysics Data System (ADS)

    Paolucci, Roberto; Stupazzini, Marco

    2008-07-01

    Near-fault effects have been widely recognised to produce specific features of earthquake ground motion, that cannot be reliably predicted by 1D seismic wave propagation modelling, used as a standard in engineering applications. These features may have a relevant impact on the structural response, especially in the nonlinear range, that is hard to predict and to be put in a design format, due to the scarcity of significant earthquake records and of reliable numerical simulations. In this contribution a pilot study is presented for the evaluation of seismic ground-motions in the near-fault region, based on a high-performance numerical code for 3D seismic wave propagation analyses, including the seismic fault, the wave propagation path and the near-surface geological or topographical irregularity. For this purpose, the software package GeoELSE is adopted, based on the spectral element method. The set-up of the numerical benchmark of 3D ground motion simulation in the valley of Grenoble (French Alps) is chosen to study the effect of the complex interaction between basin geometry and radiation mechanism on the variability of earthquake ground motion.

  8. From structure prediction to genomic screens for novel non-coding RNAs.

    PubMed

    Gorodkin, Jan; Hofacker, Ivo L

    2011-08-01

    Non-coding RNAs (ncRNAs) are receiving more and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early for folding and prediction of RNA structure with the aim of assisting in functional analysis. With the discovery of more and more ncRNAs, it has become clear that a large fraction of these are highly structured. Interestingly, a large part of the structure is comprised of regular Watson-Crick and GU wobble base pairs. This and the increased amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristic feature. Whereas early methods focused on energy-directed folding of single sequences, comparative analysis based on structure preserving changes of base pairs has been efficient in improving accuracy, and today this constitutes a key component in genomic screens. Here, we cover the basic principles of RNA folding and touch upon some of the concepts in current methods that have been applied in genomic screens for de novo RNA structures in searches for novel ncRNA genes and regulatory RNA structure on mRNAs. We discuss the strengths and weaknesses of the different strategies and how they can complement each other.

  9. Near-fault earthquake ground motion prediction by a high-performance spectral element numerical code

    SciTech Connect

    Paolucci, Roberto; Stupazzini, Marco

    2008-07-08

    Near-fault effects have been widely recognised to produce specific features of earthquake ground motion, that cannot be reliably predicted by 1D seismic wave propagation modelling, used as a standard in engineering applications. These features may have a relevant impact on the structural response, especially in the nonlinear range, that is hard to predict and to be put in a design format, due to the scarcity of significant earthquake records and of reliable numerical simulations. In this contribution a pilot study is presented for the evaluation of seismic ground-motions in the near-fault region, based on a high-performance numerical code for 3D seismic wave propagation analyses, including the seismic fault, the wave propagation path and the near-surface geological or topographical irregularity. For this purpose, the software package GeoELSE is adopted, based on the spectral element method. The set-up of the numerical benchmark of 3D ground motion simulation in the valley of Grenoble (French Alps) is chosen to study the effect of the complex interaction between basin geometry and radiation mechanism on the variability of earthquake ground motion.

  10. Performance of a municipal solid waste (MSW) incinerator predicted with a computational fluid dynamics (CFD) code

    SciTech Connect

    Anglesio, P.; Negreanu, G.P.

    1998-07-01

    The purpose of this paper is to investigate by the means of numerical simulation the performance of the MSW incinerator with of Vercelli (Italy). FLUENT, a finite-volumes commercial code for Fluid Dynamics has been used to predict the 3-D reacting flows (gaseous phase) within the incinerator geometry, in order to estimate if the three conditions settled by the Italian law (P.D. 915 / 82) are respected: (a) Flue gas temperature at the input of the secondary combustion chamber must exceed 950 C. (b) Oxygen concentration in the same section must exceed 6 %. (c) Residence time for the flue gas in the secondary combustion chamber must exceed 2 seconds. The model of the incinerator has been created using the software pre-processing facilities (wall, input, outlet and live cells), together with the set-up of boundary conditions. There are also imposed the combustion constants (stoichiometry, heat of combustion, air excess). The solving procedure transforms at the level of each live cell the partial derivative equations in algebraic equations, computing the velocities field, the temperatures, gases concentration, etc. These predicted values were compared with the design properties, and the conclusion was that the conditions (a), (b), (c), are respected in normal operation. The powerful graphic interface helps the user to visualize the magnitude of the computed parameters. These results may be successfully used for the design and operation improvements for MSW incinerators. This fact will substantially increase the efficiency, reduce pollutant emissions and optimize the plant overall performance.

  11. Analytic solution to verify code predictions of two-phase flow in a boiling water reactor core channel

    SciTech Connect

    Chen, K.F.; Olson, C.A.

    1983-09-01

    One reliable method that can be used to verify the solution scheme of a computer code is to compare the code prediction to a simplified problem for which an analytic solution can be derived. An analytic solution for the axial pressure drop as a function of the flow was obtained for the simplified problem of homogeneous equilibrium two-phase flow in a vertical, heated channel with a cosine axial heat flux shape. This analytic solution was then used to verify the predictions of the CONDOR computer code, which is used to evaluate the thermal-hydraulic performance of boiling water reactors. The results show excellent agreement between the analytic solution and CONDOR prediction.

  12. Comparison of experimental pulse-height distributions in germanium detectors with integrated-tiger-series-code predictions

    SciTech Connect

    Beutler, D.E.; Halbleib, J.A. ); Knott, D.P. )

    1989-12-01

    This paper reports pulse-height distributions in two different types of Ge detectors measured for a variety of medium-energy x-ray bremsstrahlung spectra. These measurements have been compared to predictions using the integrated tiger series (ITS) Monte Carlo electron/photon transport code. In general, the authors find excellent agreement between experiments and predictions using no free parameters. These results demonstrate that the ITS codes can predict the combined bremsstrahlung production and energy deposition with good precision (within measurement uncertainties). The one region of disagreement observed occurs for low-energy (<50 keV) photons using low-energy bremsstrahlung spectra. In this case the ITS codes appear to underestimate the produced and/or absorbed radiation by almost an order of magnitude.

  13. Predictive coding accounts of shared representations in parieto-insular networks.

    PubMed

    Ishida, Hiroaki; Suzuki, Keisuke; Grandi, Laura Clara

    2015-04-01

    The discovery of mirror neurons in the ventral premotor cortex (area F5) and inferior parietal cortex (area PFG) in the macaque monkey brain has provided the physiological evidence for direct matching of the intrinsic motor representations of the self and the visual image of the actions of others. The existence of mirror neurons implies that the brain has mechanisms reflecting shared self and other action representations. This may further imply that the neural basis self-body representations may also incorporate components that are shared with other-body representations. It is likely that such a mechanism is also involved in predicting other's touch sensations and emotions. However, the neural basis of shared body representations has remained unclear. Here, we propose a neural basis of body representation of the self and of others in both human and non-human primates. We review a series of behavioral and physiological findings which together paint a picture that the systems underlying such shared representations require integration of conscious exteroception and interoception subserved by a cortical sensory-motor network involving parieto-inner perisylvian circuits (the ventral intraparietal area [VIP]/inferior parietal area [PFG]-secondary somatosensory cortex [SII]/posterior insular cortex [pIC]/anterior insular cortex [aIC]). Based on these findings, we propose a computational mechanism of the shared body representation in the predictive coding (PC) framework. Our mechanism proposes that processes emerging from generative models embedded in these specific neuronal circuits play a pivotal role in distinguishing a self-specific body representation from a shared one. The model successfully accounts for normal and abnormal shared body phenomena such as mirror-touch synesthesia and somatoparaphrenia. In addition, it generates a set of testable experimental predictions.

  14. Rhythmic complexity and predictive coding: a novel approach to modeling rhythm and meter perception in music

    PubMed Central

    Vuust, Peter; Witek, Maria A. G.

    2014-01-01

    Musical rhythm, consisting of apparently abstract intervals of accented temporal events, has a remarkable capacity to move our minds and bodies. How does the cognitive system enable our experiences of rhythmically complex music? In this paper, we describe some common forms of rhythmic complexity in music and propose the theory of predictive coding (PC) as a framework for understanding how rhythm and rhythmic complexity are processed in the brain. We also consider why we feel so compelled by rhythmic tension in music. First, we consider theories of rhythm and meter perception, which provide hierarchical and computational approaches to modeling. Second, we present the theory of PC, which posits a hierarchical organization of brain responses reflecting fundamental, survival-related mechanisms associated with predicting future events. According to this theory, perception and learning is manifested through the brain’s Bayesian minimization of the error between the input to the brain and the brain’s prior expectations. Third, we develop a PC model of musical rhythm, in which rhythm perception is conceptualized as an interaction between what is heard (“rhythm”) and the brain’s anticipatory structuring of music (“meter”). Finally, we review empirical studies of the neural and behavioral effects of syncopation, polyrhythm and groove, and propose how these studies can be seen as special cases of the PC theory. We argue that musical rhythm exploits the brain’s general principles of prediction and propose that pleasure and desire for sensorimotor synchronization from musical rhythm may be a result of such mechanisms. PMID:25324813

  15. ER-Worker: A computer code to predict remediation worker exposure and safety hazards

    SciTech Connect

    Blaylock, B.P.; Campbell, A.C.; Hutchison, J.F.; Simek, M.A.P.; Sutherland, J.F.; Legg, J.L.

    1994-12-31

    The U.S. Department of Energy (DOE) has generated and disposed of large quantities of waste as a result of 50 years of nuclear weapons production. This waste has been disposed of in waste sites such as burial grounds, waste pits, holding ponds, and landfills. Many of these waste sites have begun to release contamination offsite and potentially pose risks to humans living or working in the vicinity of these sites. By 2019, DOE must meet its goals to achieve timely compliance with all applicable environmental requirements, clean up the 1989 inventory of hazardous and radioactive wastes at inactive sites and facilities, and safely and efficiently treat, store, and dispose of the waste generated by remediation and operating facilities. Remediation of DOE`s 13,000 facilities, and management of the current and future waste streams, will require the effort of thousands of workers. Workers, as defined here, are persons who directly participate in the cleanup or remediation of DOE sites. Remediation activities include the use of remediation technologies such as bioremediation, surface water controls, and contaminated soil excavation. This document describes a worker health risk evaluation methodology and computer code designed to predict risks associated with Environmental Restoration (ER) activities that are yet to be undertaken. The computer code, designated ER-WORKER, can be used to estimate worker risks across the DOE complex on a site-specific, installation-wide, or programmatic level. This approach generally follows the guidance suggested in the Risk Assessment Guidance for Superfund (RAGS) (EPA 1989a). Key principles from other important Environmental Protection Agency (EPA) and DOE guidance documents are incorporated into the methodology.

  16. User's guide for a flat wake rotor inflow/wake velocity prediction code, DOWN

    NASA Technical Reports Server (NTRS)

    Wilson, John C.

    1991-01-01

    A computer code named DOWN was created to implement a flat wake theory for the calculation of rotor inflow and wake velocities. A brief description of the code methodology and instructions for its use are given. The code will be available from NASA's Computer Software Management and Information Center (COSMIC).

  17. A thermal NO(x) prediction model - Scalar computation module for CFD codes with fluid and kinetic effects

    NASA Technical Reports Server (NTRS)

    Mcbeath, Giorgio; Ghorashi, Bahman; Chun, Kue

    1993-01-01

    A thermal NO(x) prediction model is developed to interface with a CFD, k-epsilon based code. A converged solution from the CFD code is the input to the postprocessing model for prediction of thermal NO(x). The model uses a decoupled analysis to estimate the equilibrium level of (NO(x))e which is the constant rate limit. This value is used to estimate the flame (NO(x)) and in turn predict the rate of formation at each node using a two-step Zeldovich mechanism. The rate is fixed on the NO(x) production rate plot by estimating the time to reach equilibrium by a differential analysis based on the reaction: O + N2 = NO + N. The rate is integrated in the nonequilibrium time space based on the residence time at each node in the computational domain. The sum of all nodal predictions yields the total NO(x) level.

  18. Self-consistent modeling of DEMOs with 1.5D BALDUR integrated predictive modeling code

    NASA Astrophysics Data System (ADS)

    Wisitsorasak, A.; Somjinda, B.; Promping, J.; Onjun, T.

    2017-02-01

    Self-consistent simulations of four DEMO designs proposed by teams from China, Europe, India, and Korea are carried out using the BALDUR integrated predictive modeling code in which theory-based models are used, for both core transport and boundary conditions. In these simulations, a combination of the NCLASS neoclassical transport and multimode (MMM95) anomalous transport model is used to compute a core transport. The boundary is taken to be at the top of the pedestal, where the pedestal values are described using a pedestal temperature model based on a combination of magnetic and flow shear stabilization, pedestal width scaling and an infinite- n ballooning pressure gradient model and a pedestal density model based on a line average density. Even though an optimistic scenario is considered, the simulation results suggest that, with the exclusion of ELMs, the fusion gain Q obtained for these reactors is pessimistic compared to their original designs, i.e. 52% for the Chinese design, 63% for the European design, 22% for the Korean design, and 26% for the Indian design. In addition, the predicted bootstrap current fractions are also found to be lower than their original designs, as fractions of their original designs, i.e. 0.49 (China), 0.66 (Europe), and 0.58 (India). Furthermore, in relation to sensitivity, it is found that increasing values of the auxiliary heating power and the electron line average density from their design values yield an enhancement of fusion performance. In addition, inclusion of sawtooth oscillation effects demonstrate positive impacts on the plasma and fusion performance in European, Indian and Korean DEMOs, but degrade the performance in the Chinese DEMO.

  19. Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

    PubMed Central

    Liao, Qi; Liu, Changning; Yuan, Xiongying; Kang, Shuli; Miao, Ruoyu; Xiao, Hui; Zhao, Guoguang; Luo, Haitao; Bu, Dechao; Zhao, Haitao; Skogerbø, Geir; Wu, Zhongdao; Zhao, Yi

    2011-01-01

    Although accumulating evidence has provided insight into the various functions of long-non-coding RNAs (lncRNAs), the exact functions of the majority of such transcripts are still unknown. Here, we report the first computational annotation of lncRNA functions based on public microarray expression profiles. A coding–non-coding gene co-expression (CNC) network was constructed from re-annotated Affymetrix Mouse Genome Array data. Probable functions for altogether 340 lncRNAs were predicted based on topological or other network characteristics, such as module sharing, association with network hubs and combinations of co-expression and genomic adjacency. The functions annotated to the lncRNAs mainly involve organ or tissue development (e.g. neuron, eye and muscle development), cellular transport (e.g. neuronal transport and sodium ion, acid or lipid transport) or metabolic processes (e.g. involving macromolecules, phosphocreatine and tyrosine). PMID:21247874

  20. 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.

  1. A 4.8 kbps code-excited linear predictive coder

    NASA Technical Reports Server (NTRS)

    Tremain, Thomas E.; Campbell, Joseph P., Jr.; Welch, Vanoy C.

    1988-01-01

    A secure voice system STU-3 capable of providing end-to-end secure voice communications (1984) was developed. The terminal for the new system will be built around the standard LPC-10 voice processor algorithm. The performance of the present STU-3 processor is considered to be good, its response to nonspeech sounds such as whistles, coughs and impulse-like noises may not be completely acceptable. Speech in noisy environments also causes problems with the LPC-10 voice algorithm. In addition, there is always a demand for something better. It is hoped that LPC-10's 2.4 kbps voice performance will be complemented with a very high quality speech coder operating at a higher data rate. This new coder is one of a number of candidate algorithms being considered for an upgraded version of the STU-3 in late 1989. The problems of designing a code-excited linear predictive (CELP) coder to provide very high quality speech at a 4.8 kbps data rate that can be implemented on today's hardware are considered.

  2. Liner Optimization Studies Using the Ducted Fan Noise Prediction Code TBIEM3D

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.; Farassat, F.

    1998-01-01

    In this paper we demonstrate the usefulness of the ducted fan noise prediction code TBIEM3D as a liner optimization design tool. Boundary conditions on the interior duct wall allow for hard walls or a locally reacting liner with axially segmented, circumferentially uniform impedance. Two liner optimization studies are considered in which farfield noise attenuation due to the presence of a liner is maximized by adjusting the liner impedance. In the first example, the dependence of optimal liner impedance on frequency and liner length is examined. Results show that both the optimal impedance and attenuation levels are significantly influenced by liner length and frequency. In the second example, TBIEM3D is used to compare radiated sound pressure levels between optimal and non-optimal liner cases at conditions designed to simulate take-off. It is shown that significant noise reduction is achieved for most of the sound field by selecting the optimal or near optimal liner impedance. Our results also indicate that there is relatively large region of the impedance plane over which optimal or near optimal liner behavior is attainable. This is an important conclusion for the designer since there are variations in liner characteristics due to manufacturing imprecisions.

  3. 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.

  4. 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).

  5. 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

  6. 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.

  7. 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…

  8. 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

  9. 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.

  10. Development of Computational Aeroacoustics Code for Jet Noise and Flow Prediction

    NASA Technical Reports Server (NTRS)

    Keith, Theo G., Jr.; Hixon, Duane R.

    2002-01-01

    Accurate prediction of jet fan and exhaust plume flow and noise generation and propagation is very important in developing advanced aircraft engines that will pass current and future noise regulations. In jet fan flows as well as exhaust plumes, two major sources of noise are present: large-scale, coherent instabilities and small-scale turbulent eddies. In previous work for the NASA Glenn Research Center, three strategies have been explored in an effort to computationally predict the noise radiation from supersonic jet exhaust plumes. In order from the least expensive computationally to the most expensive computationally, these are: 1) Linearized Euler equations (LEE). 2) Very Large Eddy Simulations (VLES). 3) Large Eddy Simulations (LES). The first method solves the linearized Euler equations (LEE). These equations are obtained by linearizing about a given mean flow and the neglecting viscous effects. In this way, the noise from large-scale instabilities can be found for a given mean flow. The linearized Euler equations are computationally inexpensive, and have produced good noise results for supersonic jets where the large-scale instability noise dominates, as well as for the tone noise from a jet engine blade row. However, these linear equations do not predict the absolute magnitude of the noise; instead, only the relative magnitude is predicted. Also, the predicted disturbances do not modify the mean flow, removing a physical mechanism by which the amplitude of the disturbance may be controlled. Recent research for isolated airfoils' indicates that this may not affect the solution greatly at low frequencies. The second method addresses some of the concerns raised by the LEE method. In this approach, called Very Large Eddy Simulation (VLES), the unsteady Reynolds averaged Navier-Stokes equations are solved directly using a high-accuracy computational aeroacoustics numerical scheme. With the addition of a two-equation turbulence model and the use of a relatively

  11. 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

  12. Verification of computational aerodynamic predictions for complex hypersonic vehicles using the INCA{trademark} code

    SciTech Connect

    Payne, J.L.; Walker, M.A.

    1995-01-01

    This paper describes a process of combining two state-of-the-art CFD tools, SPRINT and INCA, in a manner which extends the utility of both codes beyond what is possible from either code alone. The speed and efficiency of the PNS code, SPRING, has been combined with the capability of a Navier-Stokes code to model fully elliptic, viscous separated regions on high performance, high speed flight systems. The coupled SPRINT/INCA capability is applicable for design and evaluation of high speed flight vehicles in the supersonic to hypersonic speed regimes. This paper describes the codes involved, the interface process and a few selected test cases which illustrate the SPRINT/INCA coupling process. Results have shown that the combination of SPRINT and INCA produces correct results and can lead to improved computational analyses for complex, three-dimensional problems.

  13. Modification of the PARC Navier-Stokes Code to predict rocket engine nozzle performance

    NASA Technical Reports Server (NTRS)

    Collins, Frank G.; Myruski, Bryan; Orr, Joseph L.

    1990-01-01

    The PARC2D Navier-Stokes Code was modified to compute the performance parameters for rocket engine nozzles. The perfect gas code was applied to the SSME engine nozzle for inviscid, laminar and turbulent flow. Inviscid computations compare well with Rocketdyne computations. Performance degradation due to the boundary layers is very reasonable. Application of the code to nontraditional nozzle geometries and to low Reynolds nozzles is demonstrated. Modification of the code for equilibrium H2/O2 chemistry is described. Thermodynamic and equilibrium constants are determined from statistical mechanics and the transport properties from exact kinetic theory, using collison integrals determined from appropriate intermolecular potentials. The equilibrium code was used to compute the SSME flowfield. Modifications of the flowfield due to the change of composition are described.

  14. 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.

  15. 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.

  16. COSAL: A black-box compressible stability analysis code for transition prediction in three-dimensional boundary layers

    NASA Technical Reports Server (NTRS)

    Malik, M. R.

    1982-01-01

    A fast computer code COSAL for transition prediction in three dimensional boundary layers using compressible stability analysis is described. The compressible stability eigenvalue problem is solved using a finite difference method, and the code is a black box in the sense that no guess of the eigenvalue is required from the user. Several optimization procedures were incorporated into COSAL to calculate integrated growth rates (N factor) for transition correlation for swept and tapered laminar flow control wings using the well known e to the Nth power method. A user's guide to the program is provided.

  17. STGSTK: A computer code for predicting multistage axial flow compressor performance by a meanline stage stacking method

    NASA Technical Reports Server (NTRS)

    Steinke, R. J.

    1982-01-01

    A FORTRAN computer code is presented for off-design performance prediction of axial-flow compressors. Stage and compressor performance is obtained by a stage-stacking method that uses representative velocity diagrams at rotor inlet and outlet meanline radii. The code has options for: (1) direct user input or calculation of nondimensional stage characteristics; (2) adjustment of stage characteristics for off-design speed and blade setting angle; (3) adjustment of rotor deviation angle for off-design conditions; and (4) SI or U.S. customary units. Correlations from experimental data are used to model real flow conditions. Calculations are compared with experimental data.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. The rhythms of predictive coding? Pre-stimulus phase modulates the influence of shape perception on luminance judgments

    PubMed Central

    Han, Biao; VanRullen, Rufin

    2017-01-01

    Predictive coding is an influential model emphasizing interactions between feedforward and feedback signals. Here, we investigated the temporal dynamics of these interactions. Two gray disks with different versions of the same stimulus, one enabling predictive feedback (a 3D-shape) and one impeding it (random-lines), were simultaneously presented on the left and right of fixation. Human subjects judged the luminance of the two disks while EEG was recorded. The choice of 3D-shape or random-lines as the brighter disk was used to assess the influence of feedback signals on sensory processing in each trial (i.e., as a measure of post-stimulus predictive coding efficiency). Independently of the spatial response (left/right), we found that this choice fluctuated along with the pre-stimulus phase of two spontaneous oscillations: a ~5 Hz oscillation in contralateral frontal electrodes and a ~16 Hz oscillation in contralateral occipital electrodes. This pattern of results demonstrates that predictive coding is a rhythmic process, and suggests that it could take advantage of faster oscillations in low-level areas and slower oscillations in high-level areas. PMID:28262824

  7. Euler Technology Assessment for Preliminary Aircraft Design: Compressibility Predictions by Employing the Cartesian Unstructured Grid SPLITFLOW Code

    NASA Technical Reports Server (NTRS)

    Finley, Dennis B.; Karman, Steve L., Jr.

    1996-01-01

    The objective of the second phase of the Euler Technology Assessment program was to evaluate the ability of Euler computational fluid dynamics codes to predict compressible flow effects over a generic fighter wind tunnel model. This portion of the study was conducted by Lockheed Martin Tactical Aircraft Systems, using an in-house Cartesian-grid code called SPLITFLOW. The Cartesian grid technique offers several advantages, including ease of volume grid generation and reduced number of cells compared to other grid schemes. SPLITFLOW also includes grid adaption of the volume grid during the solution to resolve high-gradient regions. The SPLITFLOW code predictions of configuration forces and moments are shown to be adequate for preliminary design, including predictions of sideslip effects and the effects of geometry variations at low and high angles-of-attack. The transonic pressure prediction capabilities of SPLITFLOW are shown to be improved over subsonic comparisons. The time required to generate the results from initial surface data is on the order of several hours, including grid generation, which is compatible with the needs of the design environment.

  8. Using self-similarity compensation for improving inter-layer prediction in scalable 3D holoscopic video coding

    NASA Astrophysics Data System (ADS)

    Conti, Caroline; Nunes, Paulo; Ducla Soares, Luís.

    2013-09-01

    Holoscopic imaging, also known as integral imaging, has been recently attracting the attention of the research community, as a promising glassless 3D technology due to its ability to create a more realistic depth illusion than the current stereoscopic or multiview solutions. However, in order to gradually introduce this technology into the consumer market and to efficiently deliver 3D holoscopic content to end-users, backward compatibility with legacy displays is essential. Consequently, to enable 3D holoscopic content to be delivered and presented on legacy displays, a display scalable 3D holoscopic coding approach is required. Hence, this paper presents a display scalable architecture for 3D holoscopic video coding with a three-layer approach, where each layer represents a different level of display scalability: Layer 0 - a single 2D view; Layer 1 - 3D stereo or multiview; and Layer 2 - the full 3D holoscopic content. In this context, a prediction method is proposed, which combines inter-layer prediction, aiming to exploit the existing redundancy between the multiview and the 3D holoscopic layers, with self-similarity compensated prediction (previously proposed by the authors for non-scalable 3D holoscopic video coding), aiming to exploit the spatial redundancy inherent to the 3D holoscopic enhancement layer. Experimental results show that the proposed combined prediction can improve significantly the rate-distortion performance of scalable 3D holoscopic video coding with respect to the authors' previously proposed solutions, where only inter-layer or only self-similarity prediction is used.

  9. Assessing the Predictive Capability of the LIFEIV Nuclear Fuel Performance Code using Sequential Calibration

    SciTech Connect

    Stull, Christopher J.; Williams, Brian J.; Unal, Cetin

    2012-07-05

    This report considers the problem of calibrating a numerical model to data from an experimental campaign (or series of experimental tests). The issue is that when an experimental campaign is proposed, only the input parameters associated with each experiment are known (i.e. outputs are not known because the experiments have yet to be conducted). Faced with such a situation, it would be beneficial from the standpoint of resource management to carefully consider the sequence in which the experiments are conducted. In this way, the resources available for experimental tests may be allocated in a way that best 'informs' the calibration of the numerical model. To address this concern, the authors propose decomposing the input design space of the experimental campaign into its principal components. Subsequently, the utility (to be explained) of each experimental test to the principal components of the input design space is used to formulate the sequence in which the experimental tests will be used for model calibration purposes. The results reported herein build on those presented and discussed in [1,2] wherein Verification & Validation and Uncertainty Quantification (VU) capabilities were applied to the nuclear fuel performance code LIFEIV. In addition to the raw results from the sequential calibration studies derived from the above, a description of the data within the context of the Predictive Maturity Index (PMI) will also be provided. The PMI [3,4] is a metric initiated and developed at Los Alamos National Laboratory to quantitatively describe the ability of a numerical model to make predictions in the absence of experimental data, where it is noted that 'predictions in the absence of experimental data' is not synonymous with extrapolation. This simply reflects the fact that resources do not exist such that each and every execution of the numerical model can be compared against experimental data. If such resources existed, the justification for numerical models

  10. 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

  11. 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.

  12. Orbitofrontal Cortex Signals Expected Outcomes with Predictive Codes When Stable Contingencies Promote the Integration of Reward History.

    PubMed

    Riceberg, Justin S; Shapiro, Matthew L

    2017-02-22

    Memory can inform goal-directed behavior by linking current opportunities to past outcomes. The orbitofrontal cortex (OFC) may guide value-based responses by integrating the history of stimulus-reward associations into expected outcomes, representations of predicted hedonic value and quality. Alternatively, the OFC may rapidly compute flexible "online" reward predictions by associating stimuli with the latest outcome. OFC neurons develop predictive codes when rats learn to associate arbitrary stimuli with outcomes, but the extent to which predictive coding depends on most recent events and the integrated history of rewards is unclear. To investigate how reward history modulates OFC activity, we recorded OFC ensembles as rats performed spatial discriminations that differed only in the number of rewarded trials between goal reversals. The firing rate of single OFC neurons distinguished identical behaviors guided by different goals. When >20 rewarded trials separated goal switches, OFC ensembles developed stable and anticorrelated population vectors that predicted overall choice accuracy and the goal selected in single trials. When <10 rewarded trials separated goal switches, OFC population vectors decorrelated rapidly after each switch, but did not develop anticorrelated firing patterns or predict choice accuracy. The results show that, whereas OFC signals respond rapidly to contingency changes, they predict choices only when reward history is relatively stable, suggesting that consecutive rewarded episodes are needed for OFC computations that integrate reward history into expected outcomes.SIGNIFICANCE STATEMENT Adapting to changing contingencies and making decisions engages the orbitofrontal cortex (OFC). Previous work shows that OFC function can either improve or impair learning depending on reward stability, suggesting that OFC guides behavior optimally when contingencies apply consistently. The mechanisms that link reward history to OFC computations remain

  13. 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

  14. 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.

  15. Hyperbolic Space Sparse Coding with Its Application on Prediction of Alzheimer’s Disease in Mild Cognitive Impairment

    PubMed Central

    Zhang, Jie; Shi, Jie; Stonnington, Cynthia; Li, Qingyang; Gutman, Boris A.; Chen, Kewei; Reiman, Eric M.; Caselli, Richard J.; Thompson, Paul M.; Ye, Jieping; Wang, Yalin

    2016-01-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal age-related cognitive decline and Alzheimer’s disease (AD). Here we introduce a hyperbolic space sparse coding method to predict impending decline of MCI patients to dementia using surface measures of ventricular enlargement. First, we compute diffeomorphic mappings between ventricular surfaces using a canonical hyperbolic parameter space with consistent boundary conditions and surface tensor-based morphometry is computed to measure local surface deformations. Second, ring-shaped patches of TBM features are selected according to the geometric structure of the hyperbolic parameter space to initialize a dictionary. Sparse coding is then applied on the patch features to learn sparse codes and update the dictionary. Finally, we adopt max-pooling to reduce the feature dimensions and apply Adaboost to predict AD in MCI patients (N = 133) from the Alzheimer’s Disease Neuroimaging Initiative baseline dataset. Our work achieved an accuracy rate of 96.7% and outperformed some other morphometry measures. The hyperbolic space sparse coding method may offer a more sensitive tool to study AD and its early symptom. PMID:28066843

  16. 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.

  17. 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.

  18. A Temporal Predictive Code for Voice Motor Control: Evidence from ERP and Behavioral Responses to Pitch-shifted Auditory Feedback

    PubMed Central

    Behroozmand, Roozbeh; Sangtian, Stacey; Korzyukov, Oleg; Larson, Charles R.

    2016-01-01

    The predictive coding model suggests that voice motor control is regulated by a process in which the mismatch (error) between feedforward predictions and sensory feedback is detected and used to correct vocal motor behavior. In this study, we investigated how predictions about timing of pitch perturbations in voice auditory feedback would modulate ERP and behavioral responses during vocal production. We designed six counterbalanced blocks in which a +100 cents pitch-shift stimulus perturbed voice auditory feedback during vowel sound vocalizations. In three blocks, there was a fixed delay (500, 750 or 1000 ms) between voice and pitch-shift stimulus onset (predictable), whereas in the other three blocks, stimulus onset delay was randomized between 500, 750 and 1000 ms (unpredictable). We found that subjects produced compensatory (opposing) vocal responses that started at 80 ms after the onset of the unpredictable stimuli. However, for predictable stimuli, subjects initiated vocal responses at 20 ms before and followed the direction of pitch shifts in voice feedback. Analysis of ERPs showed that the amplitudes of the N1 and P2 components were significantly reduced in response to predictable compared with unpredictable stimuli. These findings indicate that predictions about temporal features of sensory feedback can modulate vocal motor behavior. In the context of the predictive coding model, temporally-predictable stimuli are learned and reinforced by the internal feedforward system, and as indexed by the ERP suppression, the sensory feedback contribution is reduced for their processing. These findings provide new insights into the neural mechanisms of vocal production and motor control. PMID:26835556

  19. A temporal predictive code for voice motor control: Evidence from ERP and behavioral responses to pitch-shifted auditory feedback.

    PubMed

    Behroozmand, Roozbeh; Sangtian, Stacey; Korzyukov, Oleg; Larson, Charles R

    2016-04-01

    The predictive coding model suggests that voice motor control is regulated by a process in which the mismatch (error) between feedforward predictions and sensory feedback is detected and used to correct vocal motor behavior. In this study, we investigated how predictions about timing of pitch perturbations in voice auditory feedback would modulate ERP and behavioral responses during vocal production. We designed six counterbalanced blocks in which a +100 cents pitch-shift stimulus perturbed voice auditory feedback during vowel sound vocalizations. In three blocks, there was a fixed delay (500, 750 or 1000 ms) between voice and pitch-shift stimulus onset (predictable), whereas in the other three blocks, stimulus onset delay was randomized between 500, 750 and 1000 ms (unpredictable). We found that subjects produced compensatory (opposing) vocal responses that started at 80 ms after the onset of the unpredictable stimuli. However, for predictable stimuli, subjects initiated vocal responses at 20 ms before and followed the direction of pitch shifts in voice feedback. Analysis of ERPs showed that the amplitudes of the N1 and P2 components were significantly reduced in response to predictable compared with unpredictable stimuli. These findings indicate that predictions about temporal features of sensory feedback can modulate vocal motor behavior. In the context of the predictive coding model, temporally-predictable stimuli are learned and reinforced by the internal feedforward system, and as indexed by the ERP suppression, the sensory feedback contribution is reduced for their processing. These findings provide new insights into the neural mechanisms of vocal production and motor control.

  20. A Comparison of the Predictive Capabilities of Several Turbulence Models using Upwind and Central-Difference Computer Codes

    NASA Technical Reports Server (NTRS)

    Rumsey, Christopher L.; Vatsa, Veer N.

    1993-01-01

    Four turbulence models are described and evaluated for transonic flows using the upwind code CFL3D and the central-difference code TLNS3D. In particular, the effects of recent modifications to the half-equation model of Johnson-King are explored in detail, and different versions of the model are compared. This model can obtain good results for both two-dimensional (2D) and three-dimensional (3D) separated flows. The one-equation models of Baldwin-Barth and Spalart-Allmaras perform well for separated airfoil flows, but can predict the shock too far forward at the outboard stations of a separated wing. The equilibrium model of Baldwin-Lomax predicts the shock location too far aft for both 2D and 3D separated flows, as expected. In general, all models perform well for attached or mildly separated flows.

  1. A comparison of the predictive capabilities of several turbulence models using upwind and central-difference computer codes

    NASA Technical Reports Server (NTRS)

    Rumsey, Christopher L.; Vatsa, Veer N.

    1993-01-01

    Four turbulence models are described and evaluated for transonic flows using the upwind code CFL3D and the central-difference code TLNS3D. In particular, the effects of recent modifications to the half-equation model of Johnson-King are explored in detail, and different versions of the model are compared. This model can obtain good results for both two-dimensional (2D) and three-dimensional (3D) separated flows. The one-equation models of Baldwin-Barth and Spalart-Allmaras perform well for separated airfoil flows, but can predict the shock too far forward at the outboard stations of a separated wing. The equilibrium model of Baldwin-Lomax predicts the shock location too far aft for both 2D and 3D separated flows, as expected. In general, all models perform well for attached or mildly separated flows.

  2. Development of a Mathematical Code to Predict Thermal Degradation of Fuel and Deposit Formation in a Fuel System

    DTIC Science & Technology

    1990-09-01

    MDTCAP 5,7 7 0A DCLML",," pROCESSING SHEIET srx is 5X.!iiACSTD AD- A225 415 WRDC-TR-90-2084 DEVELOPMENT OF A MATHEMATICAL CODE TO PREDICT THERMAL...R. (1983) "Studies of the Mechanism of Turbine Fuel Instability," Colorado School of Mines, NASA CR -167963. Daniel, S. R. (1985) "Jet Fuel Instability

  3. Predictive Calculation of Neutral Beam Heating Plasmas in EAST Tokamak by NUBEAM Code for Certain Parameter Ranges

    NASA Astrophysics Data System (ADS)

    Ni, Qionglin; Fan, Tieshuan; Zhang, Xing; Zhang, Cheng; Ren, Qilong; Hu, Chundong

    2010-12-01

    A predictive calculation is carried out for neutral beam heating of fusion plasmas in EAST by using NUBEAM code under certain plasma conditions. Results calculated are analyzed for different plasma parameters. Relations between major plasma parameters, such as density and temperature, are obtained and key physical processes in the neutral beam heating, including beam power deposition, trapped fraction, heating efficiency, and power loss, are simulated. Other physical processes, such as current-drive, toroidal rotation and neutron emission, are also discussed.

  4. 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

  5. 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

  6. 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

  7. 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…

  8. 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.

  9. 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.

  10. 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

  11. The expression level of small non-coding RNAs derived from the first exon of protein-coding genes is predictive of cancer status.

    PubMed

    Zovoilis, Athanasios; Mungall, Andrew J; Moore, Richard; Varhol, Richard; Chu, Andy; Wong, Tina; Marra, Marco; Jones, Steven J M

    2014-04-01

    Small non-coding RNAs (smRNAs) are known to be significantly enriched near the transcriptional start sites of genes. However, the functional relevance of these smRNAs remains unclear, and they have not been associated with human disease. Within the cancer genome atlas project (TCGA), we have generated small RNA datasets for many tumor types. In prior cancer studies, these RNAs have been regarded as transcriptional "noise," due to their apparent chaotic distribution. In contrast, we demonstrate their striking potential to distinguish efficiently between cancer and normal tissues and classify patients with cancer to subgroups of distinct survival outcomes. This potential to predict cancer status is restricted to a subset of these smRNAs, which is encoded within the first exon of genes, highly enriched within CpG islands and negatively correlated with DNA methylation levels. Thus, our data show that genome-wide changes in the expression levels of small non-coding RNAs within first exons are associated with cancer.

  12. Code requirements document: MODFLOW 2. 1: A program for predicting moderator flow patterns

    SciTech Connect

    Peterson, P.F. . Dept. of Nuclear Engineering); Paik, I.K. )

    1992-03-01

    Sudden changes in the temperature of flowing liquids can result in transient buoyancy forces which strongly impact the flow hydrodynamics via flow stratification. These effects have been studied for the case of potential flow of stratified liquids to line sinks, but not for moderator flow in SRS reactors. Standard codes, such as TRAC and COMMIX, do not have the capability to capture the stratification effect, due to strong numerical diffusion which smears away the hot/cold fluid interface. A related problem with standard codes is the inability to track plumes injected into the liquid flow, again due to numerical diffusion. The combined effects of buoyant stratification and plume dispersion have been identified as being important in operation of the Supplementary Safety System which injects neutron-poison ink into SRS reactors to provide safe shutdown in the event of safety rod failure. The MODFLOW code discussed here provides transient moderator flow pattern information with stratification effects, and tracks the location of ink plumes in the reactor. The code, written in Fortran, is compiled for Macintosh II computers, and includes subroutines for interactive control and graphical output. Removing the graphics capabilities, the code can also be compiled on other computers. With graphics, in addition to the capability to perform safety related computations, MODFLOW also provides an easy tool for becoming familiar with flow distributions in SRS reactors.

  13. Code requirements document: MODFLOW 2.1: A program for predicting moderator flow patterns

    SciTech Connect

    Peterson, P.F.; Paik, I.K.

    1992-03-01

    Sudden changes in the temperature of flowing liquids can result in transient buoyancy forces which strongly impact the flow hydrodynamics via flow stratification. These effects have been studied for the case of potential flow of stratified liquids to line sinks, but not for moderator flow in SRS reactors. Standard codes, such as TRAC and COMMIX, do not have the capability to capture the stratification effect, due to strong numerical diffusion which smears away the hot/cold fluid interface. A related problem with standard codes is the inability to track plumes injected into the liquid flow, again due to numerical diffusion. The combined effects of buoyant stratification and plume dispersion have been identified as being important in operation of the Supplementary Safety System which injects neutron-poison ink into SRS reactors to provide safe shutdown in the event of safety rod failure. The MODFLOW code discussed here provides transient moderator flow pattern information with stratification effects, and tracks the location of ink plumes in the reactor. The code, written in Fortran, is compiled for Macintosh II computers, and includes subroutines for interactive control and graphical output. Removing the graphics capabilities, the code can also be compiled on other computers. With graphics, in addition to the capability to perform safety related computations, MODFLOW also provides an easy tool for becoming familiar with flow distributions in SRS reactors.

  14. 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).

  15. 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

  16. Validation of the ASSERT subchannel code: Prediction of critical heat flux in standard and nonstandard CANDU bundle geometries

    SciTech Connect

    Carver, M.B.; Kiteley, J.C.; Zhou, R.Q.N.; Junop, S.V.; Rowe, D.S.

    1995-12-01

    The ASSERT code has been developed to address the three-dimensional computation of flow and phase distribution and fuel element surface temperatures within the horizontal subchannels of Canada uranium deuterium (CANDU) pressurized heavy water reactor fuel channels and to provide a detailed prediction of critical heat flux (CHF) distribution throughout the bundle. The ASSERT subchannel code has been validated extensively against a wide repertoire of experiments; its combination of three-dimensional prediction of local flow conditions with a comprehensive method of predicting CHF at these local conditions makes it a unique tool for predicting CHF for situations outside the existing experimental database. In particular, ASSERT is an appropriate tool to systematically investigate CHF under conditions of local geometric variations, such as pressure tube creep and fuel element strain. The numerical methodology used in ASSERT, the constitutive relationships incorporated, and the CHF assessment methodology are discussed. The evolutionary validation plan is also discussed and early validation exercises are summarized. More recent validation exercises in standard and nonstandard geometries are emphasized.

  17. Connectivity Reveals Sources of Predictive Coding Signals in Early Visual Cortex During Processing of Visual Optic Flow.

    PubMed

    Schindler, Andreas; Bartels, Andreas

    2016-05-24

    Superimposed on the visual feed-forward pathway, feedback connections convey higher level information to cortical areas lower in the hierarchy. A prominent framework for these connections is the theory of predictive coding where high-level areas send stimulus interpretations to lower level areas that compare them with sensory input. Along these lines, a growing body of neuroimaging studies shows that predictable stimuli lead to reduced blood oxygen level-dependent (BOLD) responses compared with matched nonpredictable counterparts, especially in early visual cortex (EVC) including areas V1-V3. The sources of these modulatory feedback signals are largely unknown. Here, we re-examined the robust finding of relative BOLD suppression in EVC evident during processing of coherent compared with random motion. Using functional connectivity analysis, we show an optic flow-dependent increase of functional connectivity between BOLD suppressed EVC and a network of visual motion areas including MST, V3A, V6, the cingulate sulcus visual area (CSv), and precuneus (Pc). Connectivity decreased between EVC and 2 areas known to encode heading direction: entorhinal cortex (EC) and retrosplenial cortex (RSC). Our results provide first evidence that BOLD suppression in EVC for predictable stimuli is indeed mediated by specific high-level areas, in accord with the theory of predictive coding.

  18. 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.

  19. 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

  20. 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

  1. A new code for predicting the thermo-mechanical and irradiation behavior of metallic fuels in sodium fast reactors

    NASA Astrophysics Data System (ADS)

    Karahan, Aydın; Buongiorno, Jacopo

    2010-01-01

    An engineering code to predict the irradiation behavior of U-Zr and U-Pu-Zr metallic alloy fuel pins and UO2-PuO2 mixed oxide fuel pins in sodium-cooled fast reactors was developed. The code was named Fuel Engineering and Structural analysis Tool (FEAST). FEAST has several modules working in coupled form with an explicit numerical algorithm. These modules describe fission gas release and fuel swelling, fuel chemistry and restructuring, temperature distribution, fuel-clad chemical interaction, and fuel and clad mechanical analysis including transient creep-fracture for the clad. Given the fuel pin geometry, composition and irradiation history, FEAST can analyze fuel and clad thermo-mechanical behavior at both steady-state and design-basis (non-disruptive) transient scenarios. FEAST was written in FORTRAN-90 and has a simple input file similar to that of the LWR fuel code FRAPCON. The metal-fuel version is called FEAST-METAL, and is described in this paper. The oxide-fuel version, FEAST-OXIDE is described in a companion paper. With respect to the old Argonne National Laboratory code LIFE-METAL and other same-generation codes, FEAST-METAL emphasizes more mechanistic, less empirical models, whenever available. Specifically, fission gas release and swelling are modeled with the GRSIS algorithm, which is based on detailed tracking of fission gas bubbles within the metal fuel. Migration of the fuel constituents is modeled by means of thermo-transport theory. Fuel-clad chemical interaction models based on precipitation kinetics were developed for steady-state operation and transients. Finally, a transient intergranular creep-fracture model for the clad, which tracks the nucleation and growth of the cavities at the grain boundaries, was developed for and implemented in the code. Reducing the empiricism in the constitutive models should make it more acceptable to extrapolate FEAST-METAL to new fuel compositions and higher burnup, as envisioned in advanced sodium reactors

  2. 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.

  3. 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.

  4. Prediction of dryout performance for boiling water reactor fuel assemblies based on subchannel analysis with the RINGS code

    SciTech Connect

    Knabe, P.; Wehle, F.

    1995-12-01

    A fuel assembly with a large critical power margin introduces flexibility into reload fuel management. Therefore, optimization of the bundle and spacer geometry to maximize the bundle critical power is an important design objective. With a view to reducing the extent of the complex full-scale tests usually carried out to determine the thermal-hydraulic characteristics of various assembly geometries, the subchannel analysis method was further developed with the Siemens RINGS code. The annular flow code predicts dryout power and dryout location by calculating the conditions at which the liquid film flow rate is reduced to zero, allowing for evaporation, droplet entrainment, and droplet deposition. Appropriate attention is paid to the modeling of spacer effects. Comparison with experimental data of 3 x 3 and 4 x 4 tests shows the capability of RINGS to predict the flow quality and mass flux in subchannels under typical boiling water reactor operating conditions. By using the RINGS code, experimental critical power data for 3 x 3, 4 x 4, 5 x 5, 7 x 7, 8 x 8, 9 x 9, and 10 x 10 fuel assemblies were successfully postcalculated.

  5. Lifting scheme-based method for joint coding 3D stereo digital cinema with luminace correction and optimized prediction

    NASA Astrophysics Data System (ADS)

    Darazi, R.; Gouze, A.; Macq, B.

    2009-01-01

    Reproducing a natural and real scene as we see in the real world everyday is becoming more and more popular. Stereoscopic and multi-view techniques are used for this end. However due to the fact that more information are displayed requires supporting technologies such as digital compression to ensure the storage and transmission of the sequences. In this paper, a new scheme for stereo image coding is proposed. The original left and right images are jointly coded. The main idea is to optimally exploit the existing correlation between the two images. This is done by the design of an efficient transform that reduces the existing redundancy in the stereo image pair. This approach was inspired by Lifting Scheme (LS). The novelty in our work is that the prediction step is been replaced by an hybrid step that consists in disparity compensation followed by luminance correction and an optimized prediction step. The proposed scheme can be used for lossless and for lossy coding. Experimental results show improvement in terms of performance and complexity compared to recently proposed methods.

  6. Lossless image compression based on optimal prediction, adaptive lifting, and conditional arithmetic coding.

    PubMed

    Boulgouris, N V; Tzovaras, D; Strintzis, M G

    2001-01-01

    The optimal predictors of a lifting scheme in the general n-dimensional case are obtained and applied for the lossless compression of still images using first quincunx sampling and then simple row-column sampling. In each case, the efficiency of the linear predictors is enhanced nonlinearly. Directional postprocessing is used in the quincunx case, and adaptive-length postprocessing in the row-column case. Both methods are seen to perform well. The resulting nonlinear interpolation schemes achieve extremely efficient image decorrelation. We further investigate context modeling and adaptive arithmetic coding of wavelet coefficients in a lossless compression framework. Special attention is given to the modeling contexts and the adaptation of the arithmetic coder to the actual data. Experimental evaluation shows that the best of the resulting coders produces better results than other known algorithms for multiresolution-based lossless image coding.

  7. A general code to predict the drug release kinetics from different shaped matrices.

    PubMed

    Barba, Anna Angela; d'Amore, Matteo; Chirico, Serafina; Lamberti, Gaetano; Titomanlio, Giuseppe

    2009-02-15

    This work deals with the modeling of drug release from solid pharmaceutical systems (matrices) for oral delivery. The attention was paid to the behavior of matrices made of hydrogels and drug, and the modeling was devoted to reproduce all the relevant phenomena (water up-take, gel swelling, diffusivity increase, drug diffusion and polymer erosion). Thus, the transient mass balances (for both drug and water), with the proper initial and boundary conditions were written, and a generalized numerical code was formulated; it is able to describe several geometries (slab, sphere, infinite and finite cylinders; this latter was done by an approximation which reduces the 2D problem to an 1D scheme). The main phenomena observed in drug delivery from hydrogel-based matrix, i.e. polymer swelling and erosion, were taken into account. The code was validated by comparison with analytical solutions, available for some simplified situation, and then it was tested with some experimental data taken from literature.

  8. WINCOF-I code for prediction of fan compressor unit with water ingestion

    NASA Technical Reports Server (NTRS)

    Murthy, S. N. B.; Mullican, A.

    1990-01-01

    The PURDUE-WINCOF code, which provides a numerical method of obtaining the performance of a fan-compressor unit of a jet engine with water ingestion into the inlet, was modified to take into account: (1) the scoop factor, (2) the time required for the setting-in of a quasi-steady distribution of water, and (3) the heat and mass transfer processes over the time calculated under 2. The modified code, named WINCOF-I was utilized to obtain the performance of a fan-compressor unit of a generic jet engine. The results illustrate the manner in which quasi-equilibrium conditions become established in the machine and the redistribution of ingested water in various stages in the form of a film out of the casing wall, droplets across the span, and vapor due to mass transfer.

  9. RCS Predictions From a Method of Moments and a Finite-Element Code for Several Targets

    DTIC Science & Technology

    2010-07-01

    01803 14. ABSTRACT This report presents results of radar cross section (RCS) calculations for several interesting targets using a method-of-moments...TERMS radar cross section, method of moments, finite element, modeling 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18... radar cross section (RCS) simulation that require an exact code for solution. In this report, we compare RCS calculations with two very different

  10. Flexible Radiation Codes for Numerical Weather Prediction Across Space and Time Scales

    DTIC Science & Technology

    2013-09-30

    time and space scales, especially from regional models to global models. OBJECTIVES We are adapting radiation codes developed for climate ...PSrad is now complete, thorougly tested and debugged, is functioning as the radiation scheme in the climate model ECHAM 6.2 developed at the Max Planck...statiically significant change at most stations, indicating that errors in most places are not primarily driven by radiation errors. We are working

  11. Predictive Fallout Composition Modeling: Improvements and Applications of the Defense Land Fallout Interpretive Code

    SciTech Connect

    Hooper, David A; Jodoin, Vincent J; Lee, Ronald W; Monterial, Mateusz

    2012-01-01

    This paper outlines several improvements to the Particle Activity Module of the Defense Land Fallout Interpretive Code (DELFIC). The modeling of each phase of the fallout process is discussed within DELFIC to demonstrate the capabilities and limitations with the code for modeling and simulation. Expansion of the DELFIC isotopic library to include actinides and light elements is shown. Several key features of the new library are demonstrated, including compliance with ENDF/B-VII standards, augmentation of hardwired activated soil and actinide decay calculations with exact Bateman calculations, and full physical and chemical fractionation of all material inventories. Improvements to the radionuclide source term are demonstrated, including the ability to specify heterogeneous fission types and the ability to import source terms from irradiation calculations using the Oak Ridge Isotope Generation (ORIGEN) code. Additionally, the dose, kerma, and effective dose conversion factors are revised. Finally, the application of DELFIC for consequence management planning and forensic analysis is presented. For consequence management, DELFIC is shown to provide disaster recovery teams with simulations of real-time events, including the location, composition, time of arrival, activity rates, and dose rates of fallout, accounting for site-specific atmospheric effects. The results from DELFIC are also demonstrated for use by nuclear forensics teams to plan collection routes (including the determination of optimal collection locations), estimate dose rates to collectors, and anticipate the composition of material at collection sites. These capabilities give mission planners the ability to maximize their effectiveness in the field while minimizing risk to their collectors.

  12. Improved NASA-ANOPP Noise Prediction Computer Code for Advanced Subsonic Propulsion Systems

    NASA Technical Reports Server (NTRS)

    Kontos, K. B.; Janardan, B. A.; Gliebe, P. R.

    1996-01-01

    Recent experience using ANOPP to predict turbofan engine flyover noise suggests that it over-predicts overall EPNL by a significant amount. An improvement in this prediction method is desired for system optimization and assessment studies of advanced UHB engines. An assessment of the ANOPP fan inlet, fan exhaust, jet, combustor, and turbine noise prediction methods is made using static engine component noise data from the CF6-8OC2, E(3), and QCSEE turbofan engines. It is shown that the ANOPP prediction results are generally higher than the measured GE data, and that the inlet noise prediction method (Heidmann method) is the most significant source of this overprediction. Fan noise spectral comparisons show that improvements to the fan tone, broadband, and combination tone noise models are required to yield results that more closely simulate the GE data. Suggested changes that yield improved fan noise predictions but preserve the Heidmann model structure are identified and described. These changes are based on the sets of engine data mentioned, as well as some CFM56 engine data that was used to expand the combination tone noise database. It should be noted that the recommended changes are based on an analysis of engines that are limited to single stage fans with design tip relative Mach numbers greater than one.

  13. Temporal Uncertainty and Temporal Estimation Errors Affect Insular Activity and the Frontostriatal Indirect Pathway during Action Update: A Predictive Coding Study

    PubMed Central

    Limongi, Roberto; Pérez, Francisco J.; Modroño, Cristián; González-Mora, José L.

    2016-01-01

    Action update, substituting a prepotent behavior with a new action, allows the organism to counteract surprising environmental demands. However, action update fails when the organism is uncertain about when to release the substituting behavior, when it faces temporal uncertainty. Predictive coding states that accurate perception demands minimization of precise prediction errors. Activity of the right anterior insula (rAI) is associated with temporal uncertainty. Therefore, we hypothesize that temporal uncertainty during action update would cause the AI to decrease the sensitivity to ascending prediction errors. Moreover, action update requires response inhibition which recruits the frontostriatal indirect pathway associated with motor control. Therefore, we also hypothesize that temporal estimation errors modulate frontostriatal connections. To test these hypotheses, we collected fMRI data when participants performed an action-update paradigm within the context of temporal estimation. We fit dynamic causal models to the imaging data. Competing models comprised the inferior occipital gyrus (IOG), right supramarginal gyrus (rSMG), rAI, right presupplementary motor area (rPreSMA), and the right striatum (rSTR). The winning model showed that temporal uncertainty drove activity into the rAI and decreased insular sensitivity to ascending prediction errors, as shown by weak connectivity strength of rSMG→rAI connections. Moreover, temporal estimation errors weakened rPreSMA→rSTR connections and also modulated rAI→rSTR connections, causing the disruption of action update. Results provide information about the neurophysiological implementation of the so-called horse-race model of action control. We suggest that, contrary to what might be believed, unsuccessful action update could be a homeostatic process that represents a Bayes optimal encoding of uncertainty. PMID:27445737

  14. Temporal Uncertainty and Temporal Estimation Errors Affect Insular Activity and the Frontostriatal Indirect Pathway during Action Update: A Predictive Coding Study.

    PubMed

    Limongi, Roberto; Pérez, Francisco J; Modroño, Cristián; González-Mora, José L

    2016-01-01

    Action update, substituting a prepotent behavior with a new action, allows the organism to counteract surprising environmental demands. However, action update fails when the organism is uncertain about when to release the substituting behavior, when it faces temporal uncertainty. Predictive coding states that accurate perception demands minimization of precise prediction errors. Activity of the right anterior insula (rAI) is associated with temporal uncertainty. Therefore, we hypothesize that temporal uncertainty during action update would cause the AI to decrease the sensitivity to ascending prediction errors. Moreover, action update requires response inhibition which recruits the frontostriatal indirect pathway associated with motor control. Therefore, we also hypothesize that temporal estimation errors modulate frontostriatal connections. To test these hypotheses, we collected fMRI data when participants performed an action-update paradigm within the context of temporal estimation. We fit dynamic causal models to the imaging data. Competing models comprised the inferior occipital gyrus (IOG), right supramarginal gyrus (rSMG), rAI, right presupplementary motor area (rPreSMA), and the right striatum (rSTR). The winning model showed that temporal uncertainty drove activity into the rAI and decreased insular sensitivity to ascending prediction errors, as shown by weak connectivity strength of rSMG→rAI connections. Moreover, temporal estimation errors weakened rPreSMA→rSTR connections and also modulated rAI→rSTR connections, causing the disruption of action update. Results provide information about the neurophysiological implementation of the so-called horse-race model of action control. We suggest that, contrary to what might be believed, unsuccessful action update could be a homeostatic process that represents a Bayes optimal encoding of uncertainty.

  15. 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

  16. 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.

  17. Diagnostic Coding for Epilepsy.

    PubMed

    Williams, Korwyn; Nuwer, Marc R; Buchhalter, Jeffrey R

    2016-02-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  18. Small Engine Technology (SET) Task 23 ANOPP Noise Prediction for Small Engines, Wing Reflection Code

    NASA Technical Reports Server (NTRS)

    Lieber, Lysbeth; Brown, Daniel; Golub, Robert A. (Technical Monitor)

    2000-01-01

    The work performed under Task 23 consisted of the development and demonstration of improvements for the NASA Aircraft Noise Prediction Program (ANOPP), specifically targeted to the modeling of engine noise enhancement due to wing reflection. This report focuses on development of the model and procedure to predict the effects of wing reflection, and the demonstration of the procedure, using a representative wing/engine configuration.

  19. Truncation Depth Rule-of-Thumb for Convolutional Codes

    NASA Technical Reports Server (NTRS)

    Moision, Bruce

    2009-01-01

    In this innovation, it is shown that a commonly used rule of thumb (that the truncation depth of a convolutional code should be five times the memory length, m, of the code) is accurate only for rate 1/2 codes. In fact, the truncation depth should be 2.5 m/(1 - r), where r is the code rate. The accuracy of this new rule is demonstrated by tabulating the distance properties of a large set of known codes. This new rule was derived by bounding the losses due to truncation as a function of the code rate. With regard to particular codes, a good indicator of the required truncation depth is the path length at which all paths that diverge from a particular path have accumulated the minimum distance of the code. It is shown that the new rule of thumb provides an accurate prediction of this depth for codes of varying rates.

  20. Issues in Automatic Object Recognition: Linking Geometry and Material Data to Predictive Signature Codes

    DTIC Science & Technology

    1991-03-01

    dirbuild() opens the databse -file and builds the in-core database table of contents. rt-gettree0 adds a database sub-tree to the active model space, and...and- Chemical 7.mmand ATTN: SMCAR-ESP-L I Dir, VLAMO Rock Island, IL 61299-5000 ATTN: AMSLC-VL-D Director 10 Dir, BRL U.S. Army Aviation Research ATTN...Center ATTN: Louis E. Smith ATTN: Dr. Paul C. St. Hilaire University Park -Code 1210 Denver, CO 80208 Bethesda, MD 20084-5000 1 Dow Chemical , U.S.A

  1. Monitoring Cosmic Radiation Risk: Comparisons between Observations and Predictive Codes for Naval Aviation

    DTIC Science & Technology

    2009-01-01

    various materials can be found by use of the SRIM code [17]. F. Pions/Muons The pion, originally referred to as the π meson , was one of the earliest...These are the lightest mesons and have a very short half- life. In atmospheric interactions, they help produce muons and neutrinos [17]. The π+ is...keV/micron High Varies Pions Mesons π0 π+ π- π+,- : +-e π0 : 0 ᝺ keV/micron Low π+,- : 2.6x10-8 π0 : 0.84x10-16 Muons Leptons μ- μ+ +1, -1 ᝺

  2. Monitoring Cosmic Radiation Risk: Comparisons Between Observations and Predictive Codes for Naval Aviation

    DTIC Science & Technology

    2009-07-05

    materials can be found by use of the SRIM code [17]. F. Pions/Muons The pion, originally referred to as the π meson , was one of the earliest...These are the lightest mesons and have a very short half- life. In atmospheric interactions, they help produce muons and neutrinos [17]. The π+ is...micron High Varies Pions Mesons π0 π+ π- π+,- : +-e π0 : 0 ᝺ keV/micron Low π+,- : 2.6x10-8 π0 : 0.84x10-16 Muons Leptons μ- μ+ +1, -1 ᝺ keV

  3. 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

  4. 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

  5. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation

    PubMed Central

    Raj, Towfique; McGeachie, Michael J.; Qiu, Weiliang; Ziniti, John P.; Stubbs, Benjamin J.; Liang, Liming; Martinez, Fernando D.; Strunk, Robert C.; Lemanske, Robert F.; Liu, Andrew H.; Stranger, Barbara E.; Carey, Vincent J.; Raby, Benjamin A.

    2015-01-01

    Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial efforts to develop a predictive model of disease-associated variants leveraging eQTL information. We first catalogued cis-acting eQTLs (SNPs within 100kb of target gene transcripts) by meta-analyzing four studies of three blood-derived tissues (n = 586). At a false discovery rate < 5%, we mapped eQTLs for 6,535 genes; these were enriched for disease-associated genes (P < 10−04), particularly those related to immune diseases and metabolic traits. Based on eQTL information and other variant annotations (distance from target gene transcript, minor allele frequency, and chromatin state), we created multivariate logistic regression models to predict SNP membership in reported GWAS. The complete model revealed independent contributions of specific annotations as strong predictors, including evidence for an eQTL (odds ratio (OR) = 1.2–2.0, P < 10−11) and the chromatin states of active promoters, different classes of strong or weak enhancers, or transcriptionally active regions (OR = 1.5–2.3, P < 10−11). This complete prediction model including eQTL association information ultimately allowed for better discrimination of SNPs with higher probabilities of GWAS membership (6.3–10.0%, compared to 3.5% for a random SNP) than the other two models excluding eQTL information. This eQTL-based prediction model of disease relevance can help systematically prioritize non-coding GWAS SNPs for further functional characterization. PMID:26474488

  6. Predicting CYP2C19 catalytic parameters for enantioselective oxidations using artificial neural networks and a chirality code.

    PubMed

    Hartman, Jessica H; Cothren, Steven D; Park, Sun-Ha; Yun, Chul-Ho; Darsey, Jerry A; Miller, Grover P

    2013-07-01

    Cytochromes P450 (CYP for isoforms) play a central role in biological processes especially metabolism of chiral molecules; thus, development of computational methods to predict parameters for chiral reactions is important for advancing this field. In this study, we identified the most optimal artificial neural networks using conformation-independent chirality codes to predict CYP2C19 catalytic parameters for enantioselective reactions. Optimization of the neural networks required identifying the most suitable representation of structure among a diverse array of training substrates, normalizing distribution of the corresponding catalytic parameters (k(cat), K(m), and k(cat)/K(m)), and determining the best topology for networks to make predictions. Among different structural descriptors, the use of partial atomic charges according to the CHelpG scheme and inclusion of hydrogens yielded the most optimal artificial neural networks. Their training also required resolution of poorly distributed output catalytic parameters using a Box-Cox transformation. End point leave-one-out cross correlations of the best neural networks revealed that predictions for individual catalytic parameters (k(cat) and K(m)) were more consistent with experimental values than those for catalytic efficiency (k(cat)/K(m)). Lastly, neural networks predicted correctly enantioselectivity and comparable catalytic parameters measured in this study for previously uncharacterized CYP2C19 substrates, R- and S-propranolol. Taken together, these seminal computational studies for CYP2C19 are the first to predict all catalytic parameters for enantioselective reactions using artificial neural networks and thus provide a foundation for expanding the prediction of cytochrome P450 reactions to chiral drugs, pollutants, and other biologically active compounds.

  7. Assessment of a 3-D boundary layer code to predict heat transfer and flow losses in a turbine

    NASA Technical Reports Server (NTRS)

    Vatsa, V. N.

    1983-01-01

    The prediction of the complete flow field in a turbine passage is an extremely difficult task due to the complex three dimensional pattern which contains separation and attachment lines, a saddle point and horseshoe vortex. Whereas, in principle such a problem can be solved using full Navier-Stokes equations, in reality methods based on a Navier-Stokes solution procedure encounter difficulty in accurately predicting surface quantities (e.g., heat transfer) due to grid limitations imposed by the speed and size of the existing computers. On the other hand the overall problem is strongly three dimensional and too complex to be analyzed by the current design methods based on inviscid and/or viscous strip theories. Thus there is a strong need for enhancing the current prediction techniques through inclusion of 3-D viscous effects. A potentially simple and cost effective way to achieve this is to use a prediction method based on three dimensional boundary layer (3-DBL) theory. The major objective of this program is to assess the applicability of such a 3-DBL approach for the prediction of heat loads, boundary layer growth, pressure losses and streamline skewing in critical areas of a turbine passage. A brief discussion of the physical problem addressed here along with the overall approach is presented.

  8. 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

  9. Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

    NASA Astrophysics Data System (ADS)

    Yu, Jia-Feng; Sui, Tian-Xiang; Wang, Hong-Mei; Wang, Chun-Ling; Jing, Li; Wang, Ji-Hua

    2015-12-01

    Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, t