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Sample records for formation predictability maps

  1. RESIDUA UPGRADING EFFICIENCY IMPROVEMENT MODELS: COKE FORMATION PREDICTABILITY MAPS

    SciTech Connect

    John F. Schabron; A. Troy Pauli; Joseph F. Rovani Jr.

    2002-05-01

    The dispersed particle solution model of petroleum residua structure was used to develop predictors for pyrolytic coke formation. Coking Indexes were developed in prior years that measure how near a pyrolysis system is to coke formation during the coke formation induction period. These have been demonstrated to be universally applicable for residua regardless of the source of the material. Coking onset is coincidental with the destruction of the ordered structure and the formation of a multiphase system. The amount of coke initially formed appears to be a function of the free solvent volume of the original residua. In the current work, three-dimensional coke make predictability maps were developed at 400 C, 450 C, and 500 C (752 F, 842 F, and 932 F). These relate residence time and free solvent volume to the amount of coke formed at a particular pyrolysis temperature. Activation energies for two apparent types of zero-order coke formation reactions were estimated. The results provide a new tool for ranking residua, gauging proximity to coke formation, and predicting initial coke make tendencies.

  2. Compressor map prediction tool

    NASA Astrophysics Data System (ADS)

    Ravi, Arjun; Sznajder, Lukasz; Bennett, Ian

    2015-08-01

    Shell Global Solutions uses an in-house developed system for remote condition monitoring of centrifugal compressors. It requires field process data collected during operation to calculate and assess the machine's performance. Performance is assessed by comparing live results of polytropic head and efficiency versus design compressor curves provided by the Manufacturer. Typically, these design curves are given for specific suction conditions. The further these conditions on site deviate from those prescribed at design, the less accurate the health assessment of the compressor becomes. To address this specified problem, a compressor map prediction tool is proposed. The original performance curves of polytropic head against volumetric flow for varying rotational speeds are used as an input to define a range of Mach numbers within which the non-dimensional invariant performance curve of head and volume flow coefficient is generated. The new performance curves of polytropic head vs. flow for desired set of inlet conditions are then back calculated using the invariant non-dimensional curve. Within the range of Mach numbers calculated from design data, the proposed methodology can predict polytropic head curves at a new set of inlet conditions within an estimated 3% accuracy. The presented methodology does not require knowledge of detailed impeller geometry such as throat areas, blade number, blade angles, thicknesses nor other aspects of the aerodynamic design - diffusion levels, flow angles, etc. The only required mechanical design feature is the first impeller tip diameter. Described method makes centrifugal compressor surveillance activities more accurate, enabling precise problem isolation affecting machine's performance.

  3. Star Formation for Predictive Primordial Galaxy Formation

    NASA Astrophysics Data System (ADS)

    Milosavljević, Miloš; Safranek-Shrader, Chalence

    The elegance of inflationary cosmology and cosmological perturbation theory ends with the formation of the first stars and galaxies, the initial sources of light that launched the phenomenologically rich process of cosmic reionization. Here we review the current understanding of early star formation, emphasizing unsolved problems and technical challenges. We begin with the first generation of stars to form after the Big Bang and trace how they influenced subsequent star formation. The onset of chemical enrichment coincided with a sharp increase in the overall physical complexity of star forming systems. Ab-initio computational treatments are just now entering the domain of the predictive and are establishing contact with local observations of the relics of this ancient epoch.

  4. Motion Predicts Clinical Callus Formation

    PubMed Central

    Elkins, Jacob; Marsh, J. Lawrence; Lujan, Trevor; Peindl, Richard; Kellam, James; Anderson, Donald D.; Lack, William

    2016-01-01

    Background: Mechanotransduction is theorized to influence fracture-healing, but optimal fracture-site motion is poorly defined. We hypothesized that three-dimensional (3-D) fracture-site motion as estimated by finite element (FE) analysis would influence callus formation for a clinical series of supracondylar femoral fractures treated with locking-plate fixation. Methods: Construct-specific FE modeling simulated 3-D fracture-site motion for sixty-six supracondylar femoral fractures (OTA/AO classification of 33A or 33C) treated at a single institution. Construct stiffness and directional motion through the fracture were investigated to assess the validity of construct stiffness as a surrogate measure of 3-D motion at the fracture site. Callus formation was assessed radiographically for all patients at six, twelve, and twenty-four weeks postoperatively. Univariate and multivariate linear regression analyses examined the effects of longitudinal motion, shear (transverse motion), open fracture, smoking, and diabetes on callus formation. Construct types were compared to determine whether their 3-D motion profile was associated with callus formation. Results: Shear disproportionately increased relative to longitudinal motion with increasing bridge span, which was not predicted by our assessment of construct stiffness alone. Callus formation was not associated with open fracture, smoking, or diabetes at six, twelve, or twenty-four weeks. However, callus formation was associated with 3-D fracture-site motion at twelve and twenty-four weeks. Longitudinal motion promoted callus formation at twelve and twenty-four weeks (p = 0.017 for both). Shear inhibited callus formation at twelve and twenty-four weeks (p = 0.017 and p = 0.022, respectively). Titanium constructs with a short bridge span demonstrated greater longitudinal motion with less shear than did the other constructs, and this was associated with greater callus formation (p < 0.001). Conclusions: In this study of

  5. Kernel-Based Equiprobabilistic Topographic Map Formation.

    PubMed

    Van Hulle MM

    1998-09-15

    We introduce a new unsupervised competitive learning rule, the kernel-based maximum entropy learning rule (kMER), which performs equiprobabilistic topographic map formation in regular, fixed-topology lattices, for use with nonparametric density estimation as well as nonparametric regression analysis. The receptive fields of the formal neurons are overlapping radially symmetric kernels, compatible with radial basis functions (RBFs); but unlike other learning schemes, the radii of these kernels do not have to be chosen in an ad hoc manner: the radii are adapted to the local input density, together with the weight vectors that define the kernel centers, so as to produce maps of which the neurons have an equal probability to be active (equiprobabilistic maps). Both an "online" and a "batch" version of the learning rule are introduced, which are applied to nonparametric density estimation and regression, respectively. The application envisaged is blind source separation (BSS) from nonlinear, noisy mixtures.

  6. Crop Biometric Maps: The Key to Prediction

    PubMed Central

    Rovira-Más, Francisco; Sáiz-Rubio, Verónica

    2013-01-01

    The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular “identity.” This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed. PMID:24064605

  7. Galaxy Interactions with FIRE: Mapping Star Formation

    NASA Astrophysics Data System (ADS)

    Moreno, Jorge

    2016-01-01

    We utilize a suite of 75 simulations of galaxies in idealised major mergers (stellar mass ratio ~2.5:1), with a wide range of orbital parameters, to investigate the spatial extent of interaction-induced star formation. Two versions are used, one based on a Kennicult-like subgrid model (Gadget, Springel & Hernquist 2003); the other based on the new Feedback In Realistic Environments model (FIRE, Hopkins et al. 2014). Although the total star formation in galaxy encounters is generally elevated relative to isolated galaxies, we find that this elevation is a combination of intense enhancements within the central kpc and moderately suppressed activity at large galacto-centric radii. This effect appears to be stronger in the older Gadget model. Suppression is the disk is also found in the FIRE runs, but at larger scales. This is because tidal torques are weaker in the newer FIRE model, leading to a more extended nuclear starburt. Our predictions of the radial dependence of triggered star formation, and specifically the suppression of star formation beyond kpc-scales, will be testable with the next generation of integral-field spectroscopic surveys.

  8. Accuracy, resolution, and cost comparisons between small format and mapping cameras for environmental mapping

    NASA Technical Reports Server (NTRS)

    Clegg, R. H.; Scherz, J. P.

    1975-01-01

    Successful aerial photography depends on aerial cameras providing acceptable photographs within cost restrictions of the job. For topographic mapping where ultimate accuracy is required only large format mapping cameras will suffice. For mapping environmental patterns of vegetation, soils, or water pollution, 9-inch cameras often exceed accuracy and cost requirements, and small formats may be better. In choosing the best camera for environmental mapping, relative capabilities and costs must be understood. This study compares resolution, photo interpretation potential, metric accuracy, and cost of 9-inch, 70mm, and 35mm cameras for obtaining simultaneous color and color infrared photography for environmental mapping purposes.

  9. Predicting Droplet Formation on Centrifugal Microfluidic Platforms

    NASA Astrophysics Data System (ADS)

    Moebius, Jacob Alfred

    Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system. Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzable solution. Volume definition is one such step. The focus of this thesis is the development of a model predicting monodispersed droplet formation and the application of droplets as a technique for volume definition. First, a background of droplet microfluidic platforms is presented, along with current biological analysis technologies and the advantages of integrating such technologies onto microfluidic platforms. Second, background and theories of centrifugal microfluidics is given, followed by theories relevant to droplet emulsions. Third, fabrication techniques for centrifugal microfluidic designs are discussed. Finally, the development of a model for predicting droplet formation on the centrifugal microfluidic platform are presented for the rest of the thesis. Predicting droplet formation analytically based on the volumetric flow rates of the continuous and dispersed phases, the ratios of these two flow rates, and the interfacial tension between the continuous and dispersed phases presented many challenges, which will be discussed in this work. Experimental validation was completed using continuous phase solutions of different interfacial tensions. To conclude, prospective applications are discussed with expected challenges.

  10. Model predictive formation control of helicopter systems

    NASA Astrophysics Data System (ADS)

    Saffarian, Mehdi

    In this thesis, a robust formation control framework for formation control of a group of helicopters is proposed and designed. The dynamic model of the helicopter has been developed and verified through simulations. The control framework is constructed using two main control schemes for navigation of a helicopter group in three-dimensional (3D) environments. Two schemes are designed to maintain the position of one helicopter with respect to one or two other neighboring members, respectively. The developed parameters can uniquely define the position of the helicopters with respect to each other and can be used for any other aerial and under water vehicles such as airplanes, spacecrafts and submarines. Also, since this approach is modular, it is possible to use it for desired number and form of the group helicopters. Using the defined control parameters, two decentralized controllers are designed based on Nonlinear Model Predictive Control (NMPC) algorithm technique. The framework performance has been tested through simulation of different formation scenarios.

  11. Bilingual Knowledge Maps (BiK Maps) as a Presentation Format: Delayed Recall and Training Effects

    ERIC Educational Resources Information Center

    Bahr, G. Sussane; Dansereau, Donald F.

    2005-01-01

    The use of bilingual graphic organizers (bilingual knowledge maps [BiK maps]) as a presentation format was investigated for the acquisition of foreign language vocabulary. Participants were assigned to 1 of 4 conditions for the task of studying 32 German-English word pairs. Participants in each condition were trained on either lists or BiK maps…

  12. Bilingual Knowledge Maps (BiK Maps) as a Presentation Format: Delayed Recall and Training Effects

    ERIC Educational Resources Information Center

    Bahr, G. Sussane; Dansereau, Donald F.

    2005-01-01

    The use of bilingual graphic organizers (bilingual knowledge maps [BiK maps]) as a presentation format was investigated for the acquisition of foreign language vocabulary. Participants were assigned to 1 of 4 conditions for the task of studying 32 German-English word pairs. Participants in each condition were trained on either lists or BiK maps…

  13. Prediction of collective opinion in consensus formation

    NASA Astrophysics Data System (ADS)

    Hou, Lei; Liu, Jianguo; Pan, Xue; Song, Wen-Jun; Li, Xu-Dong

    2014-12-01

    In the consensus formation dynamics, the effect of leaders and interventions have been widely studied for it has many applications such as in politics and commerce. However, the problem is how to know if it is necessary for one to make an intervention. In this paper, we theoretically propose a method for predicting the tendency and final state of collective opinion. By giving each agent a conviction ci which measures the ability to insist on his opinion, we present an opinion formation model in which agents with high convictions naturally show up properties of the opinion leaders. Results reveal that, although each agent initially gets an opinion evenly distributed in the range [-1, 1], the collective opinion of the steady-state may deviate to the positive or negative direction because of the initial bias of the leaders' opinions. We further get the correlation coefficient of the linear relationship between the collective opinion and the initial bias according to both the experimental and theoretical analysis. Thus, we could predict the final state at the very beginning of the dynamic only if we get the opinions of a small portion of the population. The prediction would afford us more time and opportunities to make reactions and interventions.

  14. IsoMAP (Isoscape Modeling, Analysis, and Prediction)

    NASA Astrophysics Data System (ADS)

    Miller, C. C.; Bowen, G. J.; Zhang, T.; Zhao, L.; West, J. B.; Liu, Z.; Rapolu, N.

    2009-12-01

    IsoMAP is a TeraGrid-based web portal aimed at building the infrastructure that brings together distributed multi-scale and multi-format geospatial datasets to enable statistical analysis and modeling of environmental isotopes. A typical workflow enabled by the portal includes (1) data source exploration and selection, (2) statistical analysis and model development; (3) predictive simulation of isotope distributions using models developed in (1) and (2); (4) analysis and interpretation of simulated spatial isotope distributions (e.g., comparison with independent observations, pattern analysis). The gridded models and data products created by one user can be shared and reused among users within the portal, enabling collaboration and knowledge transfer. This infrastructure and the research it fosters can lead to fundamental changes in our knowledge of the water cycle and ecological and biogeochemical processes through analysis of network-based isotope data, but it will be important A) that those with whom the data and models are shared can be sure of the origin, quality, inputs, and processing history of these products, and B) the system is agile and intuitive enough to facilitate this sharing (rather than just ‘allow’ it). IsoMAP researchers are therefore building into the portal’s architecture several components meant to increase the amount of metadata about users’ products and to repurpose those metadata to make sharing and discovery more intuitive and robust to both expected, professional users as well as unforeseeable populations from other sectors.

  15. Bifurcation of learning and structure formation in neuronal maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Faust-Ellsässer, Carmen; Starke, Jens; van Hemmen, J. Leo

    2014-11-01

    Most learning processes in neuronal networks happen on a much longer time scale than that of the underlying neuronal dynamics. It is therefore useful to analyze slowly varying macroscopic order parameters to explore a network's learning ability. We study the synaptic learning process giving rise to map formation in the laminar nucleus of the barn owl's auditory system. Using equation-free methods, we perform a bifurcation analysis of spatio-temporal structure formation in the associated synaptic-weight matrix. This enables us to analyze learning as a bifurcation process and follow the unstable states as well. A simple time translation of the learning window function shifts the bifurcation point of structure formation and goes along with traveling waves in the map, without changing the animal's sound localization performance.

  16. Transcriptional regulation of mouse hypoglossal motor neuron somatotopic map formation.

    PubMed

    Chen, Xin; Wang, Jae Woong; Salin-Cantegrel, Adele; Dali, Rola; Stifani, Stefano

    2016-11-01

    Somatic motor neurons in the hypoglossal nucleus innervate tongue muscles controlling vital functions such as chewing, swallowing and respiration. Formation of functional hypoglossal nerve circuits depends on the establishment of precise hypoglossal motor neuron maps correlating with specific tongue muscle innervations. Little is known about the molecular mechanisms controlling mammalian hypoglossal motor neuron topographic map formation. Here we show that combinatorial expression of transcription factors Runx1, SCIP and FoxP1 defines separate mouse hypoglossal motor neuron groups with different topological, neurotransmitter and calcium-buffering phenotypes. Runx1 and SCIP are coexpressed in ventromedial hypoglossal motor neurons involved in control of tongue protrusion whereas FoxP1 is expressed in dorsomedial motor neurons associated with tongue retraction. Establishment of separate hypoglossal motor neuron maps depends in part on Runx1-mediated suppression of ventrolateral and dorsomedial motor neuron phenotypes and regulation of FoxP1 expression pattern. These findings suggest that combinatorial actions of Runx1, SCIP and FoxP1 are important for mouse hypoglossal nucleus somatotopic map formation.

  17. Temporal Map Formation in the Barn Owl's Brain

    NASA Astrophysics Data System (ADS)

    Leibold, Christian; Kempter, Richard; van Hemmen, J. Leo

    2001-12-01

    Barn owls provide an experimentally well-specified example of a temporal map, a neuronal representation of the outside world in the brain by means of time. Their laminar nucleus exhibits a place code of interaural time differences, a cue which is used to determine the azimuthal location of a sound stimulus, e.g., prey. We analyze a model of synaptic plasticity that explains the formation of such a representation in the young bird and show how in a large parameter regime a combination of local and nonlocal synaptic plasticity yields the temporal map as found experimentally. Our analysis includes the effect of nonlinearities as well as the influence of neuronal noise.

  18. Can Selforganizing Maps Accurately Predict Photometric Redshifts?

    NASA Technical Reports Server (NTRS)

    Way, Michael J.; Klose, Christian

    2012-01-01

    We present an unsupervised machine-learning approach that can be employed for estimating photometric redshifts. The proposed method is based on a vector quantization called the self-organizing-map (SOM) approach. A variety of photometrically derived input values were utilized from the Sloan Digital Sky Survey's main galaxy sample, luminous red galaxy, and quasar samples, along with the PHAT0 data set from the Photo-z Accuracy Testing project. Regression results obtained with this new approach were evaluated in terms of root-mean-square error (RMSE) to estimate the accuracy of the photometric redshift estimates. The results demonstrate competitive RMSE and outlier percentages when compared with several other popular approaches, such as artificial neural networks and Gaussian process regression. SOM RMSE results (using delta(z) = z(sub phot) - z(sub spec)) are 0.023 for the main galaxy sample, 0.027 for the luminous red galaxy sample, 0.418 for quasars, and 0.022 for PHAT0 synthetic data. The results demonstrate that there are nonunique solutions for estimating SOM RMSEs. Further research is needed in order to find more robust estimation techniques using SOMs, but the results herein are a positive indication of their capabilities when compared with other well-known methods

  19. Stochasticity and predictability in terrestrial planet formation

    NASA Astrophysics Data System (ADS)

    Hoffmann, Volker; Grimm, Simon L.; Moore, Ben; Stadel, Joachim

    2017-02-01

    Terrestrial planets are thought to be the result of a vast number of gravitational interactions and collisions between smaller bodies. We use numerical simulations to show that practically identical initial conditions result in a wide array of final planetary configurations. This is a result of the chaotic evolution of trajectories which are highly sensitive to minuscule displacements. We determine that differences between systems evolved from virtually identical initial conditions can be larger than the differences between systems evolved from very different initial conditions. This implies that individual simulations lack predictive power. For example, there is not a reproducible mapping between the initial and final surface density profiles. However, some key global properties can still be extracted if the statistical spread across many simulations is considered. Based on these spreads, we explore the collisional growth and orbital properties of terrestrial planets, which assemble from different initial conditions (we vary the initial planetesimal distribution, planetesimal masses, and giant planet orbits.). Confirming past work, we find that the resulting planetary systems are sculpted by sweeping secular resonances. Configurations with giant planets on eccentric orbits produce fewer and more massive terrestrial planets on tighter orbits than those with giants on circular orbits. This is further enhanced if the initial mass distribution is biased to the inner regions. In all cases, the outer edge of the system is set by the final location of the ν6 resonance and we find that the mass distribution peaks at the ν5 resonance. Using existing observations, we find that extrasolar systems follow similar trends. Although differences between our numerical modelling and exoplanetary systems remain, we suggest that CoRoT-7, HD 20003 and HD 20781 may host undetected giant planets.

  20. Development of predictive mapping techniques for soil survey and salinity mapping

    NASA Astrophysics Data System (ADS)

    Elnaggar, Abdelhamid A.

    Conventional soil maps represent a valuable source of information about soil characteristics, however they are subjective, very expensive, and time-consuming to prepare. Also, they do not include explicit information about the conceptual mental model used in developing them nor information about their accuracy, in addition to the error associated with them. Decision tree analysis (DTA) was successfully used in retrieving the expert knowledge embedded in old soil survey data. This knowledge was efficiently used in developing predictive soil maps for the study areas in Benton and Malheur Counties, Oregon and accessing their consistency. A retrieved soil-landscape model from a reference area in Harney County was extrapolated to develop a preliminary soil map for the neighboring unmapped part of Malheur County. The developed map had a low prediction accuracy and only a few soil map units (SMUs) were predicted with significant accuracy, mostly those shallow SMUs that have either a lithic contact with the bedrock or developed on a duripan. On the other hand, the developed soil map based on field data was predicted with very high accuracy (overall was about 97%). Salt-affected areas of the Malheur County study area are indicated by their high spectral reflectance and they are easily discriminated from the remote sensing data. However, remote sensing data fails to distinguish between the different classes of soil salinity. Using the DTA method, five classes of soil salinity were successfully predicted with an overall accuracy of about 99%. Moreover, the calculated area of salt-affected soil was overestimated when mapped using remote sensing data compared to that predicted by using DTA. Hence, DTA could be a very helpful approach in developing soil survey and soil salinity maps in more objective, effective, less-expensive and quicker ways based on field data.

  1. Spatial agreement of predicted results in landslide susceptibility maps

    NASA Astrophysics Data System (ADS)

    Sterlacchini, Simone; Ballabio, Cristiano; Blahut, Jan; Masetti, Marco; Sorichetta, Alessandro

    2010-05-01

    Landslides occur worldwide in response to a broad variety of natural predisposing conditions and triggering factors that include heavy rainfalls, earthquakes, and human activity. Landslides constitute a serious source of danger causing environmental damage and substantial human and financial losses. At a regional scale, landslide susceptibility zonation constitutes the first effective step to achieve a thorough risk assessment and management and contribute to public safety. For this reason, the predicted susceptibility maps must be carefully analysed and critically reviewed before disseminating the results. The tuning of statistical techniques and the independent validation of the results are already recognized as fundamental steps in any natural hazard study to assess model accuracy and predictive power. Validation also may permit to establish the degree of confidence in the model and to compare results from different models. For this reason, the spatial agreement among susceptibility maps, produced by different models, should also be tested, especially if these models have similar prediction power. This is usually a rather common occurrence as it may happen that two or more maps with similar predictive power may not have the same agreement in term of predicted spatial patterns. This study is aimed at assessing the degree of spatial agreement among different patterns of predicted values in susceptibility maps with almost similar success and prediction rate curves and areas under curves (AUC). A data-driven Bayesian method (Weights of Evidence modelling technique) is applied and the output maps reclassified to compare the predicted results. A relative classification, based on the proportion of area classified as susceptible, is performed. Maps are investigated by Kappa Statistic, Principal Component Analysis, and Distance Weighted Entropy procedures. The results show great differences within the output spatial patterns of the predicted maps and also within the

  2. Different Ocular Dominance Map Formation Influenced by Orientation Preference Columns in Visual Cortices

    NASA Astrophysics Data System (ADS)

    Cho, Myoung Won; Kim, Seunghwan

    2005-02-01

    In animal experiments, the observed orientation preference and ocular dominance columns in the visual cortex of the brain show various pattern types. Here, we show that the different visual map formations in various species are due to the crossover behavior in anisotropic systems composed of orientational and scalar components such as easy-plane Heisenberg models. We predict the transition boundary between different pattern types with the anisotropy as a main bifurcation parameter, which is consistent with experimental observations.

  3. 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.

  4. Mapping and predicting mortality from systemic sclerosis.

    PubMed

    Elhai, Muriel; Meune, Christophe; Boubaya, Marouane; Avouac, Jérôme; Hachulla, Eric; Balbir-Gurman, Alexandra; Riemekasten, Gabriela; Airò, Paolo; Joven, Beatriz; Vettori, Serena; Cozzi, Franco; Ullman, Susanne; Czirják, László; Tikly, Mohammed; Müller-Ladner, Ulf; Caramaschi, Paola; Distler, Oliver; Iannone, Florenzo; Ananieva, Lidia P; Hesselstrand, Roger; Becvar, Radim; Gabrielli, Armando; Damjanov, Nemanja; Salvador, Maria J; Riccieri, Valeria; Mihai, Carina; Szücs, Gabriella; Walker, Ulrich A; Hunzelmann, Nicolas; Martinovic, Duska; Smith, Vanessa; Müller, Carolina de Souza; Montecucco, Carlo Maurizio; Opris, Daniela; Ingegnoli, Francesca; Vlachoyiannopoulos, Panayiotis G; Stamenkovic, Bojana; Rosato, Edoardo; Heitmann, Stefan; Distler, Jörg H W; Zenone, Thierry; Seidel, Matthias; Vacca, Alessandra; Langhe, Ellen De; Novak, Srdan; Cutolo, Maurizio; Mouthon, Luc; Henes, Jörg; Chizzolini, Carlo; Mühlen, Carlos Alberto von; Solanki, Kamal; Rednic, Simona; Stamp, Lisa; Anic, Branimir; Santamaria, Vera Ortiz; Santis, Maria De; Yavuz, Sule; Sifuentes-Giraldo, Walter Alberto; Chatelus, Emmanuel; Stork, Jiri; Laar, Jacob van; Loyo, Esthela; García de la Peña Lefebvre, Paloma; Eyerich, Kilian; Cosentino, Vanesa; Alegre-Sancho, Juan Jose; Kowal-Bielecka, Otylia; Rey, Grégoire; Matucci-Cerinic, Marco; Allanore, Yannick

    2017-11-01

    To determine the causes of death and risk factors in systemic sclerosis (SSc). Between 2000 and 2011, we examined the death certificates of all French patients with SSc to determine causes of death. Then we examined causes of death and developed a score associated with all-cause mortality from the international European Scleroderma Trials and Research (EUSTAR) database. Candidate prognostic factors were tested by Cox proportional hazards regression model by single variable analysis, followed by a multiple variable model stratified by centres. The bootstrapping technique was used for internal validation. We identified 2719 French certificates of deaths related to SSc, mainly from cardiac (31%) and respiratory (18%) causes, and an increase in SSc-specific mortality over time. Over a median follow-up of 2.3 years, 1072 (9.6%) of 11 193 patients from the EUSTAR sample died, from cardiac disease in 27% and respiratory causes in 17%. By multiple variable analysis, a risk score was developed, which accurately predicted the 3-year mortality, with an area under the curve of 0.82. The 3-year survival of patients in the upper quartile was 53%, in contrast with 98% in the first quartile. Combining two complementary and detailed databases enabled the collection of an unprecedented 3700 deaths, revealing the major contribution of the cardiopulmonary system to SSc mortality. We also developed a robust score to risk-stratify these patients and estimate their 3-year survival. With the emergence of new therapies, these important observations should help caregivers plan and refine the monitoring and management to prolong these patients' survival. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  5. Predicting km-scale shear zone formation

    NASA Astrophysics Data System (ADS)

    Gerbi, Christopher; Culshaw, Nicholas; Shulman, Deborah; Foley, Maura; Marsh, Jeffrey

    2015-04-01

    gradients but are insufficient to maintain them because the stress perturbations will dissipate with deformation. Metamorphism can unquestionably cause sufficient rheological change, but only in certain rock types: for example, granitoids have much less capacity for metamorphically induced rheologic change than do mafic rocks. The magnitude of phase geometry variation observed in natural systems suggests that morphological change (e.g., interconnection of weak phases) likely has little direct affect on strength changes, although other textural factors related to diffusion paths and crystallographic orientation could play a significant role. Thermal perturbation, mainly in the form of shear heating, remains potentially powerful but inconclusive. Taken together, these observations indicate that a simple algorithm predicting shear zone formation will not succeed in many geologically relevant instances. One significant reason may be that the inherent lithologic variation at the km scale, such as observed in the Central Gneiss belt, prevents the development of self-organized strain patterns that would form in more rheologically uniform systems.

  6. Predictive cartography of metal binders using generative topographic mapping.

    PubMed

    Baskin, Igor I; Solov'ev, Vitaly P; Bagatur'yants, Alexander A; Varnek, Alexandre

    2017-07-07

    Generative topographic mapping (GTM) approach is used to visualize the chemical space of organic molecules (L) with respect to binding a wide range of 41 different metal cations (M) and also to build predictive models for stability constants (logK) of 1:1 (M:L) complexes using "density maps," "activity landscapes," and "selectivity landscapes" techniques. A two-dimensional map describing the entire set of 2962 metal binders reveals the selectivity and promiscuity zones with respect to individual metals or groups of metals with similar chemical properties (lanthanides, transition metals, etc). The GTM-based global (for entire set) and local (for selected subsets) models demonstrate a good predictive performance in the cross-validation procedure. It is also shown that the data likelihood could be used as a definition of the applicability domain of GTM-based models. Thus, the GTM approach represents an efficient tool for the predictive cartography of metal binders, which can both visualize their chemical space and predict the affinity profile of metals for new ligands.

  7. Predictive cartography of metal binders using generative topographic mapping

    NASA Astrophysics Data System (ADS)

    Baskin, Igor I.; Solov'ev, Vitaly P.; Bagatur'yants, Alexander A.; Varnek, Alexandre

    2017-08-01

    Generative topographic mapping (GTM) approach is used to visualize the chemical space of organic molecules (L) with respect to binding a wide range of 41 different metal cations (M) and also to build predictive models for stability constants (log K) of 1:1 (M:L) complexes using "density maps," "activity landscapes," and "selectivity landscapes" techniques. A two-dimensional map describing the entire set of 2962 metal binders reveals the selectivity and promiscuity zones with respect to individual metals or groups of metals with similar chemical properties (lanthanides, transition metals, etc). The GTM-based global (for entire set) and local (for selected subsets) models demonstrate a good predictive performance in the cross-validation procedure. It is also shown that the data likelihood could be used as a definition of the applicability domain of GTM-based models. Thus, the GTM approach represents an efficient tool for the predictive cartography of metal binders, which can both visualize their chemical space and predict the affinity profile of metals for new ligands.

  8. Evaluating the Quality of Predictive Geological Maps Produced using Self-Organizing Maps

    NASA Astrophysics Data System (ADS)

    Carter-McAuslan, Angela; Farquharson, Colin

    2016-04-01

    With increased data collection, extraction of useful information from large, often multi-dimensional (where each dimension is a unique data-type), datasets becomes a challenge. Associated with the problem of extracting usable information is the need to evaluate the information extracted to determine its validity. Traditionally, geophysical data has been interpreted in map or profile form one data-type at a time using primarily visual inspection by the interpreter. This approach become increasingly difficult as the dimensionality (e.g. number of data-types) of the dataset is increased. As such, new methods for discovering patterns in multi-dimensional geophysical datasets need to be investigated. Self-organizing maps (SOMs) are a class of unsupervised artificial neural network algorithm which are used to cluster multi-dimensional data while preserving the overall topology of the original dataset. As geophysical responses measured in the field are closely linked to the local geology it is postulated that SOMs can be employed to cluster multi-dimensional geophysical data in order to produce predictive geological maps. In the development of an effective work flow for creating predictive geological maps using SOMs, synthetic and real world test cases are used so that the predictive maps can be compared to a known geology. This comparison can be done through visual inspection. However, quantitative measures of clustering quality are also desired. In this project three different types of cluster quality measures are investigated: cluster morphology measures (e.g. the Quantization Error and the Dunn Index); class/cluster concatenation measures (e.g. Cluster Purity and Normalized Mutual Information); and decision-based measures (e.g. the Rand Index and F-Measure). SOM predictive mapping was applied to mapping the Baie Verte Peninsula on the north coast of the island of Newfoundland, Canada. The Baie Verte Peninsula is a region of complex geology with good regional

  9. Neural map formation in the mouse olfactory system.

    PubMed

    Takeuchi, Haruki; Sakano, Hitoshi

    2014-08-01

    In the mouse olfactory system, odorants are detected by ~1,000 different odorant receptors (ORs) produced by olfactory sensory neurons (OSNs). Each OSN expresses only one functional OR species, which is referred to as the "one neuron-one receptor" rule. Furthermore, OSN axons bearing the same OR converge to a specific projection site in the olfactory bulb (OB) forming a glomerular structure, i.e., the "one glomerulus-one receptor" rule. Based on these basic rules, binding signals of odorants detected by OSNs are converted to topographic information of activated glomeruli in the OB. During development, the glomerular map is formed by the combination of two genetically programmed processes: one is OR-independent projection along the dorsal-ventral axis, and the other is OR-dependent projection along the anterior-posterior axis. The map is further refined in an activity-dependent manner during the neonatal period. Here, we summarize recent progress of neural map formation in the mouse olfactory system.

  10. The Dokuchaev hypothesis as a basis for predictive digital soil mapping (on the 125th anniversary of its publication)

    NASA Astrophysics Data System (ADS)

    Florinsky, I. V.

    2012-04-01

    Predictive digital soil mapping is widely used in soil science. Its objective is the prediction of the spatial distribution of soil taxonomic units and quantitative soil properties via the analysis of spatially distributed quantitative characteristics of soil-forming factors. Western pedometrists stress the scientific priority and principal importance of Hans Jenny's book (1941) for the emergence and development of predictive soil mapping. In this paper, we demonstrate that Vasily Dokuchaev explicitly defined the central idea and statement of the problem of contemporary predictive soil mapping in the year 1886. Then, we reconstruct the history of the soil formation equation from 1899 to 1941. We argue that Jenny adopted the soil formation equation from Sergey Zakharov, who published it in a well-known fundamental textbook in 1927. It is encouraging that this issue was clarified in 2011, the anniversary year for publications of Dokuchaev and Jenny.

  11. Histopathology Predicts the Mechanism of Stone Formation

    NASA Astrophysics Data System (ADS)

    Evan, Andrew P.

    2007-04-01

    About 5% of American women and 12% of men will develop a kidney stone at some time in their life and these numbers appear to be on the rise. Despite years of scientific research into the mechanisms of stone formation and growth, limited advances have been made until recently. Randall's original observations and thoughts on the mechanisms for kidney stone formation have been validated for idiopathic calcium oxalate stone formers (ICSF) but not for most other stone forming groups. Our current studies on selected groups of human stone formers using intraoperative papillary biopsies has shown overwhelming evidence for the presence of Randall's plaque in ICSF and that stone formation and growth are exclusively linked to its availability to urinary ions and proteins. Intense investigation of the plaque-stone junction is needed if we are to understand the factors leading to the overgrowth process on exposed regions of plaque. Such information should allow the development of treatment strategies to block stone formation in ICSF patients. Patients who form brushite stones, or who form apatite stones because of distal renal tubular acidosis (dRTA), or patients with calcium oxalate stones due to obesity bypass procedures, or patients with cystinuria, get plugged inner medullary collecting ducts (IMCD) which leads to total destruction of the lining cells and focal sites of interstitial fibrosis. These stone formers have plaque but at levels equal to or below non-stone formers, which would suggest that they form stones by a different mechanism than do ICSF patients.

  12. Prediction-guided quantization for video tone mapping

    NASA Astrophysics Data System (ADS)

    Le Dauphin, Agnès.; Boitard, Ronan; Thoreau, Dominique; Olivier, Yannick; Francois, Edouard; LeLéannec, Fabrice

    2014-09-01

    Tone Mapping Operators (TMOs) compress High Dynamic Range (HDR) content to address Low Dynamic Range (LDR) displays. However, before reaching the end-user, this tone mapped content is usually compressed for broadcasting or storage purposes. Any TMO includes a quantization step to convert floating point values to integer ones. In this work, we propose to adapt this quantization, in the loop of an encoder, to reduce the entropy of the tone mapped video content. Our technique provides an appropriate quantization for each mode of both the Intra and Inter-prediction that is performed in the loop of a block-based encoder. The mode that minimizes a rate-distortion criterion uses its associated quantization to provide integer values for the rest of the encoding process. The method has been implemented in HEVC and was tested over two different scenarios: the compression of tone mapped LDR video content (using the HM10.0) and the compression of perceptually encoded HDR content (HM14.0). Results show an average bit-rate reduction under the same PSNR for all the sequences and TMO considered of 20.3% and 27.3% for tone mapped content and 2.4% and 2.7% for HDR content.

  13. Statistical-mechanical analysis of self-organization and pattern formation during the development of visual maps

    NASA Astrophysics Data System (ADS)

    Obermayer, K.; Blasdel, G. G.; Schulten, K.

    1992-05-01

    We report a detailed analytical and numerical model study of pattern formation during the development of visual maps, namely, the formation of topographic maps and orientation and ocular dominance columns in the striate cortex. Pattern formation is described by a stimulus-driven Markovian process, the self-organizing feature map. This algorithm generates topologically correct maps between a space of (visual) input signals and an array of formal ``neurons,'' which in our model represents the cortex. We define order parameters that are a function of the set of visual stimuli an animal perceives, and we demonstrate that the formation of orientation and ocular dominance columns is the result of a global instability of the retinoptic projection above a critical value of these order parameters. We characterize the spatial structure of the emerging patterns by power spectra, correlation functions, and Gabor transforms, and we compare model predictions with experimental data obtained from the striate cortex of the macaque monkey with optical imaging. Above the critical value of the order parameters the model predicts a lateral segregation of the striate cortex into (i) binocular regions with linear changes in orientation preference, where iso-orientation slabs run perpendicular to the ocular dominance bands, and (ii) monocular regions with low orientation specificity, which contain the singularities of the orientation map. Some of these predictions have already been verified by experiments.

  14. Predictive spatial modelling for mapping soil salinity at continental scale

    NASA Astrophysics Data System (ADS)

    Bui, Elisabeth; Wilford, John; de Caritat, Patrice

    2017-04-01

    Soil salinity is a serious limitation to agriculture and one of the main causes of land degradation. Soil is considered saline if its electrical conductivity (EC) is > 4 dS/m. Maps of saline soil distribution are essential for appropriate land development. Previous attempts to map soil salinity over extensive areas have relied on satellite imagery, aerial electromagnetic (EM) and/or proximally sensed EM data; other environmental (climate, topographic, geologic or soil) datasets are generally not used. Having successfully modelled and mapped calcium carbonate distribution over the 0-80 cm depth in Australian soils using machine learning with point samples from the National Geochemical Survey of Australia (NGSA), we took a similar approach to map soil salinity at 90-m resolution over the continent. The input data were the EC1:5 measurements on the < 2mm fraction at 1315 georeferenced points across the continent at two depth intervals (TOS, 0-10 cm, and BOS, 60-80 cm) (see http://www.ga.gov.au/energy/projects/national-geochemical-survey/atlas.html) were log-transformed and combined with values for climate, elevation and terrain attributes, soil and lithology classes, geophysics, and MODIS vegetation indices extracted at the same locations which were used as predictors in decision tree models. The machine learning software 'Cubist' (www.rulequest.com) was used as the inference engine for the modelling, a 90:10 training:test set data split was used to validate results, and 100 randomly sampled trees were built using the training data. The results were good with an average internal correlation (r) of 0.88 between predicted and measured logEC1:5 (training data), an average external correlation of 0.48 (test subset), and a Lin's concordance correlation coefficient (which evaluates the 1:1 fit) of 0.61. Therefore, the rules derived were mapped and the mean prediction for each 90-m pixel was used for the final logEC1:5 map. This is the most detailed picture of soil salinity

  15. Geomorphically based predictive mapping of soil thickness in upland watersheds

    NASA Astrophysics Data System (ADS)

    Pelletier, Jon D.; Rasmussen, Craig

    2009-09-01

    The hydrologic response of upland watersheds is strongly controlled by soil (regolith) thickness. Despite the need to quantify soil thickness for input into hydrologic models, there is currently no widely used, geomorphically based method for doing so. In this paper we describe and illustrate a new method for predictive mapping of soil thicknesses using high-resolution topographic data, numerical modeling, and field-based calibration. The model framework works directly with input digital elevation model data to predict soil thicknesses assuming a long-term balance between soil production and erosion. Erosion rates in the model are quantified using one of three geomorphically based sediment transport models: nonlinear slope-dependent transport, nonlinear area- and slope-dependent transport, and nonlinear depth- and slope-dependent transport. The model balances soil production and erosion locally to predict a family of solutions corresponding to a range of values of two unconstrained model parameters. A small number of field-based soil thickness measurements can then be used to calibrate the local value of those unconstrained parameters, thereby constraining which solution is applicable at a particular study site. As an illustration, the model is used to predictively map soil thicknesses in two small, ˜0.1 km2, drainage basins in the Marshall Gulch watershed, a semiarid drainage basin in the Santa Catalina Mountains of Pima County, Arizona. Field observations and calibration data indicate that the nonlinear depth- and slope-dependent sediment transport model is the most appropriate transport model for this site. The resulting framework provides a generally applicable, geomorphically based tool for predictive mapping of soil thickness using high-resolution topographic data sets.

  16. Predicting episodic memory formation for movie events

    PubMed Central

    Tang, Hanlin; Singer, Jed; Ison, Matias J.; Pivazyan, Gnel; Romaine, Melissa; Frias, Rosa; Meller, Elizabeth; Boulin, Adrianna; Carroll, James; Perron, Victoria; Dowcett, Sarah; Arellano, Marlise; Kreiman, Gabriel

    2016-01-01

    Episodic memories are long lasting and full of detail, yet imperfect and malleable. We quantitatively evaluated recollection of short audiovisual segments from movies as a proxy to real-life memory formation in 161 subjects at 15 minutes up to a year after encoding. Memories were reproducible within and across individuals, showed the typical decay with time elapsed between encoding and testing, were fallible yet accurate, and were insensitive to low-level stimulus manipulations but sensitive to high-level stimulus properties. Remarkably, memorability was also high for single movie frames, even one year post-encoding. To evaluate what determines the efficacy of long-term memory formation, we developed an extensive set of content annotations that included actions, emotional valence, visual cues and auditory cues. These annotations enabled us to document the content properties that showed a stronger correlation with recognition memory and to build a machine-learning computational model that accounted for episodic memory formation in single events for group averages and individual subjects with an accuracy of up to 80%. These results provide initial steps towards the development of a quantitative computational theory capable of explaining the subjective filtering steps that lead to how humans learn and consolidate memories. PMID:27686330

  17. Predicting scale formation during electrodialytic nutrient recovery.

    PubMed

    Thompson Brewster, Emma; Ward, Andrew J; Mehta, Chirag M; Radjenovic, Jelena; Batstone, Damien J

    2017-03-01

    Electro-concentration of nutrients from waste streams is a promising technology to enable resource recovery, but has several operational concerns. One key concern is the formation of inorganic scale on the concentrate side of cation exchange membranes when recovering nutrients from wastewaters containing calcium, magnesium, phosphorous and carbonate, commonly present in anaerobic digester rejection water. Electrodialytic nutrient recovery was trialed on anaerobic digester rejection water in a laboratory scale electro-concentration unit without treatment (A), following struvite recovery (B), and following struvite recovery as well as concentrate controlled at pH 5 for scaling control (C). Treatment A resulted in large amount of scale, while treatment B significantly reduced the amount of scale formation with reduction in magnesium phosphates, and treatment C reduced the amount of scale further by limiting the formation of calcium carbonates. Treatment C resulted in an 87 ± 7% by weight reduction in scale compared to treatment A. A mechanistic model for the inorganic processes was validated using a previously published general precipitation model based on saturation index. The model attributed the reduction in struvite scale to the removal of phosphate during the struvite pre-treatment, and the reduction in calcium carbonate scale to pH control resulting in the stripping of carbonate as carbon dioxide gas. This indicates that multiple strategies may be required to control precipitation, and that mechanistic models can assist in developing a combined approach.

  18. Predictions from star formation in the multiverse

    SciTech Connect

    Bousso, Raphael; Leichenauer, Stefan

    2010-03-15

    We compute trivariate probability distributions in the landscape, scanning simultaneously over the cosmological constant, the primordial density contrast, and spatial curvature. We consider two different measures for regulating the divergences of eternal inflation, and three different models for observers. In one model, observers are assumed to arise in proportion to the entropy produced by stars; in the others, they arise at a fixed time (5 or 10x10{sup 9} years) after star formation. The star formation rate, which underlies all our observer models, depends sensitively on the three scanning parameters. We employ a recently developed model of star formation in the multiverse, a considerable refinement over previous treatments of the astrophysical and cosmological properties of different pocket universes. For each combination of observer model and measure, we display all single and bivariate probability distributions, both with the remaining parameter(s) held fixed and marginalized. Our results depend only weakly on the observer model but more strongly on the measure. Using the causal diamond measure, the observed parameter values (or bounds) lie within the central 2{sigma} of nearly all probability distributions we compute, and always within 3{sigma}. This success is encouraging and rather nontrivial, considering the large size and dimension of the parameter space. The causal patch measure gives similar results as long as curvature is negligible. If curvature dominates, the causal patch leads to a novel runaway: it prefers a negative value of the cosmological constant, with the smallest magnitude available in the landscape.

  19. Predicting episodic memory formation for movie events.

    PubMed

    Tang, Hanlin; Singer, Jed; Ison, Matias J; Pivazyan, Gnel; Romaine, Melissa; Frias, Rosa; Meller, Elizabeth; Boulin, Adrianna; Carroll, James; Perron, Victoria; Dowcett, Sarah; Arellano, Marlise; Kreiman, Gabriel

    2016-09-30

    Episodic memories are long lasting and full of detail, yet imperfect and malleable. We quantitatively evaluated recollection of short audiovisual segments from movies as a proxy to real-life memory formation in 161 subjects at 15 minutes up to a year after encoding. Memories were reproducible within and across individuals, showed the typical decay with time elapsed between encoding and testing, were fallible yet accurate, and were insensitive to low-level stimulus manipulations but sensitive to high-level stimulus properties. Remarkably, memorability was also high for single movie frames, even one year post-encoding. To evaluate what determines the efficacy of long-term memory formation, we developed an extensive set of content annotations that included actions, emotional valence, visual cues and auditory cues. These annotations enabled us to document the content properties that showed a stronger correlation with recognition memory and to build a machine-learning computational model that accounted for episodic memory formation in single events for group averages and individual subjects with an accuracy of up to 80%. These results provide initial steps towards the development of a quantitative computational theory capable of explaining the subjective filtering steps that lead to how humans learn and consolidate memories.

  20. A Comparison of Alternate Formats for the Portrayal of Terrain Relief on Military Maps

    DTIC Science & Technology

    1979-11-01

    Experiments I and 11 22 Effects of User Experience Level .. ....................... 23 Interactions Between Map Format and User Experience Level . 23... user experience levels ..... ................ 19 4. Experiment 11: Summary of statistically significant effects of map format for time scores...must be identified. - 14- Experiment II was essentially a replication of Experiment I, but the overall map user experience level was lower. The

  1. Advancements in predictive plasma formation modeling

    NASA Astrophysics Data System (ADS)

    Purvis, Michael A.; Schafgans, Alexander; Brown, Daniel J. W.; Fomenkov, Igor; Rafac, Rob; Brown, Josh; Tao, Yezheng; Rokitski, Slava; Abraham, Mathew; Vargas, Mike; Rich, Spencer; Taylor, Ted; Brandt, David; Pirati, Alberto; Fisher, Aaron; Scott, Howard; Koniges, Alice; Eder, David; Wilks, Scott; Link, Anthony; Langer, Steven

    2016-03-01

    We present highlights from plasma simulations performed in collaboration with Lawrence Livermore National Labs. This modeling is performed to advance the rate of learning about optimal EUV generation for laser produced plasmas and to provide insights where experimental results are not currently available. The goal is to identify key physical processes necessary for an accurate and predictive model capable of simulating a wide range of conditions. This modeling will help to drive source performance scaling in support of the EUV Lithography roadmap. The model simulates pre-pulse laser interaction with the tin droplet and follows the droplet expansion into the main pulse target zone. Next, the interaction of the expanded droplet with the main laser pulse is simulated. We demonstrate the predictive nature of the code and provide comparison with experimental results.

  2. Detailed forest formation mapping in the land cover map series for the Caribbean islands

    NASA Astrophysics Data System (ADS)

    Helmer, E. H.; Schill, S.; Pedreros, D. H.; Tieszen, L. L.; Kennaway, T.; Cushing, M.; Ruzycki, T.

    2006-12-01

    Forest formation and land cover maps for several Caribbean islands were developed from Landsat ETM+ imagery as part of a multi-organizational project. The spatially explicit data on forest formation types will permit more refined estimates of some forest attributes. The woody vegetation classification scheme relates closely to that of Areces-Malea et al. (1), who classify Caribbean vegetation according to standards of the US Federal Geographic Data Committee (FGDC, 1997), with modifications similar to those in Helmer et al. (2). For several of the islands, we developed image mosaics that filled cloudy parts of scenes with data from other scene dates after using regression tree normalization (3). The regression tree procedure permitted us to develop mosaics for wet and drought seasons for a few of the islands. The resulting multiseason imagery facilitated separation between classes such as seasonal evergreen forest, semi-deciduous forest (including semi-evergreen forest), and drought deciduous forest or woodland formations. We used decision tree classification methods to classify the Landsat image mosaics to detailed forest formations and land cover for Puerto Rico (4), St. Kitts and Nevis, St. Lucia, St. Vincent and the Grenadines and Grenada. The decision trees classified a stack of raster layers for each mapping area that included the Landsat image bands and various ancillary raster data layers. For Puerto Rico, for example, the ancillary data included climate parameters (5). For some islands, the ancillary data included topographic derivatives such as aspect, slope and slope position, SRTM (6) or other topographic data. Mapping forest formations with decision tree classifiers, ancillary geospatial data, and cloud-free image mosaics, accurately distinguished spectrally similar forest formations, without the aid of ecological zone maps, on the islands where the approach was used. The approach resulted in maps of forest formations with comparable or better detail

  3. Predicting and mapping soil available water capacity in Korea.

    PubMed

    Hong, Suk Young; Minasny, Budiman; Han, Kyung Hwa; Kim, Yihyun; Lee, Kyungdo

    2013-01-01

    The knowledge on the spatial distribution of soil available water capacity at a regional or national extent is essential, as soil water capacity is a component of the water and energy balances in the terrestrial ecosystem. It controls the evapotranspiration rate, and has a major impact on climate. This paper demonstrates a protocol for mapping soil available water capacity in South Korea at a fine scale using data available from surveys. The procedures combined digital soil mapping technology with the available soil map of 1:25,000. We used the modal profile data from the Taxonomical Classification of Korean Soils. The data consist of profile description along with physical and chemical analysis for the modal profiles of the 380 soil series. However not all soil samples have measured bulk density and water content at -10 and -1500 kPa. Thus they need to be predicted using pedotransfer functions. Furthermore, water content at -10 kPa was measured using ground samples. Thus a correction factor is derived to take into account the effect of bulk density. Results showed that Andisols has the highest mean water storage capacity, followed by Entisols and Inceptisols which have loamy texture. The lowest water retention is Entisols which are dominated by sandy materials. Profile available water capacity to a depth of 1 m was calculated and mapped for Korea. The western part of the country shows higher available water capacity than the eastern part which is mountainous and has shallower soils. The highest water storage capacity soils are the Ultisols and Alfisols (mean of 206 and 205 mm, respectively). Validation of the maps showed promising results. The map produced can be used as an indication of soil physical quality of Korean soils.

  4. Predicting and mapping soil available water capacity in Korea

    PubMed Central

    Hong, Suk Young; Han, Kyung Hwa; Kim, Yihyun; Lee, Kyungdo

    2013-01-01

    The knowledge on the spatial distribution of soil available water capacity at a regional or national extent is essential, as soil water capacity is a component of the water and energy balances in the terrestrial ecosystem. It controls the evapotranspiration rate, and has a major impact on climate. This paper demonstrates a protocol for mapping soil available water capacity in South Korea at a fine scale using data available from surveys. The procedures combined digital soil mapping technology with the available soil map of 1:25,000. We used the modal profile data from the Taxonomical Classification of Korean Soils. The data consist of profile description along with physical and chemical analysis for the modal profiles of the 380 soil series. However not all soil samples have measured bulk density and water content at −10 and −1500 kPa. Thus they need to be predicted using pedotransfer functions. Furthermore, water content at −10 kPa was measured using ground samples. Thus a correction factor is derived to take into account the effect of bulk density. Results showed that Andisols has the highest mean water storage capacity, followed by Entisols and Inceptisols which have loamy texture. The lowest water retention is Entisols which are dominated by sandy materials. Profile available water capacity to a depth of 1 m was calculated and mapped for Korea. The western part of the country shows higher available water capacity than the eastern part which is mountainous and has shallower soils. The highest water storage capacity soils are the Ultisols and Alfisols (mean of 206 and 205 mm, respectively). Validation of the maps showed promising results. The map produced can be used as an indication of soil physical quality of Korean soils. PMID:23646290

  5. Two-phase flow regime map predictions under microgravity

    SciTech Connect

    Karri, S.B.R.; Mathur, V.K.

    1988-01-01

    In this paper, the widely used models of Taitel-Dukler and Weisman et al. are extrapolated to microgravity levels to compare predicted flow pattern boundaries for horizontal and vertical flows. Efforts have been made to analyze how the two-phase flow models available in the literature predict flow regime transitions in microgravity. The models of Taitel-Dukler and Weisman et al. have been found to be more suitable for extrapolation to a wide range of system parameters than the other two-phase flow regime maps available in the literature. The original criteria for all cases are used to predict the transition lines, except for the transition to dispersed flow regime in case of the Weisman model for horizontal flow. The constant 0.97 on the righthand side of this correlation should be two times that value, i.e., 1.94, in order to match this transition line in their original paper.

  6. Evaluation of formation water chemistry and scale prediction: Bakken Shale

    SciTech Connect

    Thyne, Geoffrey; Brady, Patrick

    2016-10-24

    Determination of in situ formation water chemistry is an essential component of reservoir management. This study details the use of thermodynamic computer models to calculate reservoir pH and restore produced water analyses for prediction of scale formation. Bakken produced water samples were restored to formation conditions and calculations of scale formation performed. In situ pH is controlled by feldspar-clay equilibria. Calcite scale is readily formed due to changes in pH during pressure drop from in situ to surface conditions. The formation of anhydrite and halite scale, which has been observed, was predicted only for the most saline samples. Finally, in addition, the formation of anhydrite and/or halite may be related to the localized conditions of increased salinity as water is partitioned into the gas phase during production.

  7. Evaluation of formation water chemistry and scale prediction: Bakken Shale

    DOE PAGES

    Thyne, Geoffrey; Brady, Patrick

    2016-10-24

    Determination of in situ formation water chemistry is an essential component of reservoir management. This study details the use of thermodynamic computer models to calculate reservoir pH and restore produced water analyses for prediction of scale formation. Bakken produced water samples were restored to formation conditions and calculations of scale formation performed. In situ pH is controlled by feldspar-clay equilibria. Calcite scale is readily formed due to changes in pH during pressure drop from in situ to surface conditions. The formation of anhydrite and halite scale, which has been observed, was predicted only for the most saline samples. Finally, inmore » addition, the formation of anhydrite and/or halite may be related to the localized conditions of increased salinity as water is partitioned into the gas phase during production.« less

  8. MAPPING CHILDREN'S POLITICS: SPATIAL STORIES, DIALOGIC RELATIONS AND POLITICAL FORMATION.

    PubMed

    Elwood, Sarah; Mitchell, Katharyne

    2012-03-01

    This article confronts a persistent challenge in research on children's geographies and politics: the difficulty of recognizing forms of political agency and practice that by definition fall outside of existing political theory. Children are effectively "always already" positioned outside most of the structures and ideals of modernist democratic theory, such as the public sphere and abstracted notions of communicative action or "rational" speech. Recent emphases on embodied tactics of everyday life have offered important ways to recognize children's political agency and practice. However, we argue here that a focus on spatial practices and critical knowledge alone cannot capture the full range of children's politics, and show how representational and dialogic practices remain a critical element of their politics in everyday life. Drawing on de Certeau's notion of spatial stories, and Bakhtin's concept of dialogic relations, we argue that children's representations and dialogues comprise a significant space of their political agency and formation, in which they can make and negotiate social meanings, subjectivities, and relationships. We develop these arguments with evidence from an after-school activity programme we conducted with 10-13 year olds in Seattle, Washington, in which participants explored, mapped, wrote and spoke about the spaces and experiences of their everyday lives. Within these practices, children negotiate autonomy and self-determination, and forward ideas, representations, and expressions of agreement or disagreement that are critical to their formation as political actors.

  9. Isomorphic semantic mapping of variant call format (VCF2RDF).

    PubMed

    Penha, Emanuel Diego S; Iriabho, Egiebade; Dussaq, Alex; de Oliveira, Diana Magalhães; Almeida, Jonas S

    2016-10-25

    The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework. RDF is advanced by the World Wide Web Consortium (W3C) to enable representations of linked data that are both distributed and discoverable. The resulting ability to decompose VCF reports of genomic variation without loss of context addresses the need to modularize and govern NGS pipelines for Precision Medicine. Specifically, it provides the flexibility (i.e. the indexing) needed to support the wide variety of clinical scenarios and patient-facing governance where only part of the VCF data is fitting.

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

    PubMed

    Schneider, Gisbert; Schneider, Petra

    2017-03-01

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

  11. Mapping of Estimations and Prediction Intervals Using Extreme Learning Machines

    NASA Astrophysics Data System (ADS)

    Leuenberger, Michael; Kanevski, Mikhail

    2015-04-01

    Due to the large amount and complexity of data available nowadays in environmental sciences, we face the need to apply more robust methodology allowing analyses and understanding of the phenomena under study. One particular but very important aspect of this understanding is the reliability of generated prediction models. From the data collection to the prediction map, several sources of error can occur and affect the final result. Theses sources are mainly identified as uncertainty in data (data noise), and uncertainty in the model. Their combination leads to the so-called prediction interval. Quantifying these two categories of uncertainty allows a finer understanding of phenomena under study and a better assessment of the prediction accuracy. The present research deals with a methodology combining a machine learning algorithm (ELM - Extreme Learning Machine) with a bootstrap-based procedure. Developed by G.-B. Huang et al. (2006), ELM is an artificial neural network following the structure of a multilayer perceptron (MLP) with one single hidden layer. Compared to classical MLP, ELM has the ability to learn faster without loss of accuracy, and need only one hyper-parameter to be fitted (that is the number of nodes in the hidden layer). The key steps of the proposed method are as following: sample from the original data a variety of subsets using bootstrapping; from these subsets, train and validate ELM models; and compute residuals. Then, the same procedure is performed a second time with only the squared training residuals. Finally, taking into account the two modeling levels allows developing the mean prediction map, the model uncertainty variance, and the data noise variance. The proposed approach is illustrated using geospatial data. References Efron B., and Tibshirani R. 1986, Bootstrap Methods for Standard Errors, Confidence Intervals, and Other Measures of Statistical accuracy, Statistical Science, vol. 1: 54-75. Huang G.-B., Zhu Q.-Y., and Siew C.-K. 2006

  12. Search strategy selection in the Morris water maze indicates allocentric map formation during learning that underpins spatial memory formation.

    PubMed

    Rogers, Jake; Churilov, Leonid; Hannan, Anthony J; Renoir, Thibault

    2017-03-01

    Using a Matlab classification algorithm, we demonstrate that a highly salient distal cue array is required for significantly increased likelihoods of spatial search strategy selection during Morris water maze spatial learning. We hypothesized that increased spatial search strategy selection during spatial learning would be the key measure demonstrating the formation of an allocentric map to the escape location. Spatial memory, as indicated by quadrant preference for the area of the pool formally containing the hidden platform, was assessed as the main measure that this allocentric map had formed during spatial learning. Our C57BL/6J wild-type (WT) mice exhibit quadrant preference in the highly salient cue paradigm but not the low, corresponding with a 120% increase in the odds of a spatial search strategy selection during learning. In contrast, quadrant preference remains absent in serotonin 1A receptor (5-HT1AR) knockout (KO) mice, who exhibit impaired search strategy selection during spatial learning. Additionally, we also aimed to assess the impact of the quality of the distal cue array on the spatial learning curves of both latency to platform and path length using mixed-effect regression models and found no significant associations or interactions. In contrast, we demonstrated that the spatial learning curve for search strategy selection was absent during training in the low saliency paradigm. Therefore, we propose that allocentric search strategy selection during spatial learning is the learning parameter in mice that robustly indicates the formation of a cognitive map for the escape goal location. These results also suggest that both latency to platform and path length spatial learning curves do not discriminate between allocentric and egocentric spatial learning and do not reliably predict spatial memory formation. We also show that spatial memory, as indicated by the absolute time in the quadrant formerly containing the hidden platform alone (without

  13. Using dominant eigenvalue analysis to predict formation of alternans in the heart

    NASA Astrophysics Data System (ADS)

    Kakade, Virendra; Zhao, Xiaopeng; Tolkacheva, Elena G.

    2013-11-01

    Ventricular fibrillation at the whole heart level is often preceded by the alternation of action potential duration (APD), i.e., alternans, at the cellular level. As proven in many experiments, traditional approaches based on the slope of the restitution curve have not been successful in predicting alternans formation. Recently, a technique has been theoretically developed based on dominant eigenvalue analysis to predict alternans formation in isolated cardiac myocytes. Here, we aimed to demonstrate that this technique can be applied to predict alternans formation at the whole heart level. Optical mapping was performed in Langendorff-perfused hearts from New Zealand white rabbits (n = 4), which were paced at decreasing basic cycle lengths to introduce APD alternans. In each heart, the basic cycle length corresponding to the local onset of alternans, Bonset, was determined and two regions of the heart were identified at Bonset: one region which exhibited alternans (1:1alt) and one which did not (1:1). Corresponding two-dimensional eigenvalue (λ) maps were generated using principal component analysis by analyzing action potentials after short perturbations from the steady state, and mean eigenvalues (λ¯) were calculated separately for the 1:1 and 1:1alt regions. We demonstrated that λ¯ calculated at Bonset was significantly different (p<0.05) between the two regions. Our results suggest that this dominant eigenvalue technique can be used to successfully predict the local alternans formation in the heart.

  14. The geologic mapping of Venus using C-1 format: Sheets 75N254, 60N263

    NASA Technical Reports Server (NTRS)

    Shalimov, I. V.

    1992-01-01

    The results of geologic mapping of Venus, produced on the base of Magellan images, are presented. We submit two C-1 format geologic maps with the appropriate legend. The mapping territory was taken from Venera 15 and 16 missions and geologic maps were composed. Magellan images allow us to divide some types of the plains units to determine the lava flow direction and to map with better accuracy.

  15. Connecting CO intensity mapping to molecular gas and star formation in the epoch of galaxy assembly

    SciTech Connect

    Li, Tony Y.; Wechsler, Risa H.; Devaraj, Kiruthika; Church, Sarah E.

    2016-01-29

    Intensity mapping, which images a single spectral line from unresolved galaxies across cosmological volumes, is a promising technique for probing the early universe. Here we present predictions for the intensity map and power spectrum of the CO(1–0) line from galaxies at $z\\sim 2.4$–2.8, based on a parameterized model for the galaxy–halo connection, and demonstrate the extent to which properties of high-redshift galaxies can be directly inferred from such observations. We find that our fiducial prediction should be detectable by a realistic experiment. Motivated by significant modeling uncertainties, we demonstrate the effect on the power spectrum of varying each parameter in our model. Using simulated observations, we infer constraints on our model parameter space with an MCMC procedure, and show corresponding constraints on the ${L}_{\\mathrm{IR}}$–${L}_{\\mathrm{CO}}$ relation and the CO luminosity function. These constraints would be complementary to current high-redshift galaxy observations, which can detect the brightest galaxies but not complete samples from the faint end of the luminosity function. Furthermore, by probing these populations in aggregate, CO intensity mapping could be a valuable tool for probing molecular gas and its relation to star formation in high-redshift galaxies.

  16. Connecting CO Intensity Mapping to Molecular Gas and Star Formation in the Epoch of Galaxy Assembly

    NASA Astrophysics Data System (ADS)

    Li, Tony Y.; Wechsler, Risa H.; Devaraj, Kiruthika; Church, Sarah E.

    2016-02-01

    Intensity mapping, which images a single spectral line from unresolved galaxies across cosmological volumes, is a promising technique for probing the early universe. Here we present predictions for the intensity map and power spectrum of the CO(1-0) line from galaxies at z˜ 2.4-2.8, based on a parameterized model for the galaxy-halo connection, and demonstrate the extent to which properties of high-redshift galaxies can be directly inferred from such observations. We find that our fiducial prediction should be detectable by a realistic experiment. Motivated by significant modeling uncertainties, we demonstrate the effect on the power spectrum of varying each parameter in our model. Using simulated observations, we infer constraints on our model parameter space with an MCMC procedure, and show corresponding constraints on the {L}{IR}-{L}{CO} relation and the CO luminosity function. These constraints would be complementary to current high-redshift galaxy observations, which can detect the brightest galaxies but not complete samples from the faint end of the luminosity function. By probing these populations in aggregate, CO intensity mapping could be a valuable tool for probing molecular gas and its relation to star formation in high-redshift galaxies.

  17. Connecting CO intensity mapping to molecular gas and star formation in the epoch of galaxy assembly

    DOE PAGES

    Li, Tony Y.; Wechsler, Risa H.; Devaraj, Kiruthika; ...

    2016-01-29

    Intensity mapping, which images a single spectral line from unresolved galaxies across cosmological volumes, is a promising technique for probing the early universe. Here we present predictions for the intensity map and power spectrum of the CO(1–0) line from galaxies atmore » $$z\\sim 2.4$$–2.8, based on a parameterized model for the galaxy–halo connection, and demonstrate the extent to which properties of high-redshift galaxies can be directly inferred from such observations. We find that our fiducial prediction should be detectable by a realistic experiment. Motivated by significant modeling uncertainties, we demonstrate the effect on the power spectrum of varying each parameter in our model. Using simulated observations, we infer constraints on our model parameter space with an MCMC procedure, and show corresponding constraints on the $${L}_{\\mathrm{IR}}$$–$${L}_{\\mathrm{CO}}$$ relation and the CO luminosity function. These constraints would be complementary to current high-redshift galaxy observations, which can detect the brightest galaxies but not complete samples from the faint end of the luminosity function. Furthermore, by probing these populations in aggregate, CO intensity mapping could be a valuable tool for probing molecular gas and its relation to star formation in high-redshift galaxies.« less

  18. Artificial Intelligence Techniques for Predicting and Mapping Daily Pan Evaporation

    NASA Astrophysics Data System (ADS)

    Arunkumar, R.; Jothiprakash, V.; Sharma, Kirty

    2017-08-01

    In this study, Artificial Intelligence techniques such as Artificial Neural Network (ANN), Model Tree (MT) and Genetic Programming (GP) are used to develop daily pan evaporation time-series (TS) prediction and cause-effect (CE) mapping models. Ten years of observed daily meteorological data such as maximum temperature, minimum temperature, relative humidity, sunshine hours, dew point temperature and pan evaporation are used for developing the models. For each technique, several models are developed by changing the number of inputs and other model parameters. The performance of each model is evaluated using standard statistical measures such as Mean Square Error, Mean Absolute Error, Normalized Mean Square Error and correlation coefficient (R). The results showed that daily TS-GP (4) model predicted better with a correlation coefficient of 0.959 than other TS models. Among various CE models, CE-ANN (6-10-1) resulted better than MT and GP models with a correlation coefficient of 0.881. Because of the complex non-linear inter-relationship among various meteorological variables, CE mapping models could not achieve the performance of TS models. From this study, it was found that GP performs better for recognizing single pattern (time series modelling), whereas ANN is better for modelling multiple patterns (cause-effect modelling) in the data.

  19. Flood Water Level Mapping and Prediction Due to Dam Failures

    NASA Astrophysics Data System (ADS)

    Musa, S.; Adnan, M. S.; Ahmad, N. A.; Ayob, S.

    2016-07-01

    Sembrong dam has undergone overflow failure. Flooding has been reported to hit the town, covering an area of up to Parit Raja, located in the district of Batu Pahat. This study aims to identify the areas that will be affected by flood in the event of a dam failure in Sembrong Dam, Kluang, Johor at a maximum level. To grasp the extent, the flood inundation maps have been generated by using the InfoWorks ICM and GIS software. By using these maps, information such as the depth and extent of floods can be identified the main ares flooded. The flood map was created starting with the collection of relevant data such as measuring the depth of the river and a maximum flow rate for Sembrong Dam. The data were obtained from the Drainage and Irrigation Department Malaysia and the Department of Survey and Mapping and HLA Associates Sdn. Bhd. Then, the data were analyzed according to the established Info Works ICM method. The results found that the flooded area were listed at Sri Lalang, Parit Sagil, Parit Sonto, Sri Paya, Parit Raja, Parit Sempadan, Talang Bunut, Asam Bubok, Tanjung Sembrong, Sungai Rambut and Parit Haji Talib. Flood depth obtained for the related area started from 0.5 m up to 1.2 m. As a conclusion, the flood emanating from this study include the area around the town of Ayer Hitam up to Parit Raja approximately of more than 20 km distance. This may give bad implication to residents around these areas. In future studies, other rivers such as Sungai Batu Pahat should be considered for this study to predict and reduce the yearly flood victims for this area.

  20. Hansen solubility parameter as a tool to predict cocrystal formation.

    PubMed

    Mohammad, Mohammad Amin; Alhalaweh, Amjad; Velaga, Sitaram P

    2011-04-04

    The objective of this study was to investigate whether the miscibility of a drug and coformer, as predicted by Hansen solubility parameters (HSPs), can indicate cocrystal formation and guide cocrystal screening. It was also our aim to evaluate various HSPs-based approaches in miscibility prediction. HSPs for indomethacin (the model drug) and over thirty coformers were calculated according to the group contribution method. Differences in the HSPs between indomethacin and each coformer were then calculated using three established approaches, and the miscibility was predicted. Subsequently, differential scanning calorimetry was used to investigate the experimental miscibility and cocrystal formation. The formation of cocrystals was also verified using liquid-assisted grinding. All except one of the drug-coformers that were predicted to be miscible were confirmed experimentally as miscible. All tested theoretical approaches were in agreement in predicting miscibility. All systems that formed cocrystals were miscible. Remarkably, two new cocrystals of indomethacin were discovered in this study. Though it may be necessary to test this approach in a wide range of different coformer and drug compound types for accurate generalizations, the trends with tested systems were clear and suggest that the drug and coformer should be miscible for cocrystal formation. Thus, predicting the miscibility of cocrystal components using solubility parameters can guide the selection of potential coformers prior to exhaustive cocrystal screening work.

  1. Evaluating, predicting and mapping belowground carbon stores in Kenyan mangroves.

    PubMed

    Gress, Selena K; Huxham, Mark; Kairo, James G; Mugi, Lilian M; Briers, Robert A

    2017-01-01

    Despite covering only approximately 138 000 km(2) , mangroves are globally important carbon sinks with carbon density values three to four times that of terrestrial forests. A key challenge in evaluating the carbon benefits from mangrove forest conservation is the lack of rigorous spatially resolved estimates of mangrove sediment carbon stocks; most mangrove carbon is stored belowground. Previous work has focused on detailed estimations of carbon stores over relatively small areas, which has obvious limitations in terms of generality and scope of application. Most studies have focused only on quantifying the top 1 m of belowground carbon (BGC). Carbon stored at depths beyond 1 m, and the effects of mangrove species, location and environmental context on these stores, are poorly studied. This study investigated these variables at two sites (Gazi and Vanga in the south of Kenya) and used the data to produce a country-specific BGC predictive model for Kenya and map BGC store estimates throughout Kenya at spatial scales relevant for climate change research, forest management and REDD+ (reduced emissions from deforestation and degradation). The results revealed that mangrove species was the most reliable predictor of BGC; Rhizophora muronata had the highest mean BGC with 1485.5 t C ha(-1) . Applying the species-based predictive model to a base map of species distribution in Kenya for the year 2010 with a 2.5 m(2) resolution produced an estimate of 69.41 Mt C [±9.15 95% confidence interval (C.I.)] for BGC in Kenyan mangroves. When applied to a 1992 mangrove distribution map, the BGC estimate was 75.65 Mt C (±12.21 95% C.I.), an 8.3% loss in BGC stores between 1992 and 2010 in Kenya. The country-level mangrove map provides a valuable tool for assessing carbon stocks and visualizing the distribution of BGC. Estimates at the 2.5 m(2) resolution provide sufficient details for highlighting and prioritizing areas for mangrove conservation and restoration.

  2. Web-Based Support for Constructing Competence Maps: Design and Formative Evaluation

    ERIC Educational Resources Information Center

    Stoof, Angela; Martens, Rob L.; van Merrienboer, Jeroen J. G.

    2007-01-01

    This article describes the design and formative evaluation of a Web-based tool that supports curriculum developers in constructing competence maps. Competence maps describe final attainment levels of educational programs in terms of--interrelated--competencies. Key requirements for the competence-mapping tool were validity and practicality.…

  3. Heliospheric current sheet inclinations predicted from source surface maps

    NASA Technical Reports Server (NTRS)

    Shodhan, S.; Crooker, N. U.; Hughes, W. J.; Siscoe, G. L.

    1994-01-01

    The inclinations of the neutral line at the ecliptic plane derived from source surface model maps of coronal fields are measured for the interval from June 1976 to March 1992. The mean and median values of 53 deg and 57 deg are close to the average inclinations determined earlier from minimum variance analyses of solar wind measurements at sector boundaries, but the mode falls in the 80 deg - 90 deg bin. This result, which is based on the model assumptions implicit in deriving the source surface maps, predicts that the heliospheric current sheet typically intersects the ecliptic plane nearly at right angles, even without steepening by stream interaction regions. High inclinations dominate the solar cycle for about 7 years around solar maximum. Dips to lower inclination occur near solar minimum, but high variance admits a wide range of inclinations throughout the cycle. Compared to the smooth solar cycle variation of the maximum latitudinal excursion of the neutral line, often treated as the tilt angle of a flat heliospheric current sheet, the noisy variation of the inclinations reflects the degree to which the neutral line deviates from a sine wave, implying warps and corrugations in the current sheet. About a third of the time the neutral line so deviates that it doubles back in longitude.

  4. Heliospheric current sheet inclinations predicted from source surface maps

    NASA Technical Reports Server (NTRS)

    Shodhan, S.; Crooker, N. U.; Hughes, W. J.; Siscoe, G. L.

    1994-01-01

    The inclinations of the neutral line at the ecliptic plane derived from source surface model maps of coronal fields are measured for the interval from June 1976 to March 1992. The mean and median values of 53 deg and 57 deg are close to the average inclinations determined earlier from minimum variance analyses of solar wind measurements at sector boundaries, but the mode falls in the 80 deg - 90 deg bin. This result, which is based on the model assumptions implicit in deriving the source surface maps, predicts that the heliospheric current sheet typically intersects the ecliptic plane nearly at right angles, even without steepening by stream interaction regions. High inclinations dominate the solar cycle for about 7 years around solar maximum. Dips to lower inclination occur near solar minimum, but high variance admits a wide range of inclinations throughout the cycle. Compared to the smooth solar cycle variation of the maximum latitudinal excursion of the neutral line, often treated as the tilt angle of a flat heliospheric current sheet, the noisy variation of the inclinations reflects the degree to which the neutral line deviates from a sine wave, implying warps and corrugations in the current sheet. About a third of the time the neutral line so deviates that it doubles back in longitude.

  5. The digital geologic map of Wyoming in ARC/INFO format

    USGS Publications Warehouse

    Green, G.N.; Drouillard, P.H.

    1994-01-01

    This geologic map was prepared as part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Wyoming (Love and Christiansen, 1985). Consequently, the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the State base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1985 geologic map. Descriptors: The Digital Geologic Map of Wyoming in ARC/INFO Format Open-File Report 94-0425

  6. Geologic Mapping of the Medusae Fossae Formation, Mars, and the Northern Lowland Plains, Venus

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.

    2010-01-01

    This report summarizes the status of mapping projects supported by NASA grant NNX07AP42G, through the Planetary Geology and Geophysics (PGG) program. The PGG grant is focused on 1:2M-scale mapping of portions of the Medusae Fossae Formation (MFF) on Mars. Also described below is the current status of two Venus geologic maps, generated under an earlier PGG mapping grant.

  7. Geologic Mapping of the Medusae Fossae Formation on Mars and the Northern Lowland Plains of Venus

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.

    2009-01-01

    This report summarizes the status of mapping projects supported by NASA grant NNX07AP42G, through the Planetary Geology and Geophysics (PGG) program. The PGG grant is focused on 1:2M-scale mapping of portions of the Medusae Fossae Formation (MFF) on Mars. Also described below is the current status of two Venus geo-logic maps, generated under an earlier PGG mapping grant.

  8. The Star Formation in Radio Survey: Mapping Star Formation in Nearby Galaxies with 33GHz Emission

    NASA Astrophysics Data System (ADS)

    Dong, Dillon; Murphy, Eric J.; Momjian, Emmanuel; Nyland, Kristina; Condon, James J.; Helou, George; Meier, David S.; Ott, Juergen; Schinnerer, Eva; Turner, Jean

    2015-01-01

    We present initial results from the 33GHz phase of the Star Formation in Radio Survey (SFRS), including a gallery of 2" resolution Jansky Very Large Array (VLA) images and spatially resolved thermal / synchrotron emission models in a subset of sources. The SFRS is targeting 118 galaxy nuclei and extranuclear star-forming regions in 56 nearby (d < 30Mpc) galaxies included in the Spitzer/SINGS and Herschel/KINGFISH legacy programs. VLA observations of the entire sample have recently been completed at 3GHz (S band), 15GHz (Ku band) and 33GHz (Ka band). For an initial subset of 9 targets, we have also obtained 90GHz ALMA continuum and line imaging during cycle 1 observations.The frequency spacing of our complete radio data set will allow us to accurately measure the radio spectral index of these targets, in order to model the physical processes that produce the radio emission. In particular, 33GHz observations of HII regions probe free-free emission, providing a sensitive, dust-unbiased measure of the current star formation activity in each complex. We can use the differences between 33GHz derived star formation rates and those derived with other tracers such as synchrotron radiation, extinction corrected UV and Hα emission, and infrared luminosity to examine the dependence of each tracer on separately measured variables such as extinction, metallicity and ionizing radiation field strength. Consequently, these data will help calibrate other empirically-derived star formation rate diagnostics that are more easily measured for high redshift studies, and help interpret rest-frame 33GHz observations from a new generation of deep high frequency (>10GHz) radio surveys.As an example of the science that can be done with SFRS data, we have used our images along with an archival 1.4GHz and a new 5GHz VLA image to map the spectral index, spectral curvature, and the separated thermal and synchrotron components of NGC1266, a low level AGN with a mass outflow rate of > 50 M⊙ / yr

  9. Formative Assessment of Classroom Concept Maps: The Reasonable Fallible Analyser

    ERIC Educational Resources Information Center

    Conlon, Tom

    2006-01-01

    Concept mapping is a powerful learning technique that can be enhanced by computer technology. Software tools are already available for the preparation of concept maps but as yet, few systems provide feedback on their content. The claim made by this article is that by enlisting the student as an assessment partner, computer-based feedback becomes…

  10. Predicting Lake Depths from Topography to Map Global Lake Volume

    NASA Astrophysics Data System (ADS)

    Holtzman, N.; Pavelsky, T.

    2016-12-01

    The depth of a lake affects its role in climate and biogeochemical cycling. There is a lack of lake depth data due to the difficulty of measuring bathymetry, which impedes the accurate inclusion of lakes in climate models and the assessment of global water resources and carbon storage. However, lake depths can be estimated from land topography, for which remotely-sensed DEM data is available. We develop a simple statistical model to predict lake depth from two explanatory variables: the mean relief above the lake surface of a buffer surrounding the lake, and whether the lake's location was glaciated in the last ice age. The model is based on 328 lakes with known depths, located on all continents but Antarctica, and has an r2 of 0.57. We then apply this model to a set of over 200,000 lakes from the Global Lakes and Wetlands Database to produce global gridded maps of predicted total lake volume and average depth. The realistic depth estimates provided by our model may improve the accuracy of future studies of climate and water resources.

  11. Predicting the size of the progeny mapping population required to positionally clone a gene.

    PubMed

    Dinka, Stephen J; Campbell, Matthew A; Demers, Tyler; Raizada, Manish N

    2007-08-01

    A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.

  12. Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism.

    PubMed

    Tong, Chunfa; Shen, Lianying; Lv, Yafei; Wang, Zhong; Wang, Xiaoling; Feng, Sisi; Li, Xin; Sui, Yihan; Pang, Xiaoming; Wu, Rongling

    2014-01-01

    Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation.

  13. Unbiased atlas formation via large deformations metric mapping.

    PubMed

    Lorenzen, Peter; Davis, Brad; Joshi, Sarang

    2005-01-01

    The construction of population atlases is a key issue in medical image analysis, and particularly in brain mapping. Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and to facilitate tissue and object segmentation via registration of anatomical labels. We formulate the unbiased atlas construction problem as a Fréchet mean estimation in the space of diffeomorphisms via large deformations metric mapping. A novel method for computing constant speed velocity fields and an analysis of atlas stability and robustness using entropy are presented. We address the question: how many images are required to build a stable brain atlas?

  14. QSPR for predicting chloroform formation in drinking water disinfection.

    PubMed

    Luilo, G B; Cabaniss, S E

    2011-01-01

    Chlorination is the most widely used technique for water disinfection, but may lead to the formation of chloroform (trichloromethane; TCM) and other by-products. This article reports the first quantitative structure-property relationship (QSPR) for predicting the formation of TCM in chlorinated drinking water. Model compounds (n = 117) drawn from 10 literature sources were divided into training data (n = 90, analysed by five-way leave-many-out internal cross-validation) and external validation data (n = 27). QSPR internal cross-validation had Q² = 0.94 and root mean square error (RMSE) of 0.09 moles TCM per mole compound, consistent with external validation Q2 of 0.94 and RMSE of 0.08 moles TCM per mole compound, and met criteria for high predictive power and robustness. In contrast, log TCM QSPR performed poorly and did not meet the criteria for predictive power. The QSPR predictions were consistent with experimental values for TCM formation from tannic acid and for model fulvic acid structures. The descriptors used are consistent with a relatively small number of important TCM precursor structures based upon 1,3-dicarbonyls or 1,3-diphenols.

  15. Predictive model for ice formation on superhydrophobic surfaces.

    PubMed

    Bahadur, Vaibhav; Mishchenko, Lidiya; Hatton, Benjamin; Taylor, J Ashley; Aizenberg, Joanna; Krupenkin, Tom

    2011-12-06

    The prevention and control of ice accumulation has important applications in aviation, building construction, and energy conversion devices. One area of active research concerns the use of superhydrophobic surfaces for preventing ice formation. The present work develops a physics-based modeling framework to predict ice formation on cooled superhydrophobic surfaces resulting from the impact of supercooled water droplets. This modeling approach analyzes the multiple phenomena influencing ice formation on superhydrophobic surfaces through the development of submodels describing droplet impact dynamics, heat transfer, and heterogeneous ice nucleation. These models are then integrated together to achieve a comprehensive understanding of ice formation upon impact of liquid droplets at freezing conditions. The accuracy of this model is validated by its successful prediction of the experimental findings that demonstrate that superhydrophobic surfaces can fully prevent the freezing of impacting water droplets down to surface temperatures of as low as -20 to -25 °C. The model can be used to study the influence of surface morphology, surface chemistry, and fluid and thermal properties on dynamic ice formation and identify parameters critical to achieving icephobic surfaces. The framework of the present work is the first detailed modeling tool developed for the design and analysis of surfaces for various ice prevention/reduction strategies. © 2011 American Chemical Society

  16. Predictive Mapping of Forest Attributes on the Fishlake National Forest

    Treesearch

    Tracey S. Frescino; Gretchen G. Moisen

    2005-01-01

    Forest land managers increasingly need maps of forest characteristics to aid in planning and management. A set of 30-m resolution maps was prepared for the Fishlake National Forest by modeling FIA plot variables as nonparametric functions of ancillary digital data. The set includes maps of volume, biomass, growth, stand age, size, crown cover, and various aspen...

  17. Active plasma source formation in the MAP diode

    SciTech Connect

    Lamppa, K.P.; Stinnett, R.W.; Renk, T.J.

    1995-07-01

    The Ion Beam Surface Treatment (IBEST) program is exploring using ion beams to treat the surface of a wide variety of materials. These experiments have shown that improved corrosion resistance, surface hardening, grain size modification, polishing and surface cleaning can all be achieved using a pulsed 0.4-0.8 MeV ion beam delivering 1-10 J/cm{sup 2}. The Magnetically-confined Anode Plasma (MAP) diode, developed at Cornell University, produces an active plasma which can be used to treat the surfaces of materials. The diode consists of a fast puff valve as the source of gas to produce the desired ions and two capacitively driven B-fields. A slow magnetic field is used for electron insulation and a fast field is used to both ionize the puffed gas and to position the plasma in the proper spatial location in the anode prior to the accelerator pulse. The relative timing between subsystems is an important factor in the effective production of the active plasma source for the MAP diode system. The MAP diode has been characterized using a Langmuir probe to measure plasma arrival times at the anode annulus for hydrogen gas. This data was then used to determine the optimum operating point for the MAP diode on RHEPP-1 accelerator shots. Operation of the MAP diode system to produce an ion beam of 500 kV, 12 kA with 40% efficiency (measured at the diode) has been demonstrated.

  18. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction.

    PubMed

    Potocnakova, Lenka; Bhide, Mangesh; Pulzova, Lucia Borszekova

    2016-01-01

    Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.

  19. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction

    PubMed Central

    Potocnakova, Lenka

    2016-01-01

    Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes. PMID:28127568

  20. Prediction of Standard Enthalpy of Formation by a QSPR Model

    PubMed Central

    Vatani, Ali; Mehrpooya, Mehdi; Gharagheizi, Farhad

    2007-01-01

    The standard enthalpy of formation of 1115 compounds from all chemical groups, were predicted using genetic algorithm-based multivariate linear regression (GA-MLR). The obtained multivariate linear five descriptors model by GA-MLR has correlation coefficient (R2 = 0.9830). All molecular descriptors which have entered in this model are calculated from chemical structure of any molecule. As a result, application of this model for any compound is easy and accurate.

  1. Electromagnetic wave method for mapping subterranean earth formations

    DOEpatents

    Shuck, Lowell Z.; Fasching, George E.; Balanis, Constantine A.

    1977-01-01

    The present invention is directed to a method for remotely mapping subterranean coal beds prior to and during in situ gasification operations. This method is achieved by emplacing highly directional electromagnetic wave transmitters and receivers in bore holes penetrating the coal beds and then mapping the anomalies surrounding each bore hole by selectively rotating and vertically displacing the directional transmitter in a transmitting mode within the bore hole, and thereafter, initiating the gasification of the coal at bore holes separate from those containing the transmitters and receivers and then utilizing the latter for monitoring the burn front as it progresses toward the transmitters and receivers.

  2. Predictions of Thrombus Formation Using Lattice Boltzmann Method

    NASA Astrophysics Data System (ADS)

    Tamagawa, Masaaki; Matsuo, Sumiaki

    This paper describes the prediction of index of thrombus formation in shear blood flow by computational fluid dynamics (CFD) with Lattice Boltzmann Method (LBM), applying to orifice-pipe blood flow and flow around a cylinder, which is simple model of turbulent shear stress in the high speed rotary blood pumps and complicated geometry of medical fluid machines. The results of the flow field in the orifice-pipe flow using LBM are compared with experimental data and those using finite difference method, and it is found that the reattachment length of the backward facing step flow is predicted as precise as that the experiment and the finite difference method. As for thrombus formation, from the computational data of flow around the cylinder in the channel, the thrombus formation (thickness) is estimated using (1) shear rate and adhesion force (effective distance) to the wall independently, and (2) shear rate function with adhesion force (effective distance), and it is found that the prediction method using shear rate function with adhesion force is more accurate than the method using the former one.

  3. Prediction of Peptide and Protein Propensity for Amyloid Formation.

    PubMed

    Família, Carlos; Dennison, Sarah R; Quintas, Alexandre; Phoenix, David A

    2015-01-01

    Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔG° values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation.

  4. Prediction of Peptide and Protein Propensity for Amyloid Formation

    PubMed Central

    Família, Carlos; Dennison, Sarah R.; Quintas, Alexandre; Phoenix, David A.

    2015-01-01

    Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔG° values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation. PMID:26241652

  5. Evidence for the Role of MAP1B in Axon Formation

    PubMed Central

    Gonzalez-Billault, Christian; Avila, Jesus; Cáceres, Alfredo

    2001-01-01

    Cultured neurons obtained from a hypomorphous MAP1B mutant mouse line display a selective and significant inhibition of axon formation that reflects a delay in axon outgrowth and a reduced rate of elongation. This phenomenon is paralleled by decreased microtubule formation and dynamics, which is dramatic at the distal axonal segment, as well as in growth cones, where the more recently assembled microtubule polymer normally predominates. These neurons also have aberrant growth cone formation and increased actin-based protrusive activity. Taken together, this study provides direct evidence showing that by promoting microtubule dynamics and regulating cytoskeletal organization MAP1B has a crucial role in axon formation. PMID:11452005

  6. The Use of Concept Maps to Assess Preservice Teacher Understanding: A Formative Approach in Mathematics Education

    ERIC Educational Resources Information Center

    Brakoniecki, Aaron; Shah, Fahmil

    2017-01-01

    The research reported in this article explored the methods by which concept maps served as formative assessment by capturing changes in the ways preservice mathematics teachers represented their understanding of algebra. The participants were enrolled in a course on high school algebra for teachers and created the maps on the first and last day of…

  7. An application of quantile random forests for predictive mapping of forest attributes

    Treesearch

    E.A. Freeman; G.G. Moisen

    2015-01-01

    Increasingly, random forest models are used in predictive mapping of forest attributes. Traditional random forests output the mean prediction from the random trees. Quantile regression forests (QRF) is an extension of random forests developed by Nicolai Meinshausen that provides non-parametric estimates of the median predicted value as well as prediction quantiles. It...

  8. POSTERIOR PREDICTIVE MODEL CHECKS FOR DISEASE MAPPING MODELS. (R827257)

    EPA Science Inventory

    Disease incidence or disease mortality rates for small areas are often displayed on maps. Maps of raw rates, disease counts divided by the total population at risk, have been criticized as unreliable due to non-constant variance associated with heterogeneity in base population si...

  9. Predicting Behavior from Cognitive Cause Maps of a Work Setting.

    ERIC Educational Resources Information Center

    Komocar, John

    Cognitive cause maps permit a topological investigation of the complexity of organizational events and behaviors. Because cognitive cause maps are believed to be ordered according to a givens-means-ends schema, they contain information about an individual's motivation structure. In a work setting an individual engages in several different acts.…

  10. POSTERIOR PREDICTIVE MODEL CHECKS FOR DISEASE MAPPING MODELS. (R827257)

    EPA Science Inventory

    Disease incidence or disease mortality rates for small areas are often displayed on maps. Maps of raw rates, disease counts divided by the total population at risk, have been criticized as unreliable due to non-constant variance associated with heterogeneity in base population si...

  11. The evolution of logic circuits for the purpose of protein contact map prediction.

    PubMed

    Chapman, Samuel D; Adami, Christoph; Wilke, Claus O; B Kc, Dukka

    2017-01-01

    Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.

  12. The evolution of logic circuits for the purpose of protein contact map prediction

    PubMed Central

    Chapman, Samuel D.; Adami, Christoph; Wilke, Claus O.

    2017-01-01

    Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset. PMID:28439455

  13. Understanding Visual Map Formation through Vortex Dynamics of Spin Hamiltonian Models

    NASA Astrophysics Data System (ADS)

    Cho, Myoung Won; Kim, Seunghwan

    2004-01-01

    The pattern formation in orientation and ocular dominance columns is one of the most investigated problems in the brain. From a known cortical structure, we build spinlike Hamiltonian models with long-range interactions of the Mexican hat type. These Hamiltonian models allow a coherent interpretation of the diverse phenomena in the visual map formation with the help of relaxation dynamics of spin systems. In particular, we explain various phenomena of self-organization in orientation and ocular dominance map formation including the pinwheel annihilation and its dependency on the columnar wave vector and boundary conditions.

  14. A two-stage approach for improved prediction of residue contact maps.

    PubMed

    Vullo, Alessandro; Walsh, Ian; Pollastri, Gianluca

    2006-03-30

    Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure. Although improvements have occurred over the last years, the problem of accurately predicting residue contact maps from primary sequences is still largely unsolved. Among the reasons for this are the unbalanced nature of the problem (with far fewer examples of contacts than non-contacts), the formidable challenge of capturing long-range interactions in the maps, the intrinsic difficulty of mapping one-dimensional input sequences into two-dimensional output maps. In order to alleviate these problems and achieve improved contact map predictions, in this paper we split the task into two stages: the prediction of a map's principal eigenvector (PE) from the primary sequence; the reconstruction of the contact map from the PE and primary sequence. Predicting the PE from the primary sequence consists in mapping a vector into a vector. This task is less complex than mapping vectors directly into two-dimensional matrices since the size of the problem is drastically reduced and so is the scale length of interactions that need to be learned. We develop architectures composed of ensembles of two-layered bidirectional recurrent neural networks to classify the components of the PE in 2, 3 and 4 classes from protein primary sequence, predicted secondary structure, and hydrophobicity interaction scales. Our predictor, tested on a non redundant set of 2171 proteins, achieves classification performances of up to 72.6%, 16% above a base-line statistical predictor. We design a system for the prediction of contact maps from the predicted PE. Our results show that predicting maps through the PE yields sizeable gains especially for long-range contacts which are particularly critical for accurate protein 3D reconstruction. The final predictor's accuracy on a non-redundant set of 327 targets is 35.4% and 19.8% for minimum contact separations of

  15. Predictive lithological mapping of Canada's North using Random Forest classification applied to geophysical and geochemical data

    NASA Astrophysics Data System (ADS)

    Harris, J. R.; Grunsky, E. C.

    2015-07-01

    A recent method for mapping lithology which involves the Random Forest (RF) machine classification algorithm is evaluated. Random Forests, a supervised classifier, requires training data representative of each lithology to produce a predictive or classified map. We use two training strategies, one based on the location of lake sediment geochemical samples where the rock type is recorded from a legacy geology map at each sample station and the second strategy is based on lithology recorded from field stations derived from reconnaissance field mapping. We apply the classification to interpolated major and minor lake sediment geochemical data as well as airborne total field magnetic and gamma ray spectrometer data. Using this method we produce predictions of the lithology of a large section of the Hearne Archean - Paleoproterozoic tectonic domain, in northern Canada. The results indicate that meaningful predictive lithologic maps can be produced using RF classification for both training strategies. The best results were achieved when all data were used; however, the geochemical and gamma ray data were the strongest predictors of the various lithologies. The maps generated from this research can be used to compliment field mapping activities by focusing field work on areas where the predicted geology and legacy geology do not match and as first order geological maps in poorly mapped areas.

  16. Stochastic interaction between neural activity and molecular cues in the formation of topographic maps

    PubMed Central

    Owens, Melinda T.; Feldheim, David A.; Stryker, Michael P.; Triplett, Jason W.

    2015-01-01

    SUMMARY Topographic maps in visual processing areas maintain the spatial order of the visual world. Molecular cues and neuronal activity both play critical roles in map formation, but their interaction remains unclear. Here, we demonstrate that when molecular- and activity-dependent cues are rendered nearly equal in force, they drive topographic mapping stochastically. The functional and anatomical representation of azimuth in the superior colliculus of heterozygous Islet2-EphA3 knock-in (Isl2EphA3/+) mice is variable: maps may be single, duplicated, or a combination of the two. This heterogeneity is not due to genetic differences, since map organizations in individual mutant animals often differ between colliculi. Disruption of spontaneous waves of retinal activity resulted in uniform map organization in Isl2EphA3/+ mice, demonstrating that correlated spontaneous activity is required for map heterogeneity. Computational modeling replicates this heterogeneity, revealing that molecular- and activity-dependent forces interact simultaneously and stochastically during topographic map formation. PMID:26402608

  17. Can formative quizzes predict or improve summative exam performance?

    PubMed

    Zhang, Niu; Henderson, Charles N R

    2015-03-01

    Despite wide use, the value of formative exams remains unclear. We evaluated the possible benefits of formative assessments in a physical examination course at our chiropractic college. Three hypotheses were examined: (1) Receiving formative quizzes (FQs) will increase summative exam (SX) scores, (2) writing FQ questions will further increase SE scores, and (3) FQs can predict SX scores. Hypotheses were tested across three separate iterations of the class. The SX scores for the control group (Class 3) were significantly less than those of Classes 1 and 2, but writing quiz questions and taking FQs (Class 1) did not produce significantly higher SX scores than only taking FQs (Class 2). The FQ scores were significant predictors of SX scores, accounting for 52% of the SX score. Sex, age, academic degrees, and ethnicity were not significant copredictors. Our results support the assertion that FQs can improve written SX performance, but students producing quiz questions didn't further increase SX scores. We concluded that nonthreatening FQs may be used to enhance student learning and suggest that they also may serve to identify students who, without additional remediation, will perform poorly on subsequent summative written exams.

  18. Mapping the pinhole formation pathway of S21.

    PubMed

    Pang, Ting; Park, Taehyun; Young, Ry

    2010-11-01

    Phage holins are small, lethal membrane proteins of two general types: canonical holins, like λ S105, which oligomerizes and forms large membrane holes of unprecedented size; and pinholins, like S(21) 68 of lambdoid phage 21, which forms homo-heptameric channels, or pinholes, with a lumen of <2 nm. Pinholes depolarize the membrane, leading to activation of secreted endolysins and murein degradation. S(21) 68 has two transmembrane domains, TMD1 and TMD2. TMD2 alone lines the pinhole, making heterotypic interactions involving two surfaces, A and B. Mutational analysis on S(21) 68 suggested that S(21) 68 initially forms inactive dimer, with TMD1 inhibiting TMD2 both in cis and trans. When TMD1 exits the membrane to the periplasm, it liberates TMD2 to participate in the pathway to pinhole formation. In this study, further mutational analysis suggests a refined pinhole formation pathway, with the existence of at least two intermediate states. We propose that the pathway begins in the activated dimer state, with a homotypic TMD2 interface involving the A surface. Evidence is presented for a further oligomeric state involving a heterotypic A:B interaction. Moreover, the data suggest that a glycine-zipper motif present in the A interface of TMD2 is involved in every stage downstream of the inactive dimer. © 2010 Blackwell Publishing Ltd.

  19. Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method.

    PubMed

    Nakajima, Shunsuke; Alvarez-Salgado, Emma; Kikuchi, Takeshi; Arredondo-Peter, Raúl

    2005-11-15

    Computational methods, such as the ADM (average distance map) method, have been developed to predict folding of homologous proteins. In this work we used the ADM method to predict the folding pathway and kinetics among selected plant nonsymbiotic (nsHb), symbiotic (Lb), and truncated (tHb) hemoglobins (Hbs). Results predicted that (1) folding of plant Hbs occurs throughout the formation of compact folding modules mostly formed by helices A, B, and C, and E, F, G, and H (folding modules A/C and E/H, respectively), and (2) primitive (moss) nsHbs fold in the C-->N direction, evolved (monocot and dicot) nsHbs fold either in the C-->N or N-->C direction, and Lbs and plant tHbs fold in the C-->N direction. We also predicted relative folding rates of plant Hbs from qualitative analyses of the stability of subdomains and classified plant Hbs into fast and moderate folding. ADM analysis of nsHbs predicted that prehelix A plays a role during folding of the N-terminal domain of Ceratodon nsHb, and that CD-loop plays a role in folding of primitive (Physcomitrella and Ceratodon) but not evolved nsHbs. Modeling of the rice Hb1 A/C and E/H modules showed that module E/H overlaps to the Mycobacterium tuberculosis HbO two-on-two folding. This observation suggests that module E/H is an ancient tertiary structure in plant Hbs.

  20. Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning

    PubMed Central

    Basso, Edward; Arai, Mamiko; Dabaghian, Yuri

    2016-01-01

    The mammalian hippocampus plays a crucial role in producing a cognitive map of space—an internalized representation of the animal’s environment. We have previously shown that it is possible to model this map formation using a topological framework, in which information about the environment is transmitted through the temporal organization of neuronal spiking activity, particularly those occasions in which the firing of different place cells overlaps. In this paper, we discuss how gamma rhythm, one of the main components of the extracellular electrical field potential affects the efficiency of place cell map formation. Using methods of algebraic topology and the maximal entropy principle, we demonstrate that gamma modulation synchronizes the spiking of dynamical cell assemblies, which enables learning a spatial map at faster timescales. PMID:27636199

  1. Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning.

    PubMed

    Basso, Edward; Arai, Mamiko; Dabaghian, Yuri

    2016-09-01

    The mammalian hippocampus plays a crucial role in producing a cognitive map of space-an internalized representation of the animal's environment. We have previously shown that it is possible to model this map formation using a topological framework, in which information about the environment is transmitted through the temporal organization of neuronal spiking activity, particularly those occasions in which the firing of different place cells overlaps. In this paper, we discuss how gamma rhythm, one of the main components of the extracellular electrical field potential affects the efficiency of place cell map formation. Using methods of algebraic topology and the maximal entropy principle, we demonstrate that gamma modulation synchronizes the spiking of dynamical cell assemblies, which enables learning a spatial map at faster timescales.

  2. Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions

    PubMed Central

    Pienaar, Elsje; Matern, William M.; Linderman, Jennifer J.

    2016-01-01

    Granulomas are a hallmark of tuberculosis. Inside granulomas, the pathogen Mycobacterium tuberculosis may enter a metabolically inactive state that is less susceptible to antibiotics. Understanding M. tuberculosis metabolism within granulomas could contribute to reducing the lengthy treatment required for tuberculosis and provide additional targets for new drugs. Two key adaptations of M. tuberculosis are a nonreplicating phenotype and accumulation of lipid inclusions in response to hypoxic conditions. To explore how these adaptations influence granuloma-scale outcomes in vivo, we present a multiscale in silico model of granuloma formation in tuberculosis. The model comprises host immunity, M. tuberculosis metabolism, M. tuberculosis growth adaptation to hypoxia, and nutrient diffusion. We calibrated our model to in vivo data from nonhuman primates and rabbits and apply the model to predict M. tuberculosis population dynamics and heterogeneity within granulomas. We found that bacterial populations are highly dynamic throughout infection in response to changing oxygen levels and host immunity pressures. Our results indicate that a nonreplicating phenotype, but not lipid inclusion formation, is important for long-term M. tuberculosis survival in granulomas. We used virtual M. tuberculosis knockouts to predict the impact of both metabolic enzyme inhibitors and metabolic pathways exploited to overcome inhibition. Results indicate that knockouts whose growth rates are below ∼66% of the wild-type growth rate in a culture medium featuring lipid as the only carbon source are unable to sustain infections in granulomas. By mapping metabolite- and gene-scale perturbations to granuloma-scale outcomes and predicting mechanisms of sterilization, our method provides a powerful tool for hypothesis testing and guiding experimental searches for novel antituberculosis interventions. PMID:26975995

  3. Vector Topographic Map Data over the BOREAS NSA and SSA in SIF Format

    NASA Technical Reports Server (NTRS)

    Knapp, David; Nickeson, Jaime; Hall, Forrest G. (Editor)

    2000-01-01

    This data set contains vector contours and other features of individual topographic map sheets from the National Topographic Series (NTS). The map sheet files were received in Standard Interchange Format (SIF) and cover the BOReal Ecosystem-Atmosphere Study (BOREAS) Northern Study Area (NSA) and Southern Study Area (SSA) at scales of 1:50,000 and 1:250,000. The individual files are stored in compressed Unix tar archives.

  4. Quantitative assessment of computational models for retinotopic map formation

    PubMed Central

    Sterratt, David C; Cutts, Catherine S; Willshaw, David J; Eglen, Stephen J

    2014-01-01

    ABSTRACT Molecular and activity‐based cues acting together are thought to guide retinal axons to their terminal sites in vertebrate optic tectum or superior colliculus (SC) to form an ordered map of connections. The details of mechanisms involved, and the degree to which they might interact, are still not well understood. We have developed a framework within which existing computational models can be assessed in an unbiased and quantitative manner against a set of experimental data curated from the mouse retinocollicular system. Our framework facilitates comparison between models, testing new models against known phenotypes and simulating new phenotypes in existing models. We have used this framework to assess four representative models that combine Eph/ephrin gradients and/or activity‐based mechanisms and competition. Two of the models were updated from their original form to fit into our framework. The models were tested against five different phenotypes: wild type, Isl2‐EphA3 ki/ki, Isl2‐EphA3 ki/+, ephrin‐A2,A3,A5 triple knock‐out (TKO), and Math5 −/− (Atoh7). Two models successfully reproduced the extent of the Math5 −/− anteromedial projection, but only one of those could account for the collapse point in Isl2‐EphA3 ki/+. The models needed a weak anteroposterior gradient in the SC to reproduce the residual order in the ephrin‐A2,A3,A5 TKO phenotype, suggesting either an incomplete knock‐out or the presence of another guidance molecule. Our article demonstrates the importance of testing retinotopic models against as full a range of phenotypes as possible, and we have made available MATLAB software, we wrote to facilitate this process. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 75: 641–666, 2015 PMID:25367067

  5. Applications systems verification and transfer project. Volume 8: Satellite snow mapping and runoff prediction handbook

    NASA Technical Reports Server (NTRS)

    Bowley, C. J.; Barnes, J. C.; Rango, A.

    1981-01-01

    The purpose of the handbook is to update the various snowcover interpretation techniques, document the snow mapping techniques used in the various ASVT study areas, and describe the ways snowcover data have been applied to runoff prediction. Through documentation in handbook form, the methodology developed in the Snow Mapping ASVT can be applied to other areas.

  6. Activity dependent mechanisms of visual map formation--from retinal waves to molecular regulators.

    PubMed

    Assali, Ahlem; Gaspar, Patricia; Rebsam, Alexandra

    2014-11-01

    The refinement of neural connections requires activity-dependent mechanisms in addition to the genetic program initially establishing wiring diagrams. The well-understood organization of the visual system makes it an accessible model for analyzing the contribution of activity in the formation of connectivity. Prior to visual experience, patterned spontaneous activity in the form of retinal waves has an important role for the establishment of eye-specific and retinotopic maps by acting on the refinement of axon arborization. In the present review, which focuses on experimental data obtained in mice and ferrets, we highlight the features of retinal activity that are important for visual map formation and question whether synaptic release and Hebbian based competition rules apply to this system. Recent evidence using genetic tools that allowed the manipulation of different features of neural activity have clarified the controversy on whether activity is instructive or permissive for visual map formation. Furthermore, current evidence strongly suggests that different mechanisms are at play for different types of axons (ipsilateral vs. contralateral), maps (eye-specific vs. retinotopic) or targets. Many molecules that either modulate activity or are modulated by activity are important in the formation of the visual map, such as adenylate cyclase 1, serotonin, or molecules from the immune system. Finally, new players in the game include retrograde messengers signaling from the target cell to the retinal axons as well as microglia that could help to eliminate inappropriate synapses.

  7. Formation of temporal-feature maps by axonal propagation of synaptic learning

    PubMed Central

    Kempter, Richard; Leibold, Christian; Wagner, Hermann; van Hemmen, J. Leo

    2001-01-01

    Computational maps are of central importance to a neuronal representation of the outside world. In a map, neighboring neurons respond to similar sensory features. A well studied example is the computational map of interaural time differences (ITDs), which is essential to sound localization in a variety of species and allows resolution of ITDs of the order of 10 μs. Nevertheless, it is unclear how such an orderly representation of temporal features arises. We address this problem by modeling the ontogenetic development of an ITD map in the laminar nucleus of the barn owl. We show how the owl's ITD map can emerge from a combined action of homosynaptic spike-based Hebbian learning and its propagation along the presynaptic axon. In spike-based Hebbian learning, synaptic strengths are modified according to the timing of pre- and postsynaptic action potentials. In unspecific axonal learning, a synapse's modification gives rise to a factor that propagates along the presynaptic axon and affects the properties of synapses at neighboring neurons. Our results indicate that both Hebbian learning and its presynaptic propagation are necessary for map formation in the laminar nucleus, but the latter can be orders of magnitude weaker than the former. We argue that the algorithm is important for the formation of computational maps, when, in particular, time plays a key role. PMID:11274439

  8. The Panchromatic Hubble Andromeda Treasury. XVII. Examining Obscured Star Formation with Synthetic Ultraviolet Flux Maps in M31.

    NASA Astrophysics Data System (ADS)

    Lewis, Alexia R.; Simones, Jacob E.; Johnson, Benjamin D.; Dalcanton, Julianne J.; Skillman, Evan D.; Weisz, Daniel R.; Dolphin, Andrew E.; Williams, Benjamin F.; Bell, Eric F.; Fouesneau, Morgan; Kapala, Maria; Rosenfield, Philip; Schruba, Andreas

    2017-01-01

    We present synthetic far- and near-ultraviolet ({FUV} and {NUV}) maps of M31, both with and without dust reddening. These maps were constructed from spatially resolved star formation histories (SFHs) derived from optical Hubble Space Telescope imaging of resolved stars, taken as part of the Panchromatic Hubble Andromeda Treasury program. We use stellar population synthesis modeling to generate synthetic UV maps with a spatial resolution of ∼100 pc (∼24 arcsec), projected. When reddening is included, these maps reproduce all of the main morphological features in the GALEX imaging, including rings and large star-forming complexes. The predicted UV flux also agrees well with the observed flux, with median ratios between the modeled and observed flux of {{log}}10({f}{FUV}{syn}/{f}{FUV}{obs})=0.03+/- 0.24 and {{log}}10({f}{NUV}{syn}/{f}{NUV}{obs})=-0.03+/- 0.16 in the {FUV} and {NUV}, respectively. This agreement is particularly impressive given that we used only optical photometry to construct these UV maps. Having verified the synthetic reddened maps, we use the dust-free maps to examine properties of obscured flux and star formation. We compare our dust-free and reddened maps of {FUV} flux with the observed GALEX {FUV} flux and {FUV} + 24 μm flux to examine the fraction of obscured flux. We find that the maps of synthetic flux require that ∼90% of the {FUV} flux in M31 is obscured by dust, while the GALEX -based methods suggest that ∼70% of the {FUV} flux is absorbed by dust. This 30% increase in the estimate of the obscured flux is driven by significant differences between the dust-free synthetic {FUV} flux and that derived when correcting the observed {FUV} flux for dust absorption with 24 μm emission observations. The difference is further illustrated when we compare the SFRs derived from the {FUV} + 24 μm flux with the 100 Myr average SFR from the CMD-based SFHs. We find that the 24 μm corrected {FUV} flux underestimates the SFR by a factor of 2.3–2

  9. Predictive lymphatic mapping: a method for mapping lymphatic channels in patients with advanced unilateral lymphedema using indocyanine green lymphography.

    PubMed

    Mihara, Makoto; Seki, Yukio; Hara, Hisako; Iida, Takuya; Oka, Aiko; Kikuchi, Kazuki; Narushima, Mitsunaga; Haragi, Makiko; Furniss, Dominic; Hin-Lun, Lawrence; Mitsui, Kito; Murai, Noriyuki; Koshima, Isao

    2014-01-01

    In severe lymphedema, indocyanine green lymphography cannot be used to map lymphatic channels before lymphaticovenular anastomosis (LVA) because linear lymphatics cannot be detected in a severely affected leg. Here, we describe a new method, which we refer to as predictive lymphatic mapping, to predict the location of lymphatics for anastomosis in unilateral lymphedema, thereby improving surgical accuracy and efficiency. The approach consists of marking anatomical landmarks and joining selected landmarks with fixed lines. The distance from these fixed lines to lymphatic channels mapped by indocyanine green lymphography in the unaffected leg is then measured, scaled up based on the difference in circumference between the legs, and transposed to the affected leg. To date, we have used this method in 5 cases of unilateral or asymmetric lymphedema of the lower extremities. In no cases have we failed to find a lymphatic channel suitable for LVA within a 2-cm incision. These results suggest that predictive lymphatic mapping is a useful additional tool for surgeons performing LVA under local anesthesia, which will help to improve the accuracy of incisions and the efficiency of surgery.

  10. Exploration of very high spatial resolution data for vegetation mapping using cartographic ontologies: Identifying life forms to mapping formations

    NASA Astrophysics Data System (ADS)

    Rodriguez-Gallegos, Hugo Benigno

    Vegetation mapping is often considered the process of identifying landscape patterns of individuals or clusters of species or life forms (LF). At the landscape scale, the larger pattern represented by individuals or clusters represents the conceptualization of "vegetation mapping" and can be used as a building block to describe an ecosystem. To represent these building blocks or LF a "common entity (CE)" concept is introduced to represent the components of Formations as described by the National Vegetation Classification (NVC) system. The NVC has established protocols to consistently represent plant communities and promote coordinated management, particularly across jurisdictional boundaries. However, it is not a universal standard and the methods of producing detailed maps of vegetation CE from very high spatial resolution (VHR) remote sensing data are important research questions. This research addressed how best to understand and represent plant cover in arid regions, the most effective methods of mapping vegetation cover using high spatial resolution data, how to assess the accuracy of these maps, and their value in establishing more standardized mapping protocols across ecosystems. Utilizing VHR products from the IKONOS and QuickBird sensors the study focused on the Coronado National Memorial and Chiricahua National Monument in Arizona and Los Ajos and Pinacate - Grand Desierto Biosphere Reserves in Mexico. Individual CE were semi-automatically mapped incorporating spectral, textural and geostatistical variables. The results were evaluated across sensors, study sites, and input variables. In addition, multiple methods of acquiring field data for accuracy assessment were evaluated and then an evaluation was made of a semi-automatic determination of Formation based on CE. The results of the study suggest consistency across study sites using the IKONOS data. A comparison between VHR products from the same place is feasible but sensor spectral differences may

  11. Assess, Map and Predict the Integrity, Resilience, and ...

    EPA Pesticide Factsheets

    This project will provide knowledge and adaptive management techniques to both maintain healthy waters and to improve degraded systems. It will provide scientific support for the National Aquatic Resource Surveys. Results will provide a basis for informed decision making and tools applicable to EPA program office and regional needs at national regional, and local scales. The research products, tools, models, and maps produced will be an excellent means to communicate management options with stakeholders. To share information about SSWR research projects

  12. Predicting Bed Pattern Formation at Duck, North Carolina

    NASA Astrophysics Data System (ADS)

    Dodd, N.; van Leeuwen, S. M.; Calvete, D.; Tiessen, M.; Falques, A.

    2006-12-01

    The many field campaigns over the last twenty years have given us great insight into natural beach change. The advent of ARGUS imaging techniques has further contributed enormously to our knowledge of morphological pattern formation, such as cusps, mega-cusps, and transverse, oblique and crescentic bars. More recently work on understanding the physics of the formation of such morphodynamical features has led to the development of stability models, which have yielded insight into the initial growth, and the kinematics of these bed-forms. In this presentation we shall discuss the application of such a model (MORFO60: see Calvete et al, 2005) to observations from Duck, North Carolina. Initial results over about 5 months of data from Duck indicate that results (migration rates, and pattern spacings) are consistent with observations, and that meaningful predictions cluster around periods of high wave energy. Simulations for the whole of 1998 are presently underway. The purpose is to test the viability of the approach under field conditions.

  13. Prediction of Austenite Formation Temperatures Using Artificial Neural Networks

    NASA Astrophysics Data System (ADS)

    Schulze, P.; Schmidl, E.; Grund, T.; Lampke, T.

    2016-03-01

    For the modeling and design of heat treatments, in consideration of the development/ transformation of the microstructure, different material data depending on the chemical composition, the respective microstructure/phases and the temperature are necessary. Material data are, e.g. the thermal conductivity, heat capacity, thermal expansion and transformation data etc. The quality of thermal simulations strongly depends on the accuracy of the material data. For many materials, the required data - in particular for different microstructures and temperatures - are rare in the literature. In addition, a different chemical composition within the permitted limits of the considered steel alloy cannot be predicted. A solution for this problem is provided by the calculation of material data using Artificial Neural Networks (ANN). In the present study, the start and finish temperatures of the transformation from the bcc lattice to the fcc lattice structure of hypoeutectoid steels are calculated using an Artificial Neural Network. An appropriate database containing different transformation temperatures (austenite formation temperatures) to train the ANN is selected from the literature. In order to find a suitable feedforward network, the network topologies as well as the activation functions of the hidden layers are varied and subsequently evaluated in terms of the prediction accuracy. The transformation temperatures calculated by the ANN exhibit a very good compliance compared to the experimental data. The results show that the prediction performance is even higher compared to classical empirical equations such as Andrews or Brandis. Therefore, it can be assumed that the presented ANN is a convenient tool to distinguish between bcc and fcc phases in hypoeutectoid steels.

  14. Machine and Process System Diagnostics Using One-Step Prediction Maps

    SciTech Connect

    Breeding, J.E.; Damiano, B.; Tucker, R.W., Jr.

    1999-05-10

    This paper describes a method for machine or process system diagnostics that uses one-step prediction maps. The method uses nonlinear time series analysis techniques to form a one-step prediction map that estimates the next time series data point when given a sequence of previously measured time series data point. The difference between the predicted and measured time series values is a measure of the map error. The average value of this error should remain within some bound as long as both the dynamic system and its operating condition remain unchanged. However, changes in the dynamic system or operating condition will cause an increase in average map error. Thus, for a constant operating condition, monitoring the average map error over time should indicate when a change has occurred in the dynamic system. Furthermore, the map error itself forms a time series that can be analyzed to detect changes in system dynamics. The paper provides technical background in the nonlinear analysis techniques used in the diagnostic method, describes the creation of one-step prediction maps and their application to machine or process system diagnostics, and then presents results obtained from applying the diagnostic method to simulated and measured data.

  15. Improving predictive mapping of deep-water habitats: Considering multiple model outputs and ensemble techniques

    NASA Astrophysics Data System (ADS)

    Robert, Katleen; Jones, Daniel O. B.; Roberts, J. Murray; Huvenne, Veerle A. I.

    2016-07-01

    In the deep sea, biological data are often sparse; hence models capturing relationships between observed fauna and environmental variables (acquired via acoustic mapping techniques) are often used to produce full coverage species assemblage maps. Many statistical modelling techniques are being developed, but there remains a need to determine the most appropriate mapping techniques. Predictive habitat modelling approaches (redundancy analysis, maximum entropy and random forest) were applied to a heterogeneous section of seabed on Rockall Bank, NE Atlantic, for which landscape indices describing the spatial arrangement of habitat patches were calculated. The predictive maps were based on remotely operated vehicle (ROV) imagery transects high-resolution autonomous underwater vehicle (AUV) sidescan backscatter maps. Area under the curve (AUC) and accuracy indicated similar performances for the three models tested, but performance varied by species assemblage, with the transitional species assemblage showing the weakest predictive performances. Spatial predictions of habitat suitability differed between statistical approaches, but niche similarity metrics showed redundancy analysis and random forest predictions to be most similar. As one statistical technique could not be found to outperform the others when all assemblages were considered, ensemble mapping techniques, where the outputs of many models are combined, were applied. They showed higher accuracy than any single model. Different statistical approaches for predictive habitat modelling possess varied strengths and weaknesses and by examining the outputs of a range of modelling techniques and their differences, more robust predictions, with better described variation and areas of uncertainties, can be achieved. As improvements to prediction outputs can be achieved without additional costly data collection, ensemble mapping approaches have clear value for spatial management.

  16. Modified Mercalli Intensity Maps for the 1868 Hayward Earthquake Plotted in ShakeMap Format

    USGS Publications Warehouse

    Boatwright, John; Bundock, Howard

    2008-01-01

    To construct the Modified Mercalli Intensity (MMI) ShakeMap for the 1868 Hayward earthquake, we started with two sets of damage descriptions and felt reports. The first set of 100 sites was compiled by A.A. Bullock in the Lawson (1908) report on the 1906 San Francisco earthquake. The second set of 45 sites was compiled by Toppozada et al. (1981) from an extensive search of newspaper archives. We supplemented these two sets of reports with new observations from 30 sites using surveys of cemetery damage, reports of damage to historic adobe structures, pioneer narratives, and reports from newspapers that Toppozada et al. (1981) did not retrieve. The Lawson (1908) and Toppozada et al. (1981) compilations and our contributions are assembled in the Site List.

  17. Formation of temporal-feature maps in the barn owl's auditory system

    NASA Astrophysics Data System (ADS)

    Kempter, Richard

    2000-03-01

    Computational maps are of central importance to the brain's representation of the outside world. The question of how maps are formed during ontogenetic development is a subject of intense research (Hubel & Wiesel, Proc R Soc B 198:1, 1977; Buonomano & Merzenich, Annu Rev Neurosci 21:149, 1998). The development in the primary visual cortex is in principle well explained compared to that in the auditory system, partly because the mechanisms underlying the formation of temporal-feature maps are hardly understood (Carr, Annu Rev Neurosci 16:223, 1993). Through a modelling study based on computer simulations in a system of spiking neurons a solution is offered to the problem of how a map of interaural time differences is set up in the nucleus laminaris of the barn owl, as a typical example. An array of neurons is able to represent interaural time differences in an orderly manner, viz., a map, if homosynaptic spike-based Hebbian learning (Gerstner et al, Nature 383:76, 1996; Kempter et al, Phys Rev E 59:4498, 1999) is combined with a presynaptic propagation of synaptic modifications (Fitzsimonds & Poo, Physiol Rev 78:143, 1998). The latter may be orders of magnitude weaker than the former. The algorithm is a key mechanism to the formation of temporal-feature maps on a submillisecond time scale.

  18. Improving RNA secondary structure prediction with structure mapping data.

    PubMed

    Sloma, Michael F; Mathews, David H

    2015-01-01

    Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide. © 2015 Elsevier Inc. All rights reserved.

  19. The prediction and mapping of geoidal undulations from GEOS-3 altimetry. [gravity anomalies

    NASA Technical Reports Server (NTRS)

    Kearsley, W.

    1978-01-01

    From the adjusted altimeter data an approximation to the geoid height in ocean areas is obtained. Methods are developed to produce geoid maps in these areas. Geoid heights are obtained for grid points in the region to be mapped, and two of the parameters critical to the production of an accurate map are investigated. These are the spacing of the grid, which must be related to the half-wavelength of the altimeter signal whose amplitude is the desired accuracy of the contour; and the method adopted to predict the grid values. Least squares collocation was used to find geoid undulations on a 1 deg grid in the mapping area. Twenty maps, with their associated precisions, were produced and are included. These maps cover the Indian Ocean, Southwestern and Northeastern portions of the Pacific Ocean, and Southwest Atlantic and the U.S. Calibration Area.

  20. Testing assumptions and predictions of star formation theories

    NASA Astrophysics Data System (ADS)

    González-Samaniego, Alejandro; Vázquez-Semadeni, Enrique; González, Ricardo F.; Kim, Jongsoo

    2014-05-01

    We present numerical simulations of isothermal, magnetohydrodynamic (MHD), supersonic turbulence, designed to test various hypotheses frequently assumed in star formation (SF) theories. This study complements our previous one in the non-magnetic (HD) case. We consider three simulations, each with different values of its physical size, rms sonic Mach number M_s, and Jeans parameter J, but so that all three have the same value of the virial parameter and conform with Larson's scaling relations. As in the non-magnetic case, we find that (1) no structures that are both subsonic and super-Jeans are produced; (2) that the fraction of small-scale super-Jeans structures increases when self-gravity is turned on, and the production of very dense cores by turbulence alone is very low. This implies that self-gravity is involved not only in the collapse of Jeans-unstable cores, but also in their formation. (3) We also find that denser regions tend to have a stronger velocity convergence, implying a net inwards flow towards the regions' centres. Contrary to the non-magnetic case, we find that the magnetic simulation with lowest values of M_s and J (respectively, 5 and 2) does not produce any collapsing regions for over three simulation free-fall times, in spite of being both Jeans-unstable and magnetically supercritical. We attribute this result to the combined thermal and magnetic support. Next, we compare the results of our HD and MHD simulations with the predictions from the recent SF theories by Krumholz & McKee, Padoan & Nordlund, and Hennebelle & Chabrier, using expressions recently provided by Federrath & Klessen, which extend those theories to the magnetic case. In both the HD and MHD cases, we find that the theoretical predictions tend to be larger than the SFEff measured in the simulations. In the MHD case, none of the theories captures the suppression of collapse at low values of Jeff by the additional support from the magnetic field. We conclude that randomly driven

  1. The digital geologic map of Colorado in ARC/INFO format, Part C. Explanation sheet database

    USGS Publications Warehouse

    Green, Gregory N.

    1992-01-01

    This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map. This database was developed on a MicroVAX computer system using VAX V 5.4 nd ARC/INFO 5.0 software. UPDATE: April 1995, The update was done solely for the purpose of adding the abilitly to plot to an HP650c plotter. Two new ARC/INFO plot AMLs along with a lineset and shadeset for the HP650C design jet printer have been included. These new files are COLORADO.650, INDEX.650, TWETOLIN.E00 and TWETOSHD.E00. These files were created on a UNIX platform with ARC/INFO 6.1.2. Updated versions of INDEX.E00, CONTACT.E00, LINE.E00, DECO.E00 and BORDER.E00 files that included the newly defined HP650c items are also included. * Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Descriptors: The Digital Geologic Map of Colorado in ARC/INFO Format Open-File Report 92-050

  2. The digital geologic map of Colorado in ARC/INFO format, Part A. Documentation

    USGS Publications Warehouse

    Green, Gregory N.

    1992-01-01

    This geologic map was prepared as a part of a study of digital methods and techniques as applied to complex geologic maps. The geologic map was digitized from the original scribe sheets used to prepare the published Geologic Map of Colorado (Tweto 1979). Consequently the digital version is at 1:500,000 scale using the Lambert Conformal Conic map projection parameters of the state base map. Stable base contact prints of the scribe sheets were scanned on a Tektronix 4991 digital scanner. The scanner automatically converts the scanned image to an ASCII vector format. These vectors were transferred to a VAX minicomputer, where they were then loaded into ARC/INFO. Each vector and polygon was given attributes derived from the original 1979 geologic map. This database was developed on a MicroVAX computer system using VAX V 5.4 nd ARC/INFO 5.0 software. UPDATE: April 1995, The update was done solely for the purpose of adding the abilitly to plot to an HP650c plotter. Two new ARC/INFO plot AMLs along with a lineset and shadeset for the HP650C design jet printer have been included. These new files are COLORADO.650, INDEX.650, TWETOLIN.E00 and TWETOSHD.E00. These files were created on a UNIX platform with ARC/INFO 6.1.2. Updated versions of INDEX.E00, CONTACT.E00, LINE.E00, DECO.E00 and BORDER.E00 files that included the newly defined HP650c items are also included. * Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Descriptors: The Digital Geologic Map of Colorado in ARC/INFO Format Open-File Report 92-050

  3. Fostering ontology alignment sharing: a general-purpose RDF mapping format.

    PubMed

    Anguita, Alberto; Escrich, Ana; Maojo, Victor

    2013-01-01

    RDF has established in the last years as the language for describing, publishing and sharing biomedical resources. Following this trend, a great amount of RDF-based data sources, as well as ontologies, have appeared. Using a common language as RDF has provided a unified syntactic for sharing resources, but the semantics remain as the main cause of heterogeneity, hampering data integration and homogenization efforts. To overcome this issue, ontology alignment based solutions have been typically used. However, alignment information is usually codified using ad-hoc formats. In this paper, we present a general purpose ontology mapping format, totally independent from the homogenization approach to be applied. The format is accompanied with a Java API that offers mapping construction and parsing features, as well as some basic algorithms for applying it to data translation solutions.

  4. Dependence of Initial Value on Pattern Formation for a Logistic Coupled Map Lattice

    PubMed Central

    Xu, Li; Zhang, Guang; Cui, Haoyue

    2016-01-01

    The logistic coupled map lattices (LCML) have been widely investigated as well as their pattern dynamics. The patterns formation may depend on not only fluctuations of system parameters, but variation of the initial conditions. However, the mathematical discussion is quite few for the effect of initial values so far. The present paper is concerned with the pattern formation for a two-dimensional Logistic coupled map lattice, where any initial value can be linear expressed by corresponding eigenvectors, and patterns formation can be determined by selecting the corresponding eigenvectors. A set of simulations are conducted whose results demonstrate the fact. The method utilized in the present paper could be applied to other discrete systems as well. PMID:27382964

  5. Traction force dynamics predict gap formation in activated endothelium.

    PubMed

    Valent, Erik T; van Nieuw Amerongen, Geerten P; van Hinsbergh, Victor W M; Hordijk, Peter L

    2016-09-10

    In many pathological conditions the endothelium becomes activated and dysfunctional, resulting in hyperpermeability and plasma leakage. No specific therapies are available yet to control endothelial barrier function, which is regulated by inter-endothelial junctions and the generation of acto-myosin-based contractile forces in the context of cell-cell and cell-matrix interactions. However, the spatiotemporal distribution and stimulus-induced reorganization of these integral forces remain largely unknown. Traction force microscopy of human endothelial monolayers was used to visualize contractile forces in resting cells and during thrombin-induced hyperpermeability. Simultaneously, information about endothelial monolayer integrity, adherens junctions and cytoskeletal proteins (F-actin) were captured. This revealed a heterogeneous distribution of traction forces, with nuclear areas showing lower and cell-cell junctions higher traction forces than the whole-monolayer average. Moreover, junctional forces were asymmetrically distributed among neighboring cells. Force vector orientation analysis showed a good correlation with the alignment of F-actin and revealed contractile forces in newly formed filopodia and lamellipodia-like protrusions within the monolayer. Finally, unstable areas, showing high force fluctuations within the monolayer were prone to form inter-endothelial gaps upon stimulation with thrombin. To conclude, contractile traction forces are heterogeneously distributed within endothelial monolayers and force instability, rather than force magnitude, predicts the stimulus-induced formation of intercellular gaps. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Dynamic maps of UV damage formation and repair for the human genome.

    PubMed

    Hu, Jinchuan; Adebali, Ogun; Adar, Sheera; Sancar, Aziz

    2017-06-27

    Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS-Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS-Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage.

  7. Online unsupervised formation of cell assemblies for the encoding of multiple cognitive maps.

    PubMed

    Salihoglu, Utku; Bersini, Hugues; Yamaguchi, Yoko; Molter, Colin

    2009-01-01

    Since their introduction sixty years ago, cell assemblies have proved to be a powerful paradigm for brain information processing. After their introduction in artificial intelligence, cell assemblies became commonly used in computational neuroscience as a neural substrate for content addressable memories. However, the mechanisms underlying their formation are poorly understood and, so far, there is no biologically plausible algorithms which can explain how external stimuli can be online stored in cell assemblies. We addressed this question in a previous paper [Salihoglu, U., Bersini, H., Yamaguchi, Y., Molter, C., (2009). A model for the cognitive map formation: Application of the retroaxonal theory. In Proc. IEEE international joint conference on neural networks], were, based on biologically plausible mechanisms, a novel unsupervised algorithm for online cell assemblies' creation was developed. The procedure involved simultaneously, a fast Hebbian/anti-Hebbian learning of the network's recurrent connections for the creation of new cell assemblies, and a slower feedback signal which stabilized the cell assemblies by learning the feedforward input connections. Here, we first quantify the role played by the retroaxonal feedback mechanism. Then, we show how multiple cognitive maps, composed by a set of orthogonal input stimuli, can be encoded in the network. As a result, when facing a previously learned input, the system is able to retrieve the cognitive map it belongs to. As a consequence, ambiguous inputs which could belong to multiple cognitive maps can be disambiguated by the knowledge of the context, i.e. the cognitive map.

  8. Reducing dimensionality in remote homology detection using predicted contact maps.

    PubMed

    Bedoya, Oscar; Tischer, Irene

    2015-04-01

    In this paper, a new method for remote protein homology detection is presented. Most discriminative methods concatenate the values extracted from physicochemical properties to build a model that separates homolog and non-homolog examples. Each discriminative method uses a specific strategy to represent the information extracted from the protein sequence and a different number of indices. After the vector representation is achieved, support vector machines (SVM) are usually used. Most classification techniques are not suitable in remote homology detection because they do not address high dimensional datasets. In this paper, we propose a method that reduces the high dimensionality of the vector representation using models that are defined at the 3D level. Next, the models are mapped from the protein primary sequence. The new method, called remote-C3D, is presented and tested on the SCOP 1.53 and SCOP 1.55 datasets. The remote-C3D method achieves a higher accuracy than the composition-based methods and a comparable performance with profile-based methods. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Can Self-Organizing Maps Accurately Predict Photometric Redshifts?

    NASA Astrophysics Data System (ADS)

    Way, M. J.; Klose, C. D.

    2012-03-01

    We present an unsupervised machine-learning approach that can be employed for estimating photometric redshifts. The proposed method is based on a vector quantization called the self-organizing-map (SOM) approach. A variety of photometrically derived input values were utilized from the Sloan Digital Sky Survey’s main galaxy sample, luminous red galaxy, and quasar samples, along with the PHAT0 data set from the Photo- z Accuracy Testing project. Regression results obtained with this new approach were evaluated in terms of root-mean-square error (RMSE) to estimate the accuracy of the photometric redshift estimates. The results demonstrate competitive RMSE and outlier percentages when compared with several other popular approaches, such as artificial neural networks and Gaussian process regression. SOM RMSE results (using Δz = zphot - zspec) are 0.023 for the main galaxy sample, 0.027 for the luminous red galaxy sample, 0.418 for quasars, and 0.022 for PHAT0 synthetic data. The results demonstrate that there are nonunique solutions for estimating SOM RMSEs. Further research is needed in order to find more robust estimation techniques using SOMs, but the results herein are a positive indication of their capabilities when compared with other well-known methods.

  10. Preliminary investigation of Large Format Camera photography utility in soil mapping and related agricultural applications

    NASA Technical Reports Server (NTRS)

    Pelletier, R. E.; Hudnall, W. H.

    1987-01-01

    The use of Space Shuttle Large Format Camera (LFC) color, IR/color, and B&W images in large-scale soil mapping is discussed and illustrated with sample photographs from STS 41-6 (October 1984). Consideration is given to the characteristics of the film types used; the photographic scales available; geometric and stereoscopic factors; and image interpretation and classification for soil-type mapping (detecting both sharp and gradual boundaries), soil parent material topographic and hydrologic assessment, natural-resources inventory, crop-type identification, and stress analysis. It is suggested that LFC photography can play an important role, filling the gap between aerial and satellite remote sensing.

  11. Preliminary investigation of Large Format Camera photography utility in soil mapping and related agricultural applications

    NASA Technical Reports Server (NTRS)

    Pelletier, R. E.; Hudnall, W. H.

    1987-01-01

    The use of Space Shuttle Large Format Camera (LFC) color, IR/color, and B&W images in large-scale soil mapping is discussed and illustrated with sample photographs from STS 41-6 (October 1984). Consideration is given to the characteristics of the film types used; the photographic scales available; geometric and stereoscopic factors; and image interpretation and classification for soil-type mapping (detecting both sharp and gradual boundaries), soil parent material topographic and hydrologic assessment, natural-resources inventory, crop-type identification, and stress analysis. It is suggested that LFC photography can play an important role, filling the gap between aerial and satellite remote sensing.

  12. Bone morphogenetic proteins, eye patterning, and retinocollicular map formation in the mouse

    PubMed Central

    Plas, Daniel T.; Dhande, Onkar; Lopez, Joshua E.; Murali, Deepa; Thaller, Christina; Henkemeyer, Mark; Furuta, Yasuhide; Overbeek, Paul; Crair, Michael C.

    2009-01-01

    Patterning events during early eye formation determine retinal cell fate and can dictate the behavior of retinal ganglion cell (RGC) axons as they navigate toward central brain targets. The temporally and spatially regulated expression of bone morphogenetic proteins (BMPs) and their receptors in the retina are thought to play a key role in this process, initiating gene expression cascades that distinguish different regions of the retina, particularly along the dorsoventral axis. Here, we examine the role of BMP and a potential downstream effector, EphB, in retinotopic map formation in the lateral geniculate nucleus (LGN) and superior colliculus (SC). RGC axon behaviors during retinotopic map formation in wild type mice are compared with those in several strains of mice with engineered defects of BMP and EphB signaling. Normal RGC axon sorting produces axon order in the optic tract that reflects the dorsoventral position of the parent RGCs in the eye. A dramatic consequence of disrupting BMP signaling is a missorting of RGC axons as they exit the optic chiasm. This sorting is not dependent on EphB. When BMP signaling in the developing eye is genetically modified, RGC order in the optic tract and targeting in the LGN and SC are correspondingly disrupted. These experiments show that BMP signaling regulates dorsoventral RGC cell fate, RGC axon behavior in the ascending optic tract and retinotopic map formation in the LGN and SC through mechanisms that are in part distinct from EphB signaling in the LGN and SC. PMID:18614674

  13. Two States Mapping Based Time Series Neural Network Model for Compensation Prediction Residual Error

    NASA Astrophysics Data System (ADS)

    Jung, Insung; Koo, Lockjo; Wang, Gi-Nam

    2008-11-01

    The objective of this paper was to design a model of human bio signal data prediction system for decreasing of prediction error using two states mapping based time series neural network BP (back-propagation) model. Normally, a lot of the industry has been applied neural network model by training them in a supervised manner with the error back-propagation algorithm for time series prediction systems. However, it still has got a residual error between real value and prediction result. Therefore, we designed two states of neural network model for compensation residual error which is possible to use in the prevention of sudden death and metabolic syndrome disease such as hypertension disease and obesity. We determined that most of the simulation cases were satisfied by the two states mapping based time series prediction model. In particular, small sample size of times series were more accurate than the standard MLP model.

  14. Geologic Mapping Applications Using THEMIS Data for the Medusae Fossae Formation, Mars

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.; Bender, K. C.; Harris, J. C.

    2003-01-01

    The Medusae Fossae Formation (MFF) is a regionally extensive deposit located along the equator of Mars between roughly 130 and 240 E longitude, the origin of which has stimulated a host of published hypotheses. A volcanic or aeolian origin appear most consistent with Viking and MGS data, but other hypotheses remain viable and new data, as from the Mars Odyssey spacecraft, is likely to stimulate additional hypotheses of origin. NASA is supporting geologic mapping of portions of the MFF deposits, but it is now quite clear that this on-going mapping will need considerable revision as data from the Thermal Emission Imaging System (THEMIS) on Mars Odyssey become available. The daytime IR THEMIS images hold particularly strong potential for providing a new base on which geologic mapping can be carried out, as illustrated by the examples discussed.

  15. 3-D or median map? Earthquake scenario ground-motion maps from physics-based models versus maps from ground-motion prediction equations

    NASA Astrophysics Data System (ADS)

    Porter, K.

    2015-12-01

    There are two common ways to create a ground-motion map for a hypothetical earthquake: using ground motion prediction equations (by far the more common of the two) and using 3-D physics-based modeling. The former is very familiar to engineers, the latter much less so, and the difference can present a problem because engineers tend to trust the familiar and distrust novelty. Maps for essentially the same hypothetical earthquake using the two different methods can look very different, while appearing to present the same information. Using one or the other can lead an engineer or disaster planner to very different estimates of damage and risk. The reasons have to do with depiction of variability, spatial correlation of shaking, the skewed distribution of real-world shaking, and the upward-curving relationship between shaking and damage. The scientists who develop the two kinds of map tend to specialize in one or the other and seem to defend their turf, which can aggravate the problem of clearly communicating with engineers.The USGS Science Application for Risk Reduction's (SAFRR) HayWired scenario has addressed the challenge of explaining to engineers the differences between the two maps, and why, in a disaster planning scenario, one might want to use the less-familiar 3-D map.

  16. A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

    PubMed Central

    Dabaghian, Y.; Mémoli, F.; Frank, L.; Carlsson, G.

    2012-01-01

    An animal's ability to navigate through space rests on its ability to create a mental map of its environment. The hippocampus is the brain region centrally responsible for such maps, and it has been assumed to encode geometric information (distances, angles). Given, however, that hippocampal output consists of patterns of spiking across many neurons, and downstream regions must be able to translate those patterns into accurate information about an animal's spatial environment, we hypothesized that 1) the temporal pattern of neuronal firing, particularly co-firing, is key to decoding spatial information, and 2) since co-firing implies spatial overlap of place fields, a map encoded by co-firing will be based on connectivity and adjacency, i.e., it will be a topological map. Here we test this topological hypothesis with a simple model of hippocampal activity, varying three parameters (firing rate, place field size, and number of neurons) in computer simulations of rat trajectories in three topologically and geometrically distinct test environments. Using a computational algorithm based on recently developed tools from Persistent Homology theory in the field of algebraic topology, we find that the patterns of neuronal co-firing can, in fact, convey topological information about the environment in a biologically realistic length of time. Furthermore, our simulations reveal a “learning region” that highlights the interplay between the parameters in combining to produce hippocampal states that are more or less adept at map formation. For example, within the learning region a lower number of neurons firing can be compensated by adjustments in firing rate or place field size, but beyond a certain point map formation begins to fail. We propose that this learning region provides a coherent theoretical lens through which to view conditions that impair spatial learning by altering place cell firing rates or spatial specificity. PMID:22912564

  17. Dust temperature maps of the Galactic plane: The Herschel spectral energy distribution fitting with Cloudy predictions

    NASA Astrophysics Data System (ADS)

    Zhu, Jiali; Huang, Maohai

    2014-04-01

    Context. Dust grains absorb the interstellar far ultra-violet and visible photons and re-emit them in far-infrared (FIR) wavebands. The dust FIR continuum can be predicted by a grid of models using various values of the interstellar radiation field. Aims: We analyze the dust continuum emission in two Hi-GAL science-demonstration phase (SDP) fields using both the radiative transfer code, Cloudy, and the DustEM dust model, to explore the effect of radiative transfer on dust temperature. The 500 μm sub-millimeter excess emission and the very small grain (VSG) contribution to the 70 μm intensity are investigated by spectral energy distribution (SED) fitting using the Cloudy model. Methods: By comparing the observation with the model prediction, we derive dust temperature maps of the two SDP fields by fitting the dust SED with 4-band data (SPIRE bands plus PACS 160 μm) using both Cloudy and DustEM models. Considering radiative transfer and grain physics simultaneously, we investigate the existence of a 500 μm excess and estimate the VSG contribution to the 70 μm intensity by fitting the dust SED with 3-band data (160, 250, and 350 μm) and 5-band data (SPIRE and PACS bands), respectively. Results: We confirm that the field with star formation activities have a higher temperature (18.7 ± 0.9 K) than the quiescent region (15.2 ± 0.6 K). We find that the radiative transfer affects the FIR SED of the SDP fields and results in a higher temperature distribution than the dust-only model fit. There is no significant detection of a 500 μm excess in the two SDP fields. The relative contribution from the VSGs to the 70 μm intensity can be up to 50%. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.Reduced Herschel maps (FITS) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc

  18. Feeding cosmic star formation: exploring high-redshift molecular gas with CO intensity mapping

    NASA Astrophysics Data System (ADS)

    Breysse, Patrick C.; Rahman, Mubdi

    2017-06-01

    The study of molecular gas is crucial for understanding star formation, feedback and the broader ecosystem of a galaxy as a whole. However, we have limited understanding of its physics and distribution in all but the nearest galaxies. We present a new technique for studying the composition and distribution of molecular gas in high-redshift galaxies inaccessible to existing methods. Our proposed approach is an extension of carbon monoxide intensity mapping methods, which have garnered significant experimental interest in recent years. These intensity mapping surveys target the 115 GHz 12CO (1-0) line, but also contain emission from the substantially fainter 110 GHz 13CO (1-0) transition. The method leverages the information contained in the 13CO line by cross-correlating pairs of frequency channels in an intensity mapping survey. Since 13CO is emitted from the same medium as the 12CO, but saturates at a much higher column density, this cross-correlation provides valuable information about both the gas density distribution and isotopologue ratio, inaccessible from the 12CO alone. Using a simple model of these molecular emission lines, we show that a future intensity mapping survey can constrain the abundance ratio of these two species and the fraction of emission from optically thick regions to order ˜30 per cent. These measurements cannot be made by traditional CO observations, and consequently the proposed method will provide unique insight into the physics of star formation, feedback and galactic ecology at high redshifts.

  19. NUMERICALLY PREDICTED INDIRECT SIGNATURES OF TERRESTRIAL PLANET FORMATION

    SciTech Connect

    Leinhardt, Zoë M.; Dobinson, Jack; Carter, Philip J.; Lines, Stefan

    2015-06-10

    The intermediate phases of planet formation are not directly observable due to lack of emission from planetesimals. Planet formation is, however, a dynamically active process resulting in collisions between the evolving planetesimals and the production of dust. Thus, indirect observation of planet formation may indeed be possible in the near future. In this paper we present synthetic observations based on numerical N-body simulations of the intermediate phase of planet formation including a state-of-the-art collision model, EDACM, which allows multiple collision outcomes, such as accretion, erosion, and bouncing events. We show that the formation of planetary embryos may be indirectly observable by a fully functioning ALMA telescope if the surface area involved in planetesimal evolution is sufficiently large and/or the amount of dust produced in the collisions is sufficiently high in mass.

  20. Spatial modeling for refining and predicting surface potential mapping with enhanced resolution.

    PubMed

    Zhang, Qiong; Deng, Xinwei; Qian, Peter Z G; Wang, Xudong

    2013-02-07

    Quantitatively mapping surface properties with nanometer or even subnanometer resolutions is critical for advanced scanning probe microscopy (SPM) characterization. However, the characterization performance often suffers from noises and artifacts due to instrumentation or environmental limitations. In this paper, we proposed a novel statistical approach with bivariate spatial modeling to efficiently refine and predict surface property mapping. Scanning Kelvin probe microscopy (SKPM) was selected as a representative example to test our proposed method on lateral nanowire assemblies. We revealed that the proposed method can effectively retrieve the artifact-free surface potential distribution by automatically identifying topological artifacts from surface potential maps. Furthermore, the statistical model built upon low spatial resolution was successfully used to predict the potential values from higher-resolution topography data. Compared to conventional regression model, our model is able to predict the surface potential distribution from less raw data but yields much higher accuracy. Through this means, the spatial resolution of SKPM surface potential maps can be significantly improved. This statistics-enabled predictive method opens a new route toward high-precision and high-resolution SPM characterizations without the enhancement of instrumentation capabilities.

  1. Prediction of Poly(A) Sites by Poly(A) Read Mapping

    PubMed Central

    Bonfert, Thomas; Friedel, Caroline C.

    2017-01-01

    RNA-seq reads containing part of the poly(A) tail of transcripts (denoted as poly(A) reads) provide the most direct evidence for the position of poly(A) sites in the genome. However, due to reduced coverage of poly(A) tails by reads, poly(A) reads are not routinely identified during RNA-seq mapping. Nevertheless, recent studies for several herpesviruses successfully employed mapping of poly(A) reads to identify herpesvirus poly(A) sites using different strategies and customized programs. To more easily allow such analyses without requiring additional programs, we integrated poly(A) read mapping and prediction of poly(A) sites into our RNA-seq mapping program ContextMap 2. The implemented approach essentially generalizes previously used poly(A) read mapping approaches and combines them with the context-based approach of ContextMap 2 to take into account information provided by other reads aligned to the same location. Poly(A) read mapping using ContextMap 2 was evaluated on real-life data from the ENCODE project and compared against a competing approach based on transcriptome assembly (KLEAT). This showed high positive predictive value for our approach, evidenced also by the presence of poly(A) signals, and considerably lower runtime than KLEAT. Although sensitivity is low for both methods, we show that this is in part due to a high extent of spurious results in the gold standard set derived from RNA-PET data. Sensitivity improves for poly(A) sites of known transcripts or determined with a more specific poly(A) sequencing protocol and increases with read coverage on transcript ends. Finally, we illustrate the usefulness of the approach in a high read coverage scenario by a re-analysis of published data for herpes simplex virus 1. Thus, with current trends towards increasing sequencing depth and read length, poly(A) read mapping will prove to be increasingly useful and can now be performed automatically during RNA-seq mapping with ContextMap 2. PMID:28135292

  2. Prediction of Phase Formation in Nanoscale Sn-Ag-Cu Solder Alloy

    NASA Astrophysics Data System (ADS)

    Wu, Min; Lv, Bailin

    2016-01-01

    In a dynamic nonequilibrium process, the effective heat of formation allows the heat of formation to be calculated as a function of concentrations of the reacting atoms. In this work, we used the effective heat of formation rule to predict the formation and size of compound phases in a nanoscale Sn-Ag-Cu lead-free solder. We calculated the formation enthalpy and effective formation enthalpy of compounds in the Sn-Ag, Sn-Cu, and Ag-Cu systems by using the Miedema model and effective heat of formation. Our results show that, considering the surface effect of the nanoparticle, the effective heat of formation rule successfully predicts the phase formation and sizes of Ag3Sn and Cu6Sn5 compounds, which agrees well with experimental data.

  3. Formation and Evolution of Lakshmi Planum (V-7), Venus: Assessment of Models using Observations from Geological Mapping

    NASA Technical Reports Server (NTRS)

    Ivanov, M. A.; Head, James W.

    2008-01-01

    Lakshmi Planum is a high-standing plateau (3.5-4.5 km above MPR) surrounded by the highest mountain ranges on Venus. Lakshmi represents a unique type of elevated region different from dome-shaped and rifted rises and tessera-bearing crustal plateaus. The unique characteristics of Lakshmi suggest that it formed by an unusual combination of processes and played an important role in Venus geologic history. Lakshmi was studied with Venera-15/16 and Magellan data, resulting in two classes of models, divergent and convergent, to explain its unusual topographic and morphologic characteristics. Divergent models explain Lakshmi as a site of mantle upwelling due to rising and subsequent collapse of a mantle diapir; such models explain emplacement of a lava plateau inside Lakshmi and, in some circumstances, formation of the mountain ranges. The convergent models consider Lakshmi as a locus of mantle downwelling, convergence, underthrusting, and possible subduction. Key features in these models are the mountain ranges, high topography of Lakshmi interior, and the large volcanic centers in the plateau center. These divergent and convergent models entail principally different mechanisms of formation and suggest different geodynamic regimes on Venus. Almost all models make either explicit or implicit predictions about the type and sequence of major events during formation and evolution of Lakshmi and thus detailed geological mapping can be used to test them. Here we present the results of such geological mapping (the V-7 quadrangle, 50-75degN, 300-360degE; scale 1:5M) that allows testing the proposed models for Lakshmi.

  4. An Approach for Predicting Essential Genes Using Multiple Homology Mapping and Machine Learning Algorithms.

    PubMed

    Hua, Hong-Li; Zhang, Fa-Zhan; Labena, Abraham Alemayehu; Dong, Chuan; Jin, Yan-Ting; Guo, Feng-Biao

    Investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. In this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. We focused on 25 bacteria which have characterized essential genes. The predictions yielded the highest area under receiver operating characteristic (ROC) curve (AUC) of 0.9716 through tenfold cross-validation test. Proper features were utilized to construct models to make predictions in distantly related bacteria. The accuracy of predictions was evaluated via the consistency of predictions and known essential genes of target species. The highest AUC of 0.9552 and average AUC of 0.8314 were achieved when making predictions across organisms. An independent dataset from Synechococcus elongatus, which was released recently, was obtained for further assessment of the performance of our model. The AUC score of predictions is 0.7855, which is higher than other methods. This research presents that features obtained by homology mapping uniquely can achieve quite great or even better results than those integrated features. Meanwhile, the work indicates that machine learning-based method can assign more efficient weight coefficients than using empirical formula based on biological knowledge.

  5. An Approach for Predicting Essential Genes Using Multiple Homology Mapping and Machine Learning Algorithms

    PubMed Central

    Hua, Hong-Li; Zhang, Fa-Zhan; Labena, Abraham Alemayehu; Dong, Chuan; Jin, Yan-Ting

    2016-01-01

    Investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. In this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. We focused on 25 bacteria which have characterized essential genes. The predictions yielded the highest area under receiver operating characteristic (ROC) curve (AUC) of 0.9716 through tenfold cross-validation test. Proper features were utilized to construct models to make predictions in distantly related bacteria. The accuracy of predictions was evaluated via the consistency of predictions and known essential genes of target species. The highest AUC of 0.9552 and average AUC of 0.8314 were achieved when making predictions across organisms. An independent dataset from Synechococcus elongatus, which was released recently, was obtained for further assessment of the performance of our model. The AUC score of predictions is 0.7855, which is higher than other methods. This research presents that features obtained by homology mapping uniquely can achieve quite great or even better results than those integrated features. Meanwhile, the work indicates that machine learning-based method can assign more efficient weight coefficients than using empirical formula based on biological knowledge. PMID:27660763

  6. Landscape prediction and mapping of game fish biomass, an ecosystem service of Michigan rivers

    USGS Publications Warehouse

    Esselman, Peter C.; Stevenson, R Jan; Lupi, Frank; Riseng, Catherine M.; Wiley, Michael J.

    2015-01-01

    The increased integration of ecosystem service concepts into natural resource management places renewed emphasis on prediction and mapping of fish biomass as a major provisioning service of rivers. The goals of this study were to predict and map patterns of fish biomass as a proxy for the availability of catchable fish for anglers in rivers and to identify the strongest landscape constraints on fish productivity. We examined hypotheses about fish responses to total phosphorus (TP), as TP is a growth-limiting nutrient known to cause increases (subsidy response) and/or decreases (stress response) in fish biomass depending on its concentration and the species being considered. Boosted regression trees were used to define nonlinear functions that predicted the standing crops of Brook Trout Salvelinus fontinalis, Brown Trout Salmo trutta, Smallmouth Bass Micropterus dolomieu, panfishes (seven centrarchid species), and Walleye Sander vitreus by using landscape and modeled local-scale predictors. Fitted models were highly significant and explained 22–56% of the variation in validation data sets. Nonlinear and threshold responses were apparent for numerous predictors, including TP concentration, which had significant effects on all except the Walleye fishery. Brook Trout and Smallmouth Bass exhibited both subsidy and stress responses, panfish biomass exhibited a subsidy response only, and Brown Trout exhibited a stress response. Maps of reach-specific standing crop predictions showed patterns of predicted fish biomass that corresponded to spatial patterns in catchment area, water temperature, land cover, and nutrient availability. Maps illustrated predictions of higher trout biomass in coldwater streams draining glacial till in northern Michigan, higher Smallmouth Bass and panfish biomasses in warmwater systems of southern Michigan, and high Walleye biomass in large main-stem rivers throughout the state. Our results allow fisheries managers to examine the biomass

  7. Landslide susceptibility mapping & prediction using Support Vector Machine for Mandakini River Basin, Garhwal Himalaya, India

    NASA Astrophysics Data System (ADS)

    Kumar, Deepak; Thakur, Manoj; Dubey, Chandra S.; Shukla, Dericks P.

    2017-10-01

    In recent years, various machine learning techniques have been applied for landslide susceptibility mapping. In this study, three different variants of support vector machine viz., SVM, Proximal Support Vector Machine (PSVM) and L2-Support Vector Machine - Modified Finite Newton (L2-SVM-MFN) have been applied on the Mandakini River Basin in Uttarakhand, India to carry out the landslide susceptibility mapping. Eight thematic layers such as elevation, slope, aspect, drainages, geology/lithology, buffer of thrusts/faults, buffer of streams and soil along with the past landslide data were mapped in GIS environment and used for landslide susceptibility mapping in MATLAB. The study area covering 1625 km2 has merely 0.11% of area under landslides. There are 2009 pixels for past landslides out of which 50% (1000) landslides were considered as training set while remaining 50% as testing set. The performance of these techniques has been evaluated and the computational results show that L2-SVM-MFN obtains higher prediction values (0.829) of receiver operating characteristic curve (AUC-area under the curve) as compared to 0.807 for PSVM model and 0.79 for SVM. The results obtained from L2-SVM-MFN model are found to be superior than other SVM prediction models and suggest the usefulness of this technique to problem of landslide susceptibility mapping where training data is very less. However, these techniques can be used for satisfactory determination of susceptible zones with these inputs.

  8. Predictive risk mapping of schistosomiasis in Brazil using Bayesian geostatistical models.

    PubMed

    Scholte, Ronaldo G C; Gosoniu, Laura; Malone, John B; Chammartin, Frédérique; Utzinger, Jürg; Vounatsou, Penelope

    2014-04-01

    Schistosomiasis is one of the most common parasitic diseases in tropical and subtropical areas, including Brazil. A national control programme was initiated in Brazil in the mid-1970s and proved successful in terms of morbidity control, as the number of cases with hepato-splenic involvement was reduced significantly. To consolidate control and move towards elimination, there is a need for reliable maps on the spatial distribution of schistosomiasis, so that interventions can target communities at highest risk. The purpose of this study was to map the distribution of Schistosoma mansoni in Brazil. We utilized readily available prevalence data from the national schistosomiasis control programme for the years 2005-2009, derived remotely sensed climatic and environmental data and obtained socioeconomic data from various sources. Data were collated into a geographical information system and Bayesian geostatistical models were developed. Model-based maps identified important risk factors related to the transmission of S. mansoni and confirmed that environmental variables are closely associated with indices of poverty. Our smoothed predictive risk map, including uncertainty, highlights priority areas for intervention, namely the northern parts of North and Southeast regions and the eastern part of Northeast region. Our predictive risk map provides a useful tool for to strengthen existing surveillance-response mechanisms. Copyright © 2014. Published by Elsevier B.V.

  9. Predicting the intensity mapping signal for multi-J CO lines

    SciTech Connect

    Mashian, Natalie; Loeb, Abraham; Sternberg, Amiel E-mail: amiel@wise.tau.ac.il

    2015-11-01

    We present a novel approach to estimating the intensity mapping signal of any CO rotational line emitted during the Epoch of Reionization (EoR). Our approach is based on large velocity gradient (LVG) modeling, a radiative transfer modeling technique that generates the full CO spectral line energy distribution (SLED) for a specified gas kinetic temperature, volume density, velocity gradient, molecular abundance, and column density. These parameters, which drive the physics of CO transitions and ultimately dictate the shape and amplitude of the CO SLED, can be linked to the global properties of the host galaxy, mainly the star formation rate (SFR) and the SFR surface density. By further employing an empirically derived SFR−M relation for high redshift galaxies, we can express the LVG parameters, and thus the specific intensity of any CO rotational transition, as functions of the host halo mass M and redshift z. Integrating over the range of halo masses expected to host CO-luminous galaxies, we predict a mean CO(1-0) brightness temperature ranging from ∼ 0.6 μK at z = 6 to ∼ 0.03 μK at z = 10 with brightness temperature fluctuations of Δ{sub CO}{sup 2} ∼ 0.1 and 0.005 μK respectively, at k = 0.1 Mpc{sup −1}. In this model, the CO emission signal remains strong for higher rotational levels at z = 6, with ( T{sub CO} ) ∼ 0.3 and 0.05 μK for the CO J = 6arrow5 and CO J = 10arrow9 transitions respectively. Including the effects of CO photodissociation in these molecular clouds, especially at low metallicities, results in the overall reduction in the amplitude of the CO signal, with the low- and high-J lines weakening by 2–20% and 10–45%, respectively, over the redshift range 4 < z < 10.

  10. The effectiveness of digital soil mapping to predict soil properties over low-relief areas.

    PubMed

    Mosleh, Zohreh; Salehi, Mohammad Hassan; Jafari, Azam; Borujeni, Isa Esfandiarpoor; Mehnatkesh, Abdolmohammad

    2016-03-01

    This study investigates the ability of different digital soil mapping (DSM) approaches to predict some of physical and chemical topsoil properties in the Shahrekord plain of Chaharmahal-Va-Bakhtiari province, Iran. According to a semi-detailed soil survey, 120 soil samples were collected from 0 to 30 cm depth with approximate distance of 750 m. Particle size distribution, coarse fragments (CFs), electrical conductivity (EC), pH, organic carbon (OC), and calcium carbonate equivalent (CCE) were determined. Four machine learning techniques, namely, artificial neural networks (ANNs), boosted regression tree (BRT), generalized linear model (GLM), and multiple linear regression (MLR), were used to identify the relationship between soil properties and auxiliary information (terrain attributes, remote sensing indices, geology map, existing soil map, and geomorphology map). Root-mean-square error (RMSE) and mean error (ME) were considered to determine the performance of the models. Among the studied models, GLM showed the highest performance to predict pH, EC, clay, silt, sand, and CCE, whereas the best model is not necessarily able to make accurate estimation. According to RMSE%, DSM has a good efficiency to predict soil properties with low and moderate variabilities. Terrain attributes were the main predictors among different studied auxiliary information. The accuracy of the estimations with more observations is recommended to give a better understanding about the performance of DSM approach over low-relief areas.

  11. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

    PubMed

    Nabieva, Elena; Jim, Kam; Agarwal, Amit; Chazelle, Bernard; Singh, Mona

    2005-06-01

    Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps. We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks. http://compbio.cs.princeton.edu/function

  12. Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

    PubMed

    Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

    2007-09-15

    Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

  13. The high-redshift star formation history from carbon-monoxide intensity maps

    NASA Astrophysics Data System (ADS)

    Breysse, Patrick C.; Kovetz, Ely D.; Kamionkowski, Marc

    2016-03-01

    We demonstrate how cosmic star formation history can be measured with one-point statistics of carbon-monoxide intensity maps. Using a P(D) analysis, the luminosity function of CO-emitting sources can be inferred from the measured one-point intensity PDF. The star formation rate density (SFRD) can then be obtained, at several redshifts, from the CO luminosity density. We study the effects of instrumental noise, line foregrounds, and target redshift, and obtain constraints on the CO luminosity density of the order of 10 per cent. We show that the SFRD uncertainty is dominated by that of the model connecting CO luminosity and star formation. For pessimistic estimates of this model uncertainty, we obtain an error of the order of 50 per cent on SFRD for surveys targeting redshifts between two and seven with reasonable noise and foregrounds included. However, comparisons between intensity maps and galaxies could substantially reduce this model uncertainty. In this case, our constraints on SFRD at these redshifts improve to roughly 5 - 10 per cent, which is highly competitive with current measurements.

  14. Map showing structure contours on the top of the upper Jurassic Morrison Formation, Powder River basin, Wyoming and Montana

    USGS Publications Warehouse

    Crysdale, B.L.

    1991-01-01

    This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 2,429 of these wells that penetrate the Minnelusa Formation and equivalents.

  15. Genetic mapping and predictive testing for multiple endocrine neoplasia type 1 (MEN1)

    SciTech Connect

    Pandit, S.D.; Read, C.; Liu, L.

    1994-09-01

    Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder with an estimated prevalance of 20-200 per million persons. It is characterized by the combined occurence of tumors involving two or more endocrine glands, namely the parathyroid glands, the endocrine pancreas and the anterior pituitary. This disorder affects virtually all age groups with an average range of 20-60 years. Linkage analysis mapped the MEN1 locus to 11q13 near the human muscle glycogen phosphorylase (PYGM) locus. Additional genetic mapping and deletion analysis studies have refined the region containing the MEN1 locus to a 3 cM interval flanked by markers PYGM and D11S146/D11S97, a physical distance of approximately 1.5 Mb. We have identified 8 large families segregating MEN1 (71 affected from a population of 389 individuals). A high resolution reference map for the 11q13 region has been constructed using four new microsatellite markers, the CEPH reference (40 family) pedigree resource, and the CRI-MAP program package. Subsequent analyses using the LINKAGE program package and 8 MEN 1 families placed the MEN1 locus within the context of the microsatellite map. This map was used to develop a linkage-based predictive test. These markers have also been used to further refine the interval containing the MEN1 locus from the study of chromosome deletions (loss of heterozygosity, LOH studies) in paired sets of tumor and germline DNA from 87 MEN 1 affected individuals.

  16. Large scale fire whirls: Can their formation be predicted?

    Treesearch

    J. Forthofer; Bret Butler

    2010-01-01

    Large scale fire whirls have not traditionally been recognized as a frequent phenomenon on wildland fires. However, there are anecdotal data suggesting that they can and do occur with some regularity. This paper presents a brief summary of this information and an analysis of the causal factors leading to their formation.

  17. Prediction of an Autocatalytic Replication Mechanism for Micelle Formation

    NASA Astrophysics Data System (ADS)

    Pool, René; Bolhuis, Peter G.

    2006-07-01

    We report molecular simulations suggesting that the kinetics of surfactant micelle formation can be sped up significantly by a replication mechanism, in which growing micelles become unstable and split into two similar sized micelles. We argue that for certain surfactants types around the critical micelle concentration, such a mechanism becomes more dominant than the commonly accepted nucleation pathway.

  18. Science Teachers' Use of a Concept Map Marking Guide as a Formative Assessment Tool for the Concept of Energy

    ERIC Educational Resources Information Center

    Won, Mihye; Krabbe, Heiko; Ley, Siv Ling; Treagust, David F.; Fischer, Hans E.

    2017-01-01

    In this study, we investigated the value of a concept map marking guide as an alternative formative assessment tool for science teachers to adopt for the topic of energy. Eight high school science teachers marked students' concept maps using an itemized holistic marking guide. Their marking was compared with the researchers' marking and the scores…

  19. Spatial Mapping of NEO 2008 EV5 Using Small Satellite Formation Flying and Steresoscopic Technology

    NASA Astrophysics Data System (ADS)

    Gonzalez, Juan; Singh Derewa, Chrishma

    2016-10-01

    NASA is currently developing the first-ever robotic Asteroid Redirect Robotic Mission (ARRM) to the near-Earth asteroid 2008 EV5 with the objective to capture a multi-ton boulder from the asteroids surface and use its mass to redirect its parent into a CIS lunar orbit where astronauts will study its physical and chemical composition.A critical step towards achieving this mission is to effectively map the target asteroid, identify the candidate boulder for retrieval and characterize its critical parameters. Currently, ARRM utilizes a laser altimeter to characterize the height of the boulders and mapping for final autonomous control of the capture. The proposed Lava-Kusha mission provides the increased of stereoscopic imaging and mapping, not only the Earthward side of the asteroid which has been observed for possible landing sites, but mapping the whole asteroid. LKM will enhance the fidelity of the data collected by the laser altimeter and gather improved topographic data for future Orion missions to 2008 EV5 once in cis lunar space.LKM consists of two low cost small satellites (6U) as a part of the ARRM. They will launch with ARRM as an integrated part of the system. Once at the target, this formation of pathfinder satellites will image the mission critical boulder to ensure the system design can support its removal. LKM will conduct a series of flybys prior to ARRM's rendezvous. LKMs stereoscopic cameras will provide detailed surveys of the boulder's terrain and environment to ensure ARRM can operate safely, reach the location and interface with the boulder. The LKM attitude control and cold gas propulsion system will enable formation maintenance maneuvers for global mapping of asteroid 2008 EV5 at an altitude of 100 km to a high-spatial resolution imaging altitude of 5 km.LKM will demonstrate formation flying in deep space and the reliability of stereoscopic cameras to precisely identify a specific target and provide physical characterization of an asteroid. An

  20. Robotic blue-dye sentinel lymph node detection for endometrial cancer - Factors predicting successful mapping.

    PubMed

    Eitan, R; Sabah, G; Krissi, H; Raban, O; Ben-Haroush, A; Goldschmit, C; Levavi, H; Peled, Y

    2015-12-01

    Sentinel lymph node (SLN) mapping has emerged as a viable option for the treatment of patients with endometrial cancer. We report our initial experience with SLN mapping algorithm, and examine the factors predicting successful SLN mapping. We analyzed all data recorded in our institute on robotic blue-dye SLN detection mapping from the time it was first introduced to our department in January 2012-December 2014. Data included patient demographics, SLN allocation, operating room times, and pathology results. During the study period, 74 patients had robotic assisted surgery for endometrial cancer with attempted SLN mapping. SLN was found overall in 46 patients (62.1%). At first, SLN was detected in only 50% of cases, but after performing 30 cases, detection rates rose to 84.6% (OR = 3.34, CI 1.28-8.71; p = 0.003). Univariate analysis showed a higher detection rate with methylene blue than patent blue dye, 74.3% vs. 52.3% (OR = 2.744, 95% CI 1.026-7.344; p = 0.042). In multivariate analysis, high body mass index (BMI) was associated with failed mapping (OR = 0.899; 95% CI 0.808-1.00), as was the presence of lymph-vascular space invasion (LVSI) (OR = 0.126; 95% CI 0.24-0.658) and few cases per surgeon (OR = 1.083, 95% CI 1.032-1.118). Factors related to uterine pathology itself, including tumor histology, grade, method of diagnosis, the presence of an endometrial polyp, and lower uterine segment involvement were not found to be associated with successful mapping. Surgeon experience, BMI and LVSI may affect the success rate of SLN mapping for endometrial cancer. These factors should be investigated further in future studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Star Formation in Orion A : Towards Resolved Maps of SFR and SFE

    NASA Astrophysics Data System (ADS)

    Großschedl, Josefa; Alves, J.; Ascenso, J.; Bouy, H.

    2017-06-01

    The OrionA GMC is a benchmark for studying star formation. Our goal is to construct a map of SFR and SFE (with Herschel) across the entire complex, for which it is critical to have a reliable and complete sample of YSOs. In this work we present a refined catalogue of YSOs, making use of a new deep NIR survey with VISTA, complemented with archival data. The survey allows us to rule out false positives from previous samples (galaxies, cloud edges, etc.). To add new candidates we use MIR data from WISE for areas not covered by Spitzer to get a complete census of the spatial distribution of YSOs.

  2. Selected Data for Wells and Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation in the Black Hills Area, South Dakota

    DTIC Science & Technology

    1999-01-01

    Selected Data for Wells and Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison...Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation...Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation in the Black Hills Area

  3. The Formation Age of Comets: Predicted Physical and Chemical Trends

    NASA Technical Reports Server (NTRS)

    Nuth, Joesph A., III; Hill, H. G. M.

    2000-01-01

    The chemical composition of a comet has always been considered to be a function of where it formed in the nebula. We suggest that the most important factor in determining a comet's chemistry might actually be when it formed. We present specific predictions of correlations between the dust and volatile components to test our hypothesis.

  4. Mapping the Star Formation History of the Local Group with NHST

    NASA Astrophysics Data System (ADS)

    Brown, T. M.

    2003-05-01

    The color-magnitude diagram (CMD) is the most fundamental tool for studying the star formation history of nearby stellar populations. Strong constraints on the ages of stellar populations come from CMDs reaching the main sequence, and with the Hubble Space Telescope (HST), it is possible to produce such a CMD for stars at any distance within the Local Group. Unfortunately, resolving the main sequence in old populations beyond the satellites of the Milky Way requires an enormous investment of HST time, meaning that only a few pencil beams can be explored within the remaining HST mission. In strong contrast, an 8 meter UV-optical space telescope, diffraction limited at 0.5 microns, could map the star formation history of all galaxies in the Local Group: It would take only one hour to resolve the main sequence in any Local Group galaxy, allowing the exploration of hundreds of sight-lines in a reasonable program.

  5. Predicting weed migration from soil and climate maps. [Centaurea maculosa Lam

    SciTech Connect

    Chicoine, T.K.; Fay, P.K.; Nielsen, G.A.

    1985-01-01

    Soil characteristics, elevation, annual precipitation, potential evapotranspiration, length of frost-free season, and mean maximum July temperature were estimated for 116 established infestations of spotted knapweed (Centaurea maculosa Lam. number/sup 3/ CENMA) in Montana using basic land resource maps. Areas potentially vulnerable to invasion by the plant were delineated on the basis of representative edaphic and climatic characteristics. No single environmental variable was an effective predictor of sites vulnerable to invasion by spotted knapweed. Only a combination of variables was effective, indicating that the factors that regulate adaptability of this plant are complex. This technique provides a first approximation map of the regions most similar environmentally to infested sites and; therefore, most vulnerable to further invasion. This weed migration prediction technique shows promise for predicting suitable habitats of other invader species. 6 references, 4 figures, 1 table.

  6. Predictive long-range allele-specific mapping of regulatory variants and target transcripts.

    PubMed

    Lee, Kibaick; Lee, Seulkee; Bang, Hyoeun; Choi, Jung Kyoon

    2017-01-01

    Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts. With phased genotypes, much of allele-specific expression could be explained by paired allelic cis-regulation across a long range. This approach showed approximately two times greater sensitivity than QTL mapping. There are cases in which allele imbalance cannot be tested because heterozygotes are not available among reference samples. Therefore, we employed a machine learning method to predict missing positive cases based on various features shared by observed allele-specific pairs. We showed that only 10 reference samples are sufficient to achieve high prediction accuracy with a low sampling variation. In conclusion, our method enables highly sensitive fine mapping and target identification for trait-associated variants based on a small number of reference samples.

  7. Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

    SciTech Connect

    Elrod, D.W.

    1992-01-01

    Computational neural networks (CNNs) are a computational paradigm inspired by the brain's massively parallel network of highly interconnected neurons. The power of computational neural networks derives not so much from their ability to model the brain as from their ability to learn by example and to map highly complex, nonlinear functions, without the need to explicitly specify the functional relationship. Two central questions about CNNs were investigated in the context of predicting chemical reactions: (1) the mapping properties of neural networks and (2) the representation of chemical information for use in CNNs. Chemical reactivity is here considered an example of a complex, nonlinear function of molecular structure. CNN's were trained using modifications of the back propagation learning rule to map a three dimensional response surface similar to those typically observed in quantitative structure-activity and structure-property relationships. The computational neural network's mapping of the response surface was found to be robust to the effects of training sample size, noisy data and intercorrelated input variables. The investigation of chemical structure representation led to the development of a molecular structure-based connection-table representation suitable for neural network training. An extension of this work led to a BE-matrix structure representation that was found to be general for several classes of reactions. The CNN prediction of chemical reactivity and regiochemistry was investigated for electrophilic aromatic substitution reactions, Markovnikov addition to alkenes, Saytzeff elimination from haloalkanes, Diels-Alder cycloaddition, and retro Diels-Alder ring opening reactions using these connectivity-matrix derived representations. The reaction predictions made by the CNNs were more accurate than those of an expert system and were comparable to predictions made by chemists.

  8. Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps.

    PubMed

    Antolík, Ján

    2017-01-01

    Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added.

  9. Rapid Long-Range Disynaptic Inhibition Explains the Formation of Cortical Orientation Maps

    PubMed Central

    Antolík, Ján

    2017-01-01

    Competitive interactions are believed to underlie many types of cortical processing, ranging from memory formation, attention and development of cortical functional organization (e.g., development of orientation maps in primary visual cortex). In the latter case, the competitive interactions happen along the cortical surface, with local populations of neurons reinforcing each other, while competing with those displaced more distally. This specific configuration of lateral interactions is however in stark contrast with the known properties of the anatomical substrate, i.e., excitatory connections (mediating reinforcement) having longer reach than inhibitory ones (mediating competition). No satisfactory biologically plausible resolution of this conflict between anatomical measures, and assumed cortical function has been proposed. Recently a specific pattern of delays between different types of neurons in cat cortex has been discovered, where direct mono-synaptic excitation has approximately the same delay, as the combined delays of the disynaptic inhibitory interactions between excitatory neurons (i.e., the sum of delays from excitatory to inhibitory and from inhibitory to excitatory neurons). Here we show that this specific pattern of delays represents a biologically plausible explanation for how short-range inhibition can support competitive interactions that underlie the development of orientation maps in primary visual cortex. We demonstrate this statement analytically under simplifying conditions, and subsequently show using network simulations that development of orientation maps is preserved when long-range excitation, direct inhibitory to inhibitory interactions, and moderate inequality in the delays between excitatory and inhibitory pathways is added. PMID:28408869

  10. Predictive modeling of synergistic effects in nanoscale ion track formation

    DOE PAGES

    Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou; ...

    2015-08-05

    Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

  11. Predicting functional neuroanatomical maps from fusing brain networks with genetic information.

    PubMed

    Ganglberger, Florian; Kaczanowska, Joanna; Penninger, Josef M; Hess, Andreas; Bühler, Katja; Haubensak, Wulf

    2017-09-03

    Functional neuroanatomical maps provide a mesoscale reference framework for studies from molecular to systems neuroscience and psychiatry. The underlying structure-function relationships are typically derived from functional manipulations or imaging approaches. Although highly informative, these are experimentally costly. The increasing amount of publicly available brain and genetic data offers a rich source that could be mined to address this problem computationally. Here, we developed an algorithm that fuses gene expression and connectivity data with functional genetic meta data and exploits cumulative effects to derive neuroanatomical maps related to multi-genic functions. We validated the approach by using public available mouse and human data. The generated neuroanatomical maps recapture known functional anatomical annotations from literature and functional MRI data. When applied to multi-genic meta data from mouse quantitative trait loci (QTL) studies and human neuropsychiatric databases, this method predicted known functional maps underlying behavioral or psychiatric traits. Taken together, genetically weighted connectivity analysis (GWCA) allows for high throughput functional exploration of brain anatomy in silico. It maps functional genetic associations onto brain circuitry for refining functional neuroanatomy, or identifying trait-associated brain circuitry, from genetic data. Copyright © 2017. Published by Elsevier Inc.

  12. Fine-mapping of the woolly gene controlling multicellular trichome formation and embryonic development in tomato.

    PubMed

    Yang, Changxian; Li, Hanxia; Zhang, Junhong; Wang, Taotao; Ye, Zhibiao

    2011-08-01

    Trichomes are small hairs that originate from the epidermal cells of nearly all land plants, and they exist in unicellular and multicellular forms. The regulatory pathway of unicellular trichomes in Arabidopsis is well characterized. However, little is known about the multicellular trichome formation in tomato (Solanum lycopersicum). The woolly (Wo) gene controls multicellular trichome initiation and leads to embryonic lethality when homozygous in tomato. To clone and characterize Wo, the gene was fine-mapped to a DNA fragment of ~200 kb using the map-based cloning strategy. A series of sequence-based molecular markers, including simple sequence repeat, sequence characterized amplified region, and cleaved amplified polymorphic sequence were utilized in this study. Analysis of the sequence indicated that this region carries 19 putative open reading frames. These results will provide not only the important information for the isolation and characterization of Wo but also the starting point for studying the regulatory pathway responsible for trichome formation and embryonic lethality in tomato.

  13. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  14. Predictive Mapping of the Biotic Condition of Conterminous-USA Rivers and Streams.

    PubMed

    Hill, Ryan A; Fox, Eric W; Leibowitz, Scott G; Olsen, Anthony R; Thornbrugh, Darren J; Weber, Marc H

    2017-09-04

    Understanding and mapping the spatial variation in stream biological condition could provide an important tool for conservation, assessment, and restoration of stream ecosystems. The USEPA's 2008-2009 National Rivers and Streams Assessment (NRSA) summarizes the percent of stream lengths within the conterminous US that are in good, fair, or poor biological condition based on a multimetric index of benthic invertebrate assemblages. However, condition is usually summarized at regional or national scales, and these assessments do not provide substantial insight into the spatial distribution of conditions at unsampled locations. We used random forests to model and predict the probable condition of several million kilometers of streams across the conterminous US based on nearby and upstream landscape features, including human-related alterations to watersheds. To do so, we linked NRSA sample sites to the USEPA's StreamCat Dataset; a database of several hundred landscape metrics for all 1:100,000-scale streams and their associated watersheds within the conterminous US. The StreamCat data provided geospatial indicators of nearby and upstream land use, land cover, climate, and other landscape features for modeling. Nationally, the model correctly predicted the biological condition class of 75% of NRSA sites. Although model evaluations suggested good discrimination among condition classes, we present maps as predicted probabilities of good condition, given upstream and nearby landscape settings. Inversely, the maps can be interpreted as the probability of a stream being in poor condition, given human-related watershed alterations. These predictions are available for download from the USEPA's StreamCat website (https://w w w .epa. gov/national-aquatic-resource-surveys/streamcat). Finally, we illustrate how these predictions could be used to prioritize streams for conservation or restoration. This article is protected by copyright. All rights reserved. This article is

  15. Predictive modeling of synergistic effects in nanoscale ion track formation

    SciTech Connect

    Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou; Zhang, Yanwen; Weber, William J.

    2015-08-05

    Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

  16. Using global maps to predict the risk of dengue in Europe.

    PubMed

    Rogers, David J; Suk, Jonathan E; Semenza, Jan C

    2014-01-01

    This article attempts to quantify the risk to Europe of dengue, following the arrival and spread there of one of dengue's vector species Aedes (Stegomyia) albopictus. A global risk map for dengue is presented, based on a global database of the occurrence of this disease, derived from electronic literature searches. Remotely sensed satellite data (from NASA's MODIS series), interpolated meteorological data, predicted distribution maps of dengue's two main vector species, Aedes aegypti and Aedes albopictus, a digital elevation surface and human population density data were all used as potential predictor variables in a non-linear discriminant analysis modelling framework. One hundred bootstrap models were produced by randomly sub-sampling three different training sets for dengue fever, severe dengue (i.e. dengue haemorrhagic fever, DHF) and all-dengue, and output predictions were averaged to produce a single global risk map for each type of dengue. This paper concentrates on the all-dengue models. Key predictor variables were various thermal data layers, including both day- and night-time Land Surface Temperature, human population density, and a variety of rainfall variables. The relative importance of each may be shown visually using rainbow files and quantitatively using a ranking system. Vegetation Index variables (a common proxy for humidity or saturation deficit) were rarely chosen in the models. The kappa index of agreement indicated an excellent (dengue haemorrhagic fever, Cohen's kappa=0.79 ± 0.028, AUC=0.96 ± 0.007) or good fit of the top ten models in each series to the data (Cohen's kappa=0.73 ± 0.018, AUC=0.94 ± 0.007 for dengue fever and 0.74 ± 0.017, AUC=0.95 ± 0.005 for all dengue). The global risk map predicts widespread dengue risk in SE Asia and India, in Central America and parts of coastal South America, but in relatively few regions of Africa. In many cases these are less extensive predictions than those of other published dengue risk maps

  17. Predicting the external formation of callus tissues in oblique bone fractures: idealised and clinical case studies.

    PubMed

    Comiskey, D; MacDonald, B J; McCartney, W T; Synnott, K; O'Byrne, J

    2013-11-01

    It is proposed that the external asymmetric formation of callus tissues that forms naturally about an oblique bone fracture can be predicted computationally. We present an analysis of callus formation for two cases of bone fracture healing: idealised and subject-specific oblique bone fractures. Plane strain finite element (FE) models of the oblique fractures were generated to calculate the compressive strain field experienced by the immature callus tissues due to interfragmentary motion. The external formations of the calluses were phenomenologically simulated using an optimisation style algorithm that iteratively removes tissue that experiences low strains from a large domain. The resultant simulated spatial formation of the healing tissues for the two bone fracture cases showed that the calluses tended to form at an angle equivalent to the angle of the oblique fracture line. The computational results qualitatively correlated with the callus formations found in vivo. Consequently, the proposed methods show potential as a means of predicting callus formation in pre-clinical testing.

  18. Data modeling for predictive behavior hypothesis formation and testing

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Barnett, Marvin H.; Esslinger, Richard; Grover, David A.; Faucheux, Jeffrey P.; Lamkin, Kenneth

    2006-04-01

    This paper presents a novel hypothesis analysis tool building on QUEST and DANCER. Unique is the ability to convert cause/effect relationships into analytical equation transfer functions for exploitation. In this the third phase of our work, we derive Data Models for each unique word and its ontological associated unique words. We form a classical control theory transfer function using the associated words as the input vector and the assigned unique word as the output vector. Each transfer function model can be tested against new evidence to yield new output. Additionally, conjectured output can be passed through the inverse model to predict the requisite case observations required to yield the conjectured output. Hypotheses are tested using circumstantial evidence, notional similarity, evidential strength, and plausibility to determine if they are supported or rejected. Examples of solving for evidence links are provided from tool execution.

  19. XML-BSPM: an XML format for storing Body Surface Potential Map recordings

    PubMed Central

    2010-01-01

    Background The Body Surface Potential Map (BSPM) is an electrocardiographic method, for recording and displaying the electrical activity of the heart, from a spatial perspective. The BSPM has been deemed more accurate for assessing certain cardiac pathologies when compared to the 12-lead ECG. Nevertheless, the 12-lead ECG remains the most popular ECG acquisition method for non-invasively assessing the electrical activity of the heart. Although data from the 12-lead ECG can be stored and shared using open formats such as SCP-ECG, no open formats currently exist for storing and sharing the BSPM. As a result, an innovative format for storing BSPM datasets has been developed within this study. Methods The XML vocabulary was chosen for implementation, as opposed to binary for the purpose of human readability. There are currently no standards to dictate the number of electrodes and electrode positions for recording a BSPM. In fact, there are at least 11 different BSPM electrode configurations in use today. Therefore, in order to support these BSPM variants, the XML-BSPM format was made versatile. Hence, the format supports the storage of custom torso diagrams using SVG graphics. This diagram can then be used in a 2D coordinate system for retaining electrode positions. Results This XML-BSPM format has been successfully used to store the Kornreich-117 BSPM dataset and the Lux-192 BSPM dataset. The resulting file sizes were in the region of 277 kilobytes for each BSPM recording and can be deemed suitable for example, for use with any telemonitoring application. Moreover, there is potential for file sizes to be further reduced using basic compression algorithms, i.e. the deflate algorithm. Finally, these BSPM files have been parsed and visualised within a convenient time period using a web based BSPM viewer. Conclusions This format, if widely adopted could promote BSPM interoperability, knowledge sharing and data mining. This work could also be used to provide conceptual

  20. XML-BSPM: an XML format for storing Body Surface Potential Map recordings.

    PubMed

    Bond, Raymond R; Finlay, Dewar D; Nugent, Chris D; Moore, George

    2010-05-14

    The Body Surface Potential Map (BSPM) is an electrocardiographic method, for recording and displaying the electrical activity of the heart, from a spatial perspective. The BSPM has been deemed more accurate for assessing certain cardiac pathologies when compared to the 12-lead ECG. Nevertheless, the 12-lead ECG remains the most popular ECG acquisition method for non-invasively assessing the electrical activity of the heart. Although data from the 12-lead ECG can be stored and shared using open formats such as SCP-ECG, no open formats currently exist for storing and sharing the BSPM. As a result, an innovative format for storing BSPM datasets has been developed within this study. The XML vocabulary was chosen for implementation, as opposed to binary for the purpose of human readability. There are currently no standards to dictate the number of electrodes and electrode positions for recording a BSPM. In fact, there are at least 11 different BSPM electrode configurations in use today. Therefore, in order to support these BSPM variants, the XML-BSPM format was made versatile. Hence, the format supports the storage of custom torso diagrams using SVG graphics. This diagram can then be used in a 2D coordinate system for retaining electrode positions. This XML-BSPM format has been successfully used to store the Kornreich-117 BSPM dataset and the Lux-192 BSPM dataset. The resulting file sizes were in the region of 277 kilobytes for each BSPM recording and can be deemed suitable for example, for use with any telemonitoring application. Moreover, there is potential for file sizes to be further reduced using basic compression algorithms, i.e. the deflate algorithm. Finally, these BSPM files have been parsed and visualised within a convenient time period using a web based BSPM viewer. This format, if widely adopted could promote BSPM interoperability, knowledge sharing and data mining. This work could also be used to provide conceptual solutions and inspire existing formats

  1. Observation and prediction of first phase formation in binary Cu-metal thin films

    NASA Astrophysics Data System (ADS)

    Li, Jian; Strane, J. W.; Russell, S. W.; Hong, S. Q.; Mayer, J. W.; Marais, T. K.; Theron, C. C.; Pretorius, R.

    1992-10-01

    First phase formation has been determined in Cu binary thin film systems with Ti, Zr, Mg, Sb, Pd, and Pt using transmission electron microscopy and Rutherford backscattering spectrometry. CuTi, CuZr, CuMg2, Cu2Sb, Cu3Pd, and Cu3Pt are the first phases to form upon annealing the Cu/metal bilayers. The effective heat of formation model is used to predict first phase formation in 14 Cu/metal systems.

  2. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

    PubMed

    Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

    2013-05-01

    Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

  3. Predictive Multiple Model Switching Control with the Self-Organizing Map

    NASA Technical Reports Server (NTRS)

    Motter, Mark A.

    2000-01-01

    A predictive, multiple model control strategy is developed by extension of self-organizing map (SOM) local dynamic modeling of nonlinear autonomous systems to a control framework. Multiple SOMs collectively model the global response of a nonautonomous system to a finite set of representative prototype controls. Each SOM provides a codebook representation of the dynamics corresponding to a prototype control. Different dynamic regimes are organized into topological neighborhoods where the adjacent entries in the codebook represent the global minimization of a similarity metric. The SOM is additionally employed to identify the local dynamical regime, and consequently implements a switching scheme that selects the best available model for the applied control. SOM based linear models are used to predict the response to a larger family of control sequences which are clustered on the representative prototypes. The control sequence which corresponds to the prediction that best satisfies the requirements on the system output is applied as the external driving signal.

  4. Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction.

    PubMed

    Chu, Wei; Ghahramani, Zoubin; Podtelezhnikov, Alexei; Wild, David L

    2006-01-01

    In this paper, we develop a segmental semi-Markov model (SSMM) for protein secondary structure prediction which incorporates multiple sequence alignment profiles with the purpose of improving the predictive performance. The segmental model is a generalization of the hidden Markov model where a hidden state generates segments of various length and secondary structure type. A novel parameterized model is proposed for the likelihood function that explicitly represents multiple sequence alignment profiles to capture the segmental conformation. Numerical results on benchmark data sets show that incorporating the profiles results in substantial improvements and the generalization performance is promising. By incorporating the information from long range interactions in beta-sheets, this model is also capable of carrying out inference on contact maps. This is an important advantage of probabilistic generative models over the traditional discriminative approach to protein secondary structure prediction. The Web server of our algorithm and supplementary materials are available at http://public.kgi.edu/-wild/bsm.html.

  5. Predictive Brain Mechanisms in Sound-to-Meaning Mapping during Speech Processing.

    PubMed

    Lyu, Bingjiang; Ge, Jianqiao; Niu, Zhendong; Tan, Li Hai; Gao, Jia-Hong

    2016-10-19

    Spoken language comprehension relies not only on the identification of individual words, but also on the expectations arising from contextual information. A distributed frontotemporal network is known to facilitate the mapping of speech sounds onto their corresponding meanings. However, how prior expectations influence this efficient mapping at the neuroanatomical level, especially in terms of individual words, remains unclear. Using fMRI, we addressed this question in the framework of the dual-stream model by scanning native speakers of Mandarin Chinese, a language highly dependent on context. We found that, within the ventral pathway, the violated expectations elicited stronger activations in the left anterior superior temporal gyrus and the ventral inferior frontal gyrus (IFG) for the phonological-semantic prediction of spoken words. Functional connectivity analysis showed that expectations were mediated by both top-down modulation from the left ventral IFG to the anterior temporal regions and enhanced cross-stream integration through strengthened connections between different subregions of the left IFG. By further investigating the dynamic causality within the dual-stream model, we elucidated how the human brain accomplishes sound-to-meaning mapping for words in a predictive manner.

  6. Urban Mapping and Growth Prediction using Remote Sensing and GIS Techniques, Pune, India

    NASA Astrophysics Data System (ADS)

    Sivakumar, V.

    2014-11-01

    This study aims to map the urban area in and around Pune region between the year 1991 and 2010, and predict its probable future growth using remote sensing and GIS techniques. The Landsat TM and ETM+ satellite images of 1991, 2001 and 2010 were used for analyzing urban land use class. Urban class was extracted / mapped using supervised classification technique with maximum likelihood classifier. The accuracy assessment was carried out for classified maps. The achieved overall accuracy and Kappa statistics were 86.33 % & 0.76 respectively. Transition probability matrix and area change were obtained using different classified images. A plug-in was developed in QGIS software (open source) based on Markov Chain model algorithm for predicting probable urban growth for the future year 2021. Based on available data set, the result shows that urban area is expected to grow much higher in the year 2021 when compared to 2010. This study provides an insight into understanding of urban growth and aids in subsequent infrastructure planning, management and decision-making.

  7. Gis predictive mapping of terrestrial gamma radiation in the Northern State, Sudan.

    PubMed

    Hamed Bashier, E; Salih, I; Khatir Sam, A

    2012-09-01

    This study presents the evaluation of absorbed dose in air due to gamma-emitting nuclides from (238)U and (232)Th series, (40)K and (137)Cs and the corresponding geographical information system (GIS) predictive mapping for the Northern State. Activity concentration of (238)U, (232)Th , (40)K and (137)Cs in soil samples collected from different locations have been measured using high-resolution gamma spectrometry. On  average, activity concentrations were 19±4 ((238)U), 47±11 ((232)Th), 317±65 ((40)K) and 2.26 Bq kg(-1) for (137)Cs. Absorbed dose rate in air at a height of 1 m above ground surface was calculated using seven sets of dose rate conversion factors (DRCFs) and the corresponding annual effective dose was estimated. On average, the values obtained fall within a narrow range of 44 and 53 nGy h(-1), indicating that the variation in absorbed dose rate is insignificant for different DRCFs. The corresponding annual effective dose ranged from 53 to 65 µSv y(-1). Using GIS, prediction maps for concentrations of (238)U, (232)Th, (40)K and (137)Cs were produced. Also, a map for absorbed dose rate in air at a height of 1 m above the ground level was produced, which showed a trend of increasing from the west towards south-east of the State.

  8. Improved prediction accuracy for disease risk mapping using Gaussian process stacked generalization.

    PubMed

    Bhatt, Samir; Cameron, Ewan; Flaxman, Seth R; Weiss, Daniel J; Smith, David L; Gething, Peter W

    2017-09-01

    Maps of infectious disease-charting spatial variations in the force of infection, degree of endemicity and the burden on human health-provide an essential evidence base to support planning towards global health targets. Contemporary disease mapping efforts have embraced statistical modelling approaches to properly acknowledge uncertainties in both the available measurements and their spatial interpolation. The most common such approach is Gaussian process regression, a mathematical framework composed of two components: a mean function harnessing the predictive power of multiple independent variables, and a covariance function yielding spatio-temporal shrinkage against residual variation from the mean. Though many techniques have been developed to improve the flexibility and fitting of the covariance function, models for the mean function have typically been restricted to simple linear terms. For infectious diseases, known to be driven by complex interactions between environmental and socio-economic factors, improved modelling of the mean function can greatly boost predictive power. Here, we present an ensemble approach based on stacked generalization that allows for multiple nonlinear algorithmic mean functions to be jointly embedded within the Gaussian process framework. We apply this method to mapping Plasmodium falciparum prevalence data in sub-Saharan Africa and show that the generalized ensemble approach markedly outperforms any individual method. © 2017 The Author(s).

  9. The Formation Age of Comets: Predicted Physical and Chemical Trends

    NASA Technical Reports Server (NTRS)

    Nuth, Joseph A., III; Hill, Hugh G. M.

    2000-01-01

    Dust grains in Herbig Ae/Be stars are continuously replenished by infalling comets. The IR spectra of these cometary grains appear to evolve temporally from initially amorphous astronomical silicates in young protostars to crystalline olivine in much older sources. Crystalline olivine can only be produced from amorphous silicates on a time scale of months-to-years via thermal annealing at temperatures near 1000 K. Since such sustained high temperatures only occur near the central star, dust annealed at 1000 K in inner nebular regions must be continuously transported beyond the nebular snowline to be incorporated into the next generation of cometesimals. The average formation age of a comet can therefore be measured as a ratio of the annealed crystalline olivine dust component to the total dust content of the comet. Comets formed from nearly pristine interstellar materials early in the protostellar nebula stage will contain very little crystalline dust whereas comets formed towards the end of the accretion period will incorporate a much higher percentage of annealed silicate. It is unlikely that only dust grains circulate from the inner to the outer nebula; the gas associated with such dust should also find its way beyond the snowline. Since this gas and dust will have equilibrated in the higher pressure-temperature regime of the inner nebula, it will contain a much higher proportion of hydrocarbons and ammonia than more pristine interstellar ices. Therefore, in addition to a higher fraction of crystalline dust, later forming comets should also contain higher ratios of hydrocarbons to CO and ammonia to N2 than do those formed early in the history of the nebula.

  10. Estimating cross-validatory predictive p-values with integrated importance sampling for disease mapping models.

    PubMed

    Li, Longhai; Feng, Cindy X; Qiu, Shi

    2017-06-30

    An important statistical task in disease mapping problems is to identify divergent regions with unusually high or low risk of disease. Leave-one-out cross-validatory (LOOCV) model assessment is the gold standard for estimating predictive p-values that can flag such divergent regions. However, actual LOOCV is time-consuming because one needs to rerun a Markov chain Monte Carlo analysis for each posterior distribution in which an observation is held out as a test case. This paper introduces a new method, called integrated importance sampling (iIS), for estimating LOOCV predictive p-values with only Markov chain samples drawn from the posterior based on a full data set. The key step in iIS is that we integrate away the latent variables associated the test observation with respect to their conditional distribution without reference to the actual observation. By following the general theory for importance sampling, the formula used by iIS can be proved to be equivalent to the LOOCV predictive p-value. We compare iIS and other three existing methods in the literature with two disease mapping datasets. Our empirical results show that the predictive p-values estimated with iIS are almost identical to the predictive p-values estimated with actual LOOCV and outperform those given by the existing three methods, namely, the posterior predictive checking, the ordinary importance sampling, and the ghosting method by Marshall and Spiegelhalter (2003). Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  11. Bayesian Mapping Reveals That Attention Boosts Neural Responses to Predicted and Unpredicted Stimuli.

    PubMed

    Garrido, Marta I; Rowe, Elise G; Halász, Veronika; Mattingley, Jason B

    2017-04-10

    Predictive coding posits that the human brain continually monitors the environment for regularities and detects inconsistencies. It is unclear, however, what effect attention has on expectation processes, as there have been relatively few studies and the results of these have yielded contradictory findings. Here, we employed Bayesian model comparison to adjudicate between 2 alternative computational models. The "Opposition" model states that attention boosts neural responses equally to predicted and unpredicted stimuli, whereas the "Interaction" model assumes that attentional boosting of neural signals depends on the level of predictability. We designed a novel, audiospatial attention task that orthogonally manipulated attention and prediction by playing oddball sequences in either the attended or unattended ear. We observed sensory prediction error responses, with electroencephalography, across all attentional manipulations. Crucially, posterior probability maps revealed that, overall, the Opposition model better explained scalp and source data, suggesting that attention boosts responses to predicted and unpredicted stimuli equally. Furthermore, Dynamic Causal Modeling showed that these Opposition effects were expressed in plastic changes within the mismatch negativity network. Our findings provide empirical evidence for a computational model of the opposing interplay of attention and expectation in the brain.

  12. Geographical information system and predictive risk maps of urinary schistosomiasis in Ogun State, Nigeria

    PubMed Central

    Ekpo, Uwem F; Mafiana, Chiedu F; Adeofun, Clement O; Solarin, Adewale RT; Idowu, Adewumi B

    2008-01-01

    Background The control of urinary schistosomiasis in Ogun State, Nigeria remains inert due to lack of reliable data on the geographical distribution of the disease and the population at risk. To help in developing a control programme, delineating areas of risk, geographical information system and remotely sensed environmental images were used to developed predictive risk maps of the probability of occurrence of the disease and quantify the risk for infection in Ogun State, Nigeria. Methods Infection data used were derived from carefully validated morbidity questionnaires among primary school children in 2001–2002, in which school children were asked among other questions if they have experienced "blood in urine" or urinary schistosomiasis. The infection data from 1,092 schools together with remotely sensed environmental data such as rainfall, vegetation, temperature, soil-types, altitude and land cover were analysis using binary logistic regression models to identify environmental features that influence the spatial distribution of the disease. The final regression equations were then used in Arc View 3.2a GIS software to generate predictive risk maps of the distribution of the disease and population at risk in the state. Results Logistic regression analysis shows that the only significant environmental variable in predicting the presence and absence of urinary schistosomiasis in any area of the State was Land Surface Temperature (LST) (B = 0.308, p = 0.013). While LST (B = -0.478, p = 0.035), rainfall (B = -0.006, p = 0.0005), ferric luvisols (B = 0.539, p = 0.274), dystric nitosols (B = 0.133, p = 0.769) and pellic vertisols (B = 1.386, p = 0.008) soils types were the final variables in the model for predicting the probability of an area having an infection prevalence equivalent to or more than 50%. The two predictive risk maps suggest that urinary schistosomiasis is widely distributed and occurring in all the Local Government Areas (LGAs) in State. The high

  13. Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping

    NASA Astrophysics Data System (ADS)

    Frasinski, L. J.; Zhaunerchyk, V.; Mucke, M.; Squibb, R. J.; Siano, M.; Eland, J. H. D.; Linusson, P.; v. d. Meulen, P.; Salén, P.; Thomas, R. D.; Larsson, M.; Foucar, L.; Ullrich, J.; Motomura, K.; Mondal, S.; Ueda, K.; Osipov, T.; Fang, L.; Murphy, B. F.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Schorb, S.; Messerschmidt, M.; Glownia, J. M.; Cryan, J. P.; Coffee, R. N.; Takahashi, O.; Wada, S.; Piancastelli, M. N.; Richter, R.; Prince, K. C.; Feifel, R.

    2013-08-01

    When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called “partial covariance mapping” to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.

  14. Mapping the formation areas of giant molybdenum blue clusters: a spectroscopic study

    SciTech Connect

    Botar, Bogdan; Ellern, Arkady; Kogerler, Paul

    2012-05-18

    The self-assembly of soluble molybdenum blue species from simple molybdate solutions has primarily been associated with giant mixed-valent wheel-shaped cluster anions, derived from the {MoV/VI154/176} archetypes, and a {MoV/VI368} lemon-shaped cluster. The combined use of Raman spectroscopy and kinetic precipitation as self-assembly monitoring techniques and single-crystal X-ray diffraction is key to mapping the realm of molybdenum blue species by establishing spherical {MoV/VI102}-type Keplerates as an important giant molybdenum blue-type species. We additionally rationalize the empirical effect of reducing agent concentration on the formation of all three relevant skeletal types: wheel, lemon and spheres. Whereas both wheels and the lemon-shaped {MoV/VI368} cluster are obtained from weakly reduced molybdenum blue solutions, considerably higher reduced solutions lead to {MoV/VI102}-type Keplerates.

  15. Prediction of heat of formation and related parameters of high energy materials.

    PubMed

    Muthurajan, H; Sivabalan, R; Talawar, M B; Anniyappan, M; Venugopalan, S

    2006-05-20

    Heat of formation is one of the most important parameters in the performance prediction of explosive and propellant formulations and their individual ingredients. This paper reports the development of user-friendly computer code for the prediction of heat of formation based on two approaches. In first methodology, the logic of Benson's Group additivity method and in the second method, the logic of Pedley method was used for predicting the heats of formation of high energy materials (HEMs). The predicted heats of formation by Benson method for various classes of high energy materials gave deviation in the range of 2-10%, whereas nearly 10-15% deviation was observed using Pedley methodology in comparison to experimental values. The linear regression coefficient values (R(2)) of 0.9947 and 0.9637 are obtained for heat of formation values predicted by this code using methodologies I and II, respectively. The newly developed code LOTUSES (version 1.3) has been validated by calculating the heats of formation of standard explosives such as TNT, pentaerythritol tetranitrate (PETN), RDX, HMX, etc., To the best of our knowledge, no such code is reported in literature which can predict heats of formation values integrated with performance parameters of HEMs belonging to all categories of organic compounds viz. aliphatic, aromatic and heterocyclic materials. The code can also be used to obtain parameters such as velocity of detonation, C-J pressure, volume of explosion products, power index, temperature of explosion and oxygen balance of HEMs. The code has been developed in Visual Basic having enhanced Windows environment. This software namely LOTUSES 1.3 is an updated version of the earlier ones namely LOTUSES 1.1 and 1.2 which do not cater for the calculation of heat of formation and temperature of explosion of HEMs. LOTUSES 1.3 is, therefore, a totally integrated software for computing most of the vital parameters of HEMs requiring mainly the molecular structural

  16. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

  17. Predictive Factors and Risk Mapping for Rift Valley Fever Epidemics in Kenya

    PubMed Central

    Munyua, Peninah M.; Murithi, R. Mbabu; Ithondeka, Peter; Hightower, Allen; Thumbi, Samuel M.; Anyangu, Samuel A.; Kiplimo, Jusper; Bett, Bernard; Vrieling, Anton; Breiman, Robert F.; Njenga, M. Kariuki

    2016-01-01

    Background To-date, Rift Valley fever (RVF) outbreaks have occurred in 38 of the 69 administrative districts in Kenya. Using surveillance records collected between 1951 and 2007, we determined the risk of exposure and outcome of an RVF outbreak, examined the ecological and climatic factors associated with the outbreaks, and used these data to develop an RVF risk map for Kenya. Methods Exposure to RVF was evaluated as the proportion of the total outbreak years that each district was involved in prior epizootics, whereas risk of outcome was assessed as severity of observed disease in humans and animals for each district. A probability-impact weighted score (1 to 9) of the combined exposure and outcome risks was used to classify a district as high (score ≥ 5) or medium (score ≥2 - <5) risk, a classification that was subsequently subjected to expert group analysis for final risk level determination at the division levels (total = 391 divisions). Divisions that never reported RVF disease (score < 2) were classified as low risk. Using data from the 2006/07 RVF outbreak, the predictive risk factors for an RVF outbreak were identified. The predictive probabilities from the model were further used to develop an RVF risk map for Kenya. Results The final output was a RVF risk map that classified 101 of 391 divisions (26%) located in 21 districts as high risk, and 100 of 391 divisions (26%) located in 35 districts as medium risk and 190 divisions (48%) as low risk, including all 97 divisions in Nyanza and Western provinces. The risk of RVF was positively associated with Normalized Difference Vegetation Index (NDVI), low altitude below 1000m and high precipitation in areas with solonertz, luvisols and vertisols soil types (p <0.05). Conclusion RVF risk map serves as an important tool for developing and deploying prevention and control measures against the disease. PMID:26808021

  18. Predictive Factors and Risk Mapping for Rift Valley Fever Epidemics in Kenya.

    PubMed

    Munyua, Peninah M; Murithi, R Mbabu; Ithondeka, Peter; Hightower, Allen; Thumbi, Samuel M; Anyangu, Samuel A; Kiplimo, Jusper; Bett, Bernard; Vrieling, Anton; Breiman, Robert F; Njenga, M Kariuki

    2016-01-01

    To-date, Rift Valley fever (RVF) outbreaks have occurred in 38 of the 69 administrative districts in Kenya. Using surveillance records collected between 1951 and 2007, we determined the risk of exposure and outcome of an RVF outbreak, examined the ecological and climatic factors associated with the outbreaks, and used these data to develop an RVF risk map for Kenya. Exposure to RVF was evaluated as the proportion of the total outbreak years that each district was involved in prior epizootics, whereas risk of outcome was assessed as severity of observed disease in humans and animals for each district. A probability-impact weighted score (1 to 9) of the combined exposure and outcome risks was used to classify a district as high (score ≥ 5) or medium (score ≥2 - <5) risk, a classification that was subsequently subjected to expert group analysis for final risk level determination at the division levels (total = 391 divisions). Divisions that never reported RVF disease (score < 2) were classified as low risk. Using data from the 2006/07 RVF outbreak, the predictive risk factors for an RVF outbreak were identified. The predictive probabilities from the model were further used to develop an RVF risk map for Kenya. The final output was a RVF risk map that classified 101 of 391 divisions (26%) located in 21 districts as high risk, and 100 of 391 divisions (26%) located in 35 districts as medium risk and 190 divisions (48%) as low risk, including all 97 divisions in Nyanza and Western provinces. The risk of RVF was positively associated with Normalized Difference Vegetation Index (NDVI), low altitude below 1000m and high precipitation in areas with solonertz, luvisols and vertisols soil types (p <0.05). RVF risk map serves as an important tool for developing and deploying prevention and control measures against the disease.

  19. Enhanced NEXRAD Radar-based Flood Warning System with Hydraulic Prediction Feature: Floodplain Map Library (FPML)

    NASA Astrophysics Data System (ADS)

    Fang, Z.; Bedient, P. B.

    2007-12-01

    Houston is facing flood problems of a serious nature. Until more permanent solutions are found accurate and timely, early warning flood systems are vitally needed to provide the early warnings that public and private entities are demanding. The current Rice University/TMC Flood Alert System (FAS2) began to utilize higher-resolutioned Level II NEXRAD radar data (1 x 1 km) that is calibrated against local rain gauges by the end of 2004, with the real-time hydrologic model (RTHEC-1) to provide important data for predicting flood levels along Brays Bayou. The finer resolution of Level II radar rainfall data provides significantly greater details with respect to the spatial variability of rainfall. FAS2 has been tested for more than 30 events including three recent events in 2006 season with excellent performance. It has been found from 2006 season that the average difference in peak flows is 8.76%; the average difference in terms of volumes is 13.70%. The floodplain map library (FPML) as a new hydraulic prediction tool has been developed based on the radar- based FAS2 and is being integrated into FAS2 to provide inundations maps in near real time. The development of FPML includes three stages: designing rainfall based on historical rainfall data over the watershed, delineating 99 maps based on design rainfalls, and designing algorithm to link real-time NEXRAD radar rainfall to appropriate maps. The enhance system can be a prototype for other flood-prone areas along the Gulf coast, and will improve emergency personnel's ability to initiate evacuation strategies at many levels.

  20. Decision-Tree-based data mining and rule induction for predicting and mapping soil bacterial diversity.

    PubMed

    Kim, Kangsuk; Yoo, Keunje; Ki, Dongwon; Son, Il Suh; Oh, Kyong Joo; Park, Joonhong

    2011-07-01

    Soilmicrobial ecology plays a significant role in global ecosystems. Nevertheless, methods of model prediction and mapping have yet to be established for soil microbial ecology. The present study was undertaken to develop an artificial-intelligence- and geographical information system (GIS)-integrated framework for predicting and mapping soil bacterial diversity using pre-existing environmental geospatial database information, and to further evaluate the applicability of soil bacterial diversity mapping for planning construction of eco-friendly roads. Using a stratified random sampling, soil bacterial diversity was measured in 196 soil samples in a forest area where construction of an eco-friendly road was planned. Model accuracy, coherence analyses, and tree analysis were systematically performed, and four-class discretized decision tree (DT) with ordinary pair-wise partitioning (OPP) was selected as the optimal model among tested five DT model variants. GIS-based simulations of the optimal DT model with varying weights assigned to soil ecological quality showed that the inclusion of soil ecology in environmental components, which are considered in environmental impact assessment, significantly affects the spatial distributions of overall environmental quality values as well as the determination of an environmentally optimized road route. This work suggests a guideline to use systematic accuracy, coherence, and tree analyses in selecting an optimal DT model from multiple candidate model variants, and demonstrates the applicability of the OPP-improved DT integrated with GIS in rule induction for mapping bacterial diversity. These findings also provide implication on the significance of soil microbial ecology in environmental impact assessment and eco-friendly construction planning.

  1. Decoding the Formation of New Semantics: MVPA Investigation of Rapid Neocortical Plasticity during Associative Encoding through Fast Mapping

    PubMed Central

    Atir-Sharon, Tali; Gilboa, Asaf; Hazan, Hananel; Koilis, Ester; Manevitz, Larry M.

    2015-01-01

    Neocortical structures typically only support slow acquisition of declarative memory; however, learning through fast mapping may facilitate rapid learning-induced cortical plasticity and hippocampal-independent integration of novel associations into existing semantic networks. During fast mapping the meaning of new words and concepts is inferred, and durable novel associations are incidentally formed, a process thought to support early childhood's exuberant learning. The anterior temporal lobe, a cortical semantic memory hub, may critically support such learning. We investigated encoding of semantic associations through fast mapping using fMRI and multivoxel pattern analysis. Subsequent memory performance following fast mapping was more efficiently predicted using anterior temporal lobe than hippocampal voxels, while standard explicit encoding was best predicted by hippocampal activity. Searchlight algorithms revealed additional activity patterns that predicted successful fast mapping semantic learning located in lateral occipitotemporal and parietotemporal neocortex and ventrolateral prefrontal cortex. By contrast, successful explicit encoding could be classified by activity in medial and dorsolateral prefrontal and parahippocampal cortices. We propose that fast mapping promotes incidental rapid integration of new associations into existing neocortical semantic networks by activating related, nonoverlapping conceptual knowledge. In healthy adults, this is better captured by unique anterior and lateral temporal lobe activity patterns, while hippocampal involvement is less predictive of this kind of learning. PMID:26257961

  2. Decoding the Formation of New Semantics: MVPA Investigation of Rapid Neocortical Plasticity during Associative Encoding through Fast Mapping.

    PubMed

    Atir-Sharon, Tali; Gilboa, Asaf; Hazan, Hananel; Koilis, Ester; Manevitz, Larry M

    2015-01-01

    Neocortical structures typically only support slow acquisition of declarative memory; however, learning through fast mapping may facilitate rapid learning-induced cortical plasticity and hippocampal-independent integration of novel associations into existing semantic networks. During fast mapping the meaning of new words and concepts is inferred, and durable novel associations are incidentally formed, a process thought to support early childhood's exuberant learning. The anterior temporal lobe, a cortical semantic memory hub, may critically support such learning. We investigated encoding of semantic associations through fast mapping using fMRI and multivoxel pattern analysis. Subsequent memory performance following fast mapping was more efficiently predicted using anterior temporal lobe than hippocampal voxels, while standard explicit encoding was best predicted by hippocampal activity. Searchlight algorithms revealed additional activity patterns that predicted successful fast mapping semantic learning located in lateral occipitotemporal and parietotemporal neocortex and ventrolateral prefrontal cortex. By contrast, successful explicit encoding could be classified by activity in medial and dorsolateral prefrontal and parahippocampal cortices. We propose that fast mapping promotes incidental rapid integration of new associations into existing neocortical semantic networks by activating related, nonoverlapping conceptual knowledge. In healthy adults, this is better captured by unique anterior and lateral temporal lobe activity patterns, while hippocampal involvement is less predictive of this kind of learning.

  3. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

    PubMed

    N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

    2017-01-01

    Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion

  4. Mapping, Bayesian Geostatistical Analysis and Spatial Prediction of Lymphatic Filariasis Prevalence in Africa

    PubMed Central

    Slater, Hannah; Michael, Edwin

    2013-01-01

    There is increasing interest to control or eradicate the major neglected tropical diseases. Accurate modelling of the geographic distributions of parasitic infections will be crucial to this endeavour. We used 664 community level infection prevalence data collated from the published literature in conjunction with eight environmental variables, altitude and population density, and a multivariate Bayesian generalized linear spatial model that allows explicit accounting for spatial autocorrelation and incorporation of uncertainty in input data and model parameters, to construct the first spatially-explicit map describing LF prevalence distribution in Africa. We also ran the best-fit model against predictions made by the HADCM3 and CCCMA climate models for 2050 to predict the likely distributions of LF under future climate and population changes. We show that LF prevalence is strongly influenced by spatial autocorrelation between locations but is only weakly associated with environmental covariates. Infection prevalence, however, is found to be related to variations in population density. All associations with key environmental/demographic variables appear to be complex and non-linear. LF prevalence is predicted to be highly heterogenous across Africa, with high prevalences (>20%) estimated to occur primarily along coastal West and East Africa, and lowest prevalences predicted for the central part of the continent. Error maps, however, indicate a need for further surveys to overcome problems with data scarcity in the latter and other regions. Analysis of future changes in prevalence indicates that population growth rather than climate change per se will represent the dominant factor in the predicted increase/decrease and spread of LF on the continent. We indicate that these results could play an important role in aiding the development of strategies that are best able to achieve the goals of parasite elimination locally and globally in a manner that may also account

  5. Mapping, bayesian geostatistical analysis and spatial prediction of lymphatic filariasis prevalence in Africa.

    PubMed

    Slater, Hannah; Michael, Edwin

    2013-01-01

    There is increasing interest to control or eradicate the major neglected tropical diseases. Accurate modelling of the geographic distributions of parasitic infections will be crucial to this endeavour. We used 664 community level infection prevalence data collated from the published literature in conjunction with eight environmental variables, altitude and population density, and a multivariate Bayesian generalized linear spatial model that allows explicit accounting for spatial autocorrelation and incorporation of uncertainty in input data and model parameters, to construct the first spatially-explicit map describing LF prevalence distribution in Africa. We also ran the best-fit model against predictions made by the HADCM3 and CCCMA climate models for 2050 to predict the likely distributions of LF under future climate and population changes. We show that LF prevalence is strongly influenced by spatial autocorrelation between locations but is only weakly associated with environmental covariates. Infection prevalence, however, is found to be related to variations in population density. All associations with key environmental/demographic variables appear to be complex and non-linear. LF prevalence is predicted to be highly heterogenous across Africa, with high prevalences (>20%) estimated to occur primarily along coastal West and East Africa, and lowest prevalences predicted for the central part of the continent. Error maps, however, indicate a need for further surveys to overcome problems with data scarcity in the latter and other regions. Analysis of future changes in prevalence indicates that population growth rather than climate change per se will represent the dominant factor in the predicted increase/decrease and spread of LF on the continent. We indicate that these results could play an important role in aiding the development of strategies that are best able to achieve the goals of parasite elimination locally and globally in a manner that may also account

  6. A MAP3k1 SNP Predicts Survival of Gastric Cancer in a Chinese Population

    PubMed Central

    Gu, Dongying; Shen, Lili; Wang, Meilin; Xu, Zhi; Gong, Weida; Tang, Cuiju; Gao, Jinglong; Chen, Jinfei; Zhang, Zhengdong

    2014-01-01

    Objectives Genome-wide association studies (GWAS) have demonstrated that the single nucleotide polymorphism (SNP) MAP3K1 rs889312 is a genetic susceptibility marker significantly associated with a risk of hormone-related tumors such as breast cancer. Considering steroid hormone-mediated signaling pathways have an important role in the progression of gastric cancer, we hypothesized that MAP3K1 rs889312 may be associated with survival outcomes in gastric cancer. The purpose of this study was to test this hypothesis. Methods We genotyped MAP3K1 rs889312 using TaqMan in 884 gastric cancer patients who received subtotal or total gastrectomy. Kaplan-Meier survival analysis and Cox proportional hazard regression were used to analyze the association between MAP3K1 rs889312 genotypes and survival outcomes of gastric cancer. Results Our findings reveal that the rs889312 heterozygous AC genotype was significantly associated with an increased rate of mortality among patients with diffuse-type gastric cancer (log-rank P = 0.028 for AC versus AA/CC, hazard ratio [HR] = 1.32, 95% confidence interval [CI] = 1.03–1.69), compared to those carrying the homozygous variant genotypes (AA/CC). Additionally, univariate and multivariate Cox regression analysis demonstrate that rs889312 polymorphism was an independent risk factor for poor survival in these patients. Conclusions In conclusion, we demonstrate that MAP3K1 rs889312 is closely correlated with outcome among diffuse-type gastric cancer. This raises the possibility for rs889312 polymorphisms to be used as an independent indicator for predicting the prognosis of diffuse-type gastric cancer within the Chinese population. PMID:24759887

  7. Geospatial Predictive Modelling for Climate Mapping of Selected Severe Weather Phenomena Over Poland: A Methodological Approach

    NASA Astrophysics Data System (ADS)

    Walawender, Ewelina; Walawender, Jakub P.; Ustrnul, Zbigniew

    2017-02-01

    The main purpose of the study is to introduce methods for mapping the spatial distribution of the occurrence of selected atmospheric phenomena (thunderstorms, fog, glaze and rime) over Poland from 1966 to 2010 (45 years). Limited in situ observations as well the discontinuous and location-dependent nature of these phenomena make traditional interpolation inappropriate. Spatially continuous maps were created with the use of geospatial predictive modelling techniques. For each given phenomenon, an algorithm identifying its favourable meteorological and environmental conditions was created on the basis of observations recorded at 61 weather stations in Poland. Annual frequency maps presenting the probability of a day with a thunderstorm, fog, glaze or rime were created with the use of a modelled, gridded dataset by implementing predefined algorithms. Relevant explanatory variables were derived from NCEP/NCAR reanalysis and downscaled with the use of a Regional Climate Model. The resulting maps of favourable meteorological conditions were found to be valuable and representative on the country scale but at different correlation ( r) strength against in situ data (from r = 0.84 for thunderstorms to r = 0.15 for fog). A weak correlation between gridded estimates of fog occurrence and observations data indicated the very local nature of this phenomenon. For this reason, additional environmental predictors of fog occurrence were also examined. Topographic parameters derived from the SRTM elevation model and reclassified CORINE Land Cover data were used as the external, explanatory variables for the multiple linear regression kriging used to obtain the final map. The regression model explained 89 % of annual frequency of fog variability in the study area. Regression residuals were interpolated via simple kriging.

  8. Mapping Helminth Co-Infection and Co-Intensity: Geostatistical Prediction in Ghana

    PubMed Central

    Soares Magalhães, Ricardo J.; Biritwum, Nana-Kwadwo; Gyapong, John O.; Brooker, Simon; Zhang, Yaobi; Blair, Lynsey; Fenwick, Alan; Clements, Archie C. A.

    2011-01-01

    Background Morbidity due to Schistosoma haematobium and hookworm infections is marked in those with intense co-infections by these parasites. The development of a spatial predictive decision-support tool is crucial for targeting the delivery of integrated mass drug administration (MDA) to those most in need. We investigated the co-distribution of S. haematobium and hookworm infection, plus the spatial overlap of infection intensity of both parasites, in Ghana. The aim was to produce maps to assist the planning and evaluation of national parasitic disease control programs. Methodology/Principal Findings A national cross-sectional school-based parasitological survey was conducted in Ghana in 2008, using standardized sampling and parasitological methods. Bayesian geostatistical models were built, including a multinomial regression model for S. haematobium and hookworm mono- and co-infections and zero-inflated Poisson regression models for S. haematobium and hookworm infection intensity as measured by egg counts in urine and stool respectively. The resulting infection intensity maps were overlaid to determine the extent of geographical overlap of S. haematobium and hookworm infection intensity. In Ghana, prevalence of S. haematobium mono-infection was 14.4%, hookworm mono-infection was 3.2%, and S. haematobium and hookworm co-infection was 0.7%. Distance to water bodies was negatively associated with S. haematobium and hookworm co-infections, hookworm mono-infections and S. haematobium infection intensity. Land surface temperature was positively associated with hookworm mono-infections and S. haematobium infection intensity. While high-risk (prevalence >10–20%) of co-infection was predicted in an area around Lake Volta, co-intensity was predicted to be highest in foci within that area. Conclusions/Significance Our approach, based on the combination of co-infection and co-intensity maps allows the identification of communities at increased risk of severe morbidity and

  9. Mapping invasive species and spectral mixture relationships with neotropical woody formations in southeastern Brazil

    NASA Astrophysics Data System (ADS)

    Amaral, Cibele H.; Roberts, Dar A.; Almeida, Teodoro I. R.; Souza Filho, Carlos R.

    2015-10-01

    Biological invasion substantially contributes to the increasing extinction rates of native vegetative species. The remote detection and mapping of invasive species is critical for environmental monitoring. This study aims to assess the performance of a Multiple Endmember Spectral Mixture Analysis (MESMA) applied to imaging spectroscopy data for mapping Dendrocalamus sp. (bamboo) and Pinus elliottii L. (slash pine), which are invasive plant species, in a Brazilian neotropical landscape within the tropical Brazilian savanna biome. The work also investigates the spectral mixture between these exotic species and the native woody formations, including woodland savanna, submontane and alluvial seasonal semideciduous forests (SSF). Visible to Shortwave Infrared (VSWIR) imaging spectroscopy data at one-meter spatial resolution were atmospherically corrected and subset into the different spectral ranges (VIS-NIR1: 530-919 nm; and NIR2-SWIR: 1141-2352 nm). The data were further normalized via continuum removal (CR). Multiple endmember selection methods, including Interactive Endmember Selection (IES), Endmember average root mean square error (EAR), Minimum average spectral angle (MASA) and Count-based (CoB) (collectively called EMC), were employed to create endmember libraries for the targeted vegetation classes. The performance of the MESMA was assessed at the pixel and crown scales. Statistically significant differences (α = 0.05) were observed between overall accuracies that were obtained at various spectral ranges. The infrared region (IR) was critical for detecting the vegetation classes using spectral data. The invasive species endmembers exhibited spectral patterns in the IR that were not observed in the native formations. Bamboo was characterized as having a high green vegetation (GV) fraction, lower non-photosynthetic vegetation (NPV) and a low shade fraction, while pine exhibited higher NPV and shade fractions. The invasive species showed a statistically

  10. MAPPING CHILDREN’S POLITICS: SPATIAL STORIES, DIALOGIC RELATIONS AND POLITICAL FORMATION

    PubMed Central

    Elwood, Sarah; Mitchell, Katharyne

    2015-01-01

    This article confronts a persistent challenge in research on children’s geographies and politics: the difficulty of recognizing forms of political agency and practice that by definition fall outside of existing political theory. Children are effectively “always already” positioned outside most of the structures and ideals of modernist democratic theory, such as the public sphere and abstracted notions of communicative action or “rational” speech. Recent emphases on embodied tactics of everyday life have offered important ways to recognize children’s political agency and practice. However, we argue here that a focus on spatial practices and critical knowledge alone cannot capture the full range of children’s politics, and show how representational and dialogic practices remain a critical element of their politics in everyday life. Drawing on de Certeau’s notion of spatial stories, and Bakhtin’s concept of dialogic relations, we argue that children’s representations and dialogues comprise a significant space of their political agency and formation, in which they can make and negotiate social meanings, subjectivities, and relationships. We develop these arguments with evidence from an after-school activity programme we conducted with 10–13 year olds in Seattle, Washington, in which participants explored, mapped, wrote and spoke about the spaces and experiences of their everyday lives. Within these practices, children negotiate autonomy and self-determination, and forward ideas, representations, and expressions of agreement or disagreement that are critical to their formation as political actors. PMID:25642017

  11. A neural field model of the somatosensory cortex: formation, maintenance and reorganization of ordered topographic maps.

    PubMed

    Detorakis, Georgios Is; Rougier, Nicolas P

    2012-01-01

    We investigate the formation and maintenance of ordered topographic maps in the primary somatosensory cortex as well as the reorganization of representations after sensory deprivation or cortical lesion. We consider both the critical period (postnatal) where representations are shaped and the post-critical period where representations are maintained and possibly reorganized. We hypothesize that feed-forward thalamocortical connections are an adequate site of plasticity while cortico-cortical connections are believed to drive a competitive mechanism that is critical for learning. We model a small skin patch located on the distal phalangeal surface of a digit as a set of 256 Merkel ending complexes (MEC) that feed a computational model of the primary somatosensory cortex (area 3b). This model is a two-dimensional neural field where spatially localized solutions (a.k.a. bumps) drive cortical plasticity through a Hebbian-like learning rule. Simulations explain the initial formation of ordered representations following repetitive and random stimulations of the skin patch. Skin lesions as well as cortical lesions are also studied and results confirm the possibility to reorganize representations using the same learning rule and depending on the type of the lesion. For severe lesions, the model suggests that cortico-cortical connections may play an important role in complete recovery.

  12. Depth-resolved nanoscale nuclear architecture mapping for early prediction of cancer progression

    NASA Astrophysics Data System (ADS)

    Uttam, Shikhar; Pham, Hoa V.; LaFace, Justin; Hartman, Douglas J.; Liu, Yang

    2016-03-01

    Effective management of patients who are at risk of developing invasive cancer is a primary challenge in early cancer detection. Techniques that can help establish clear-cut protocols for successful triaging of at-risk patients have the potential of providing critical help in improving patient care while simultaneously reducing patient cost. We have developed such a technique for early prediction of cancer progression that uses unstained tissue sections to provide depth-resolved nanoscale nuclear architecture mapping (nanoNAM) of heterogeneity in optical density alterations manifested in precancerous lesions during cancer progression. We present nanoNAM and its application to predicting cancer progression in a well-established mouse model of spontaneous carcinogenesis: ApcMin/+ mice.

  13. Remotely mapping river water quality using multivariate regression with prediction validation.

    SciTech Connect

    Stork, Christopher Lyle; Autry, Bradley C.

    2005-07-01

    Remote spectral sensing offers an attractive means of mapping river water quality over wide spatial regions. While previous research has focused on development of spectral indices and models to predict river water quality based on remote images, little attention has been paid to subsequent validation of these predictions. To address this oversight, we describe a retrospective analysis of remote, multispectral Compact Airborne Spectrographic Imager (CASI) images of the Ohio River and its Licking River and Little Miami River tributaries. In conjunction with the CASI acquisitions, ground truth measurements of chlorophyll-a concentration and turbidity were made for a small set of locations in the Ohio River. Partial least squares regression models relating the remote river images to ground truth measurements of chlorophyll-a concentration and turbidity for the Ohio River were developed. Employing these multivariate models, chlorophyll-a concentrations and turbidity levels were predicted in river pixels lacking ground truth measurements, generating detailed estimated water quality maps. An important but often neglected step in the regression process is to validate prediction results using a spectral residual statistic. For both the chlorophyll-a and turbidity regression models, a spectral residual value was calculated for each river pixel and compared to the associated statistical confidence limit for the model. These spectral residual statistic results revealed that while the chlorophyll-a and turbidity models could validly be applied to a vast majority of Ohio River and Licking River pixels, application of these models to Little Miami River pixels was inappropriate due to an unmodeled source of spectral variation.

  14. Remotely mapping river water quality using multivariate regression with prediction validation

    NASA Astrophysics Data System (ADS)

    Stork, Chris L.; Autrey, Bradley C.

    2005-09-01

    Remote spectral sensing offers an attractive means of mapping river water quality over wide spatial regions. While previous research has focused on development of spectral indices and models to predict river water quality based on remote images, little attention has been paid to subsequent validation of these predictions. To address this oversight, we describe a retrospective analysis of remote, multispectral Compact Airborne Spectrographic Imager (CASI) images of the Ohio River and its Licking River and Little Miami River tributaries. In conjunction with the CASI acquisitions, ground truth measurements of chlorophyll-a concentration and turbidity were made for a small set of locations in the Ohio River. Partial least squares regression models relating the remote river images to ground truth measurements of chlorophyll-a concentration and turbidity for the Ohio River were developed. Employing these multivariate models, chlorophyll-a concentrations and turbidity levels were predicted in river pixels lacking ground truth measurements, generating detailed estimated water quality maps. An important but often neglected step in the regression process is to validate prediction results using a spectral residual statistic. For both the chlorophyll-a and turbidity regression models, a spectral residual value was calculated for each river pixel and compared to the associated statistical confidence limit for the model. These spectral residual statistic results revealed that while the chlorophyll-a and turbidity models could validly be applied to a vast majority of Ohio River and Licking River pixels, application of these models to Little Miami River pixels was inappropriate due to an unmodeled source of spectral variation.

  15. Satellite Mapping of Agricultural Water Requirements in California with the Terrestrial Observation and Prediction System

    NASA Astrophysics Data System (ADS)

    Melton, F. S.; Lund, C.; Johnson, L.; Michaelis, A.; Pierce, L.; Guzman, A.; Hiatt, S.; Purdy, A. J.; Rosevelt, C.; Brandt, W. T.; Votava, P.; Nemani, R. R.

    2012-12-01

    Satellite mapping of evapotranspiration (ET) from irrigated agricultural lands can provide water managers and agricultural producers with information that can be used to optimize agricultural water use, especially in regions with limited water supplies. In particular, the timely delivery of information on agricultural crop water requirements has the potential to make irrigation scheduling more practical, convenient, and accurate. We present findings from the development and deployment of a prototype system for irrigation scheduling and management support in California. The system utilizes the NASA Terrestrial Observation and Prediction System to integrate satellite observations and meteorological observations to map crop canopy development, basal crop coefficients (Kcb), and evapotranspiration (ETcb) values for multiple crop types in the Central Valley of California at the scale of individual fields. Information is distributed to agricultural producers and water managers via a web-based irrigation management decision support system and web services. We present the prototype system, including comparisons of estimates of ETcb from the prototype system against estimates of ET from other methods, including surface renewal stations and observations from wireless sensor networks deployed in operational agricultural fields across California. We discuss the potential for integration of ET from energy balance models to support near real-time mapping of consumptive water use and crop water stress.

  16. Predictive Modeling and Mapping of Fish Distributions in Small Streams of the Canadian Rocky Mountain Foothills

    NASA Astrophysics Data System (ADS)

    McCleary, R. J.; Hassan, M. A.

    2006-12-01

    An automated procedure was developed to model spatial fish distributions within small streams in the Foothills of Alberta. Native fish populations and their habitats are susceptible to impacts arising from both industrial forestry and rapid development of petroleum resources in the region. Knowledge of fish distributions and the effects of industrial activities on their habitats is required to help conserve native fish populations. Resource selection function (RSF) models were used to explain presence/absence of fish in small streams. Target species were bull trout, rainbow trout and non-native brook trout. Using GIS, the drainage network was divided into reaches with uniform slope and drainage area and then polygons for each reach were created. Predictor variables described stream size, stream energy, climate and land-use. We identified a set of candidate models and selected the best model using a standard Akaike Information Criteria approach. The best models were validated with two external data sets. Drainage area and basin slope parameters were included in all best models. This finding emphasizes the importance of controlling for the energy dimension at the basin scale in investigations into the effects of land-use on aquatic resources in this transitional landscape between the mountains and plains. The best model for bull trout indicated a relation between the presence of artificial migration barriers in downstream areas and the extirpation of the species from headwater reaches. We produced reach-scale maps by species and summarized this information within all small catchments across the 12,000 km2 study area. These maps had included three categories based on predicted probability of capture for individual reaches. The high probability category had a 78 percent accuracy for correctly predicting both fish present and fish not-present reaches. Basin scale maps highlight specific watersheds likely to support both native bull trout and invasive brook trout, while

  17. The Salient Map Analysis for Research and Teaching (SMART) method: Powerful potential as a formative assessment in the biomedical sciences

    NASA Astrophysics Data System (ADS)

    Cathcart, Laura Anne

    This dissertation consists of two studies: 1) development and characterization of the Salient Map Analysis for Research and Teaching (SMART) method as a formative assessment tool and 2) a case study exploring how a paramedic instructor's beliefs about learners affect her utilization of the SMART method and vice versa. The first study explored: How can a novel concept map analysis method be designed as an effective formative assessment tool? The SMART method improves upon existing concept map analysis methods because it does not require hierarchically structured concept maps and it preserves the rich content of the maps instead of reducing each map down to a numerical score. The SMART method is performed by comparing a set of students' maps to each other and to an instructor's map. The resulting composite map depicts, in percentages and highlighted colors, the similarities and differences between all of the maps. Some advantages of the SMART method as a formative assessment tool include its ability to highlight changes across time, problematic or alternative conceptions, and patterns of student responses at a glance. Study two explored: How do a paramedic instructor's beliefs about students and learning affect---and become affected by---her use of the SMART method as a formative assessment tool? This case study of Angel, an expert paramedic instructor, begins to address a gap in the emergency medical services (EMS) education literature, which contains almost no research on teachers or pedagogy. Angel and I worked together as participant co-researchers (Heron & Reason, 1997) exploring the affordances of the SMART method. This study, based on those interactions with Angel, involved using open coding to identify themes (Strauss & Corbin, 1998) from Angel's views of students and use of the SMART method. Angel views learning as a sense-making process. She has a multi-faceted view of her students as novices and invests substantial time trying to understand their concept

  18. MAPS

    Atmospheric Science Data Center

    2014-07-03

    ... Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle flights in 1981, ... Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

  19. Prediction of 3D chip formation in the facing cutting with lathe machine using FEM

    NASA Astrophysics Data System (ADS)

    Prasetyo, Yudhi; Tauviqirrahman, Mohamad; Rusnaldy

    2016-04-01

    This paper presents the prediction of the chip formation at the machining process using a lathe machine in a more specific way focusing on facing cutting (face turning). The main purpose is to propose a new approach to predict the chip formation with the variation of the cutting directions i.e., the backward and forward direction. In addition, the interaction between stress analysis and chip formation on cutting process was also investigated. The simulations were conducted using three dimensional (3D) finite element method based on ABAQUS software with aluminum and high speed steel (HSS) as the workpiece and the tool materials, respectively. The simulation result showed that the chip resulted using a backward direction depicts a better formation than that using a conventional (forward) direction.

  20. Performance prediction of four-contact vertical Hall-devices using a conformal mapping technique

    NASA Astrophysics Data System (ADS)

    Yang, Huang; Yue, Xu; Yufeng, Guo

    2015-12-01

    Instead of the conventional design with five contacts in the sensor active area, innovative vertical Hall devices (VHDs) with four contacts and six contacts are asymmetrical in structural design but symmetrical in the current flow that can be well fit for the spinning current technique for offset elimination. In this article, a conformal mapping calculation method is used to predict the performance of asymmetrical VHD embedded in a deep n-well with four contacts. Furthermore, to make the calculation more accurate, the junction field effect is also involved into the conformal mapping method. The error between calculated and simulated results is less than 5% for the current-related sensitivity, and approximately 13% for the voltage-related sensitivity. This proves that such calculations can be used to predict the optimal structure of the vertical Hall-devices. Project supported by the Natural Science Foundation of Jiangsu Province, China (Nos. BK20131379, BK20141431) and the Graduate Research and Innovation Projects of Jiangsu Province (No. SJLX_0373).

  1. Prediction-for-CompAction: navigation in social environments using generalized cognitive maps.

    PubMed

    Villacorta-Atienza, Jose A; Calvo, Carlos; Makarov, Valeri A

    2015-06-01

    The ultimate navigation efficiency of mobile robots in human environments will depend on how we will appraise them: merely as impersonal machines or as human-like agents. In the latter case, an agent may take advantage of the cooperative collision avoidance, given that it possesses recursive cognition, i.e., the agent's decisions depend on the decisions made by humans that in turn depend on the agent's decisions. To deal with this high-level cognitive skill, we propose a neural network architecture implementing Prediction-for-CompAction paradigm. The network predicts possible human-agent collisions and compacts the time dimension by projecting a given dynamic situation into a static map. Thereby emerging compact cognitive map can be readily used as a "dynamic GPS" for planning actions or mental evaluation of the convenience of cooperation in a given context. We provide numerical evidence that cooperation yields additional room for more efficient navigation in cluttered pedestrian flows, and the agent can choose path to the target significantly shorter than a robot treated by humans as a functional machine. Moreover, the navigation safety, i.e., the chances to avoid accidental collisions, increases under cooperation. Remarkably, these benefits yield no additional load to the mean society effort. Thus, the proposed strategy is socially compliant, and the humanoid agent can behave as "one of us."

  2. Feature maps driven no-reference image quality prediction of authentically distorted images

    NASA Astrophysics Data System (ADS)

    Ghadiyaram, Deepti; Bovik, Alan C.

    2015-03-01

    Current blind image quality prediction models rely on benchmark databases comprised of singly and synthetically distorted images, thereby learning image features that are only adequate to predict human perceived visual quality on such inauthentic distortions. However, real world images often contain complex mixtures of multiple distortions. Rather than a) discounting the effect of these mixtures of distortions on an image's perceptual quality and considering only the dominant distortion or b) using features that are only proven to be efficient for singly distorted images, we deeply study the natural scene statistics of authentically distorted images, in different color spaces and transform domains. We propose a feature-maps-driven statistical approach which avoids any latent assumptions about the type of distortion(s) contained in an image, and focuses instead on modeling the remarkable consistencies in the scene statistics of real world images in the absence of distortions. We design a deep belief network that takes model-based statistical image features derived from a very large database of authentically distorted images as input and discovers good feature representations by generalizing over different distortion types, mixtures, and severities, which are later used to learn a regressor for quality prediction. We demonstrate the remarkable competence of our features for improving automatic perceptual quality prediction on a benchmark database and on the newly designed LIVE Authentic Image Quality Challenge Database and show that our approach of combining robust statistical features and the deep belief network dramatically outperforms the state-of-the-art.

  3. Predictive coding as a model of the V1 saliency map hypothesis.

    PubMed

    Spratling, M W

    2012-02-01

    The predictive coding/biased competition (PC/BC) model is a specific implementation of the predictive coding theory that has previously been shown to provide a detailed account of the response properties of orientation tuned cells in primary visual cortex (V1). Here it is shown that the same model can successfully simulate psychophysical data relating to the saliency of unique items in search arrays, of contours embedded in random texture, and of borders between textured regions. This model thus provides a possible implementation of the hypothesis that V1 generates a bottom-up saliency map. However, PC/BC is very different from previous models of visual salience, in that it proposes that saliency results from the failure of an internal model of simple elementary image components to accurately predict the visual input. Saliency can therefore be interpreted as a mechanism by which prediction errors attract attention in an attempt to improve the accuracy of the brain's internal representation of the world. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

    PubMed Central

    Saha, Sudipto; Raghava, G. P. S.

    2006-01-01

    In this study a systematic attempt has been made to integrate various approaches in order to predict allergenic proteins with high accuracy. The dataset used for testing and training consists of 578 allergens and 700 non-allergens obtained from A. K. Bjorklund, D. Soeria-Atmadja, A. Zorzet, U. Hammerling and M. G. Gustafsson (2005) Bioinformatics, 21, 39–50. First, we developed methods based on support vector machine using amino acid and dipeptide composition and achieved an accuracy of 85.02 and 84.00%, respectively. Second, a motif-based method has been developed using MEME/MAST software that achieved sensitivity of 93.94 with 33.34% specificity. Third, a database of known IgE epitopes was searched and this predicted allergenic proteins with 17.47% sensitivity at specificity of 98.14%. Fourth, we predicted allergenic proteins by performing BLAST search against allergen representative peptides. Finally hybrid approaches have been developed, which combine two or more than two approaches. The performance of all these algorithms has been evaluated on an independent dataset of 323 allergens and on 101 725 non-allergens obtained from Swiss-Prot. A web server AlgPred has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins (). AlgPred is available at . PMID:16844994

  5. Completing the Mapping of the W3 Giant Molecular Cloud; Testing Models and the Importance of Triggered Star Formation

    NASA Astrophysics Data System (ADS)

    Moore, Toby; Allsopp, James; Jones, Huw

    2006-05-01

    It is proposed to complete the R. Gehrz's mapping of W3 at both IRAC and MIPS 24um wavelengths. W3 is an outer galaxy Giant Molecular Cloud comprising of two regions; a quiescent, spontaneously star forming region and a region compressed by the W4 OB association containing the majority of star formation and all of the high mass star formation. Currently only the high-density region, Lada( put date) is mapped, but for a scientifically-valid comparision between the triggered and spontaneous modes we require the remainder of the cloud to be mapped. Triggered star formation is vitally important as it provides a mechanism for understanding the massive disparity between the low star formation efficiencies of galaxies such as our own andmore violent events such as galaxy mergers. Currently we have mapped the majority of the cloud at 850 um using SCUBA and the whole cloud using the CO(J=1-0) with the 12CO, 13CO and C18O isotomers. From these studies we have identified and measured the masses of 230 clumps. Without Spitzer data we have no way of determining which of these clumps have formed stars. This project forms the final crucial piece which when added to our current observations of the mass in the cloud will quantify the local star formation efficiency for each region. This is the first part of an ongoing much larger study into triggered star formation. We used Aztec (1.1mm continuum) on the JCMT in January 2006 to map two more clouds and Spitzer data on these from other observers has either been recently released or is about to be. In 2007, we will expand on the knowledge gained from this with the SCUBA2 JCMT Galactic Plane Survey (JPS) in which we are collaborators.

  6. A study of photometry and image formation for application in localization and mapping

    NASA Astrophysics Data System (ADS)

    Wong, Xue Iuan

    This dissertation studies the image formation process and physically based light reflection model. Purpose of this study is to expand the concept commonly used in computer graphic community toward develop a set of surface estimation algorithm and relative navigation sensor interested by aeronautical and astronautical application. Simplified camera model has been extensively applied toward developing image based relative pose sensing algorithm who are widely used in navigation and simultaneous localization and mapping purpose. Beside of providing data of measurement, navigation sensors are also expecting to provide uncertainty measurement who describe the accuracy of output data. Since most of the image space algorithms are commonly rely on various of image processing technique such as feature extract and tracking, who are generally difficult in providing uncertainty measurement in real time, one of the major objective of this research is to develop a computational efficient method to estimate confidential level of sensor outputs. Base on the study of camera projection model and light reflection model, this dissertation develop set of three algorithms. Digital VISNAV who provide real time six degree of freedom relative pose measurement from a set of structured light beacons and a camera. Photometric stereo in motion exploit the possibility of applying photometric stereo algorithm toward estimate surface geometry model of space object. At last, a newly developed algorithm base on both camera projection model and surface reflectance model named as PhotoNAV is providing a new method for dense image base simultaneous localization and mapping application on textureless surface. Each of these proposed algorithm are providing both sensing output along with estimated uncertainty measurement of the output. Performance of these algorithms are evaluated by both simulation and experiment. Under certain constraint when real measurements are not available, the experiment is carry

  7. Predictive analysis and mapping of indoor radon concentrations in a complex environment using kernel estimation: an application to Switzerland.

    PubMed

    Kropat, Georg; Bochud, Francois; Jaboyedoff, Michel; Laedermann, Jean-Pascal; Murith, Christophe; Palacios Gruson, Martha; Baechler, Sébastien

    2015-02-01

    The aim of this study was to develop models based on kernel regression and probability estimation in order to predict and map IRC in Switzerland by taking into account all of the following: architectural factors, spatial relationships between the measurements, as well as geological information. We looked at about 240,000 IRC measurements carried out in about 150,000 houses. As predictor variables we included: building type, foundation type, year of construction, detector type, geographical coordinates, altitude, temperature and lithology into the kernel estimation models. We developed predictive maps as well as a map of the local probability to exceed 300 Bq/m(3). Additionally, we developed a map of a confidence index in order to estimate the reliability of the probability map. Our models were able to explain 28% of the variations of IRC data. All variables added information to the model. The model estimation revealed a bandwidth for each variable, making it possible to characterize the influence of each variable on the IRC estimation. Furthermore, we assessed the mapping characteristics of kernel estimation overall as well as by municipality. Overall, our model reproduces spatial IRC patterns which were already obtained earlier. On the municipal level, we could show that our model accounts well for IRC trends within municipal boundaries. Finally, we found that different building characteristics result in different IRC maps. Maps corresponding to detached houses with concrete foundations indicate systematically smaller IRC than maps corresponding to farms with earth foundation. IRC mapping based on kernel estimation is a powerful tool to predict and analyze IRC on a large-scale as well as on a local level. This approach enables to develop tailor-made maps for different architectural elements and measurement conditions and to account at the same time for geological information and spatial relations between IRC measurements. Copyright © 2014 Elsevier B.V. All rights

  8. Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism.

    PubMed

    Hughes, Tyler B; Swamidass, S Joshua

    2017-02-20

    Many adverse drug reactions are thought to be caused by electrophilically reactive drug metabolites that conjugate to nucleophilic sites within DNA and proteins, causing cancer or toxic immune responses. Quinone species, including quinone-imines, quinone-methides, and imine-methides, are electrophilic Michael acceptors that are often highly reactive and comprise over 40% of all known reactive metabolites. Quinone metabolites are created by cytochromes P450 and peroxidases. For example, cytochromes P450 oxidize acetaminophen to N-acetyl-p-benzoquinone imine, which is electrophilically reactive and covalently binds to nucleophilic sites within proteins. This reactive quinone metabolite elicits a toxic immune response when acetaminophen exceeds a safe dose. Using a deep learning approach, this study reports the first published method for predicting quinone formation: the formation of a quinone species by metabolic oxidation. We model both one- and two-step quinone formation, enabling accurate quinone formation predictions in nonobvious cases. We predict atom pairs that form quinones with an AUC accuracy of 97.6%, and we identify molecules that form quinones with 88.2% AUC. By modeling the formation of quinones, one of the most common types of reactive metabolites, our method provides a rapid screening tool for a key drug toxicity risk. The XenoSite quinone formation model is available at http://swami.wustl.edu/xenosite/p/quinone .

  9. A Stochastic Simulation Framework for the Prediction of Strategic Noise Mapping and Occupational Noise Exposure Using the Random Walk Approach

    PubMed Central

    Haron, Zaiton; Bakar, Suhaimi Abu; Dimon, Mohamad Ngasri

    2015-01-01

    Strategic noise mapping provides important information for noise impact assessment and noise abatement. However, producing reliable strategic noise mapping in a dynamic, complex working environment is difficult. This study proposes the implementation of the random walk approach as a new stochastic technique to simulate noise mapping and to predict the noise exposure level in a workplace. A stochastic simulation framework and software, namely RW-eNMS, were developed to facilitate the random walk approach in noise mapping prediction. This framework considers the randomness and complexity of machinery operation and noise emission levels. Also, it assesses the impact of noise on the workers and the surrounding environment. For data validation, three case studies were conducted to check the accuracy of the prediction data and to determine the efficiency and effectiveness of this approach. The results showed high accuracy of prediction results together with a majority of absolute differences of less than 2 dBA; also, the predicted noise doses were mostly in the range of measurement. Therefore, the random walk approach was effective in dealing with environmental noises. It could predict strategic noise mapping to facilitate noise monitoring and noise control in the workplaces. PMID:25875019

  10. A stochastic simulation framework for the prediction of strategic noise mapping and occupational noise exposure using the random walk approach.

    PubMed

    Han, Lim Ming; Haron, Zaiton; Yahya, Khairulzan; Bakar, Suhaimi Abu; Dimon, Mohamad Ngasri

    2015-01-01

    Strategic noise mapping provides important information for noise impact assessment and noise abatement. However, producing reliable strategic noise mapping in a dynamic, complex working environment is difficult. This study proposes the implementation of the random walk approach as a new stochastic technique to simulate noise mapping and to predict the noise exposure level in a workplace. A stochastic simulation framework and software, namely RW-eNMS, were developed to facilitate the random walk approach in noise mapping prediction. This framework considers the randomness and complexity of machinery operation and noise emission levels. Also, it assesses the impact of noise on the workers and the surrounding environment. For data validation, three case studies were conducted to check the accuracy of the prediction data and to determine the efficiency and effectiveness of this approach. The results showed high accuracy of prediction results together with a majority of absolute differences of less than 2 dBA; also, the predicted noise doses were mostly in the range of measurement. Therefore, the random walk approach was effective in dealing with environmental noises. It could predict strategic noise mapping to facilitate noise monitoring and noise control in the workplaces.

  11. A linkage map of maize x teosinte zea luxurians and identification of qtls controlling root aerenchyma formation

    USDA-ARS?s Scientific Manuscript database

    One-hundred and ninety five F2 individuals, derived from a cross between maize inbred line B73 x Zea luxurians, were subjected to a 107 SSR marker based QTL analysis for aerenchyma cell formation that covered 1,331 cM across all ten maize and Zea luxurians chromosomes. Composite interval mapping a...

  12. Mapping of Sand Types and Dune Morphologies in the Aeolis Dorsa Region, Western Medusae Fossae Formation, Mars

    NASA Astrophysics Data System (ADS)

    Boyd, A. S.; Burr, D. M.

    2016-06-01

    Preliminary mapping of low- and high-albedo sand deposits in the Aeolis Dorsa region, Medusae Fossae Formation (MFF), suggests sand transport from the north, consistent with sand source(s) in Elysium Mons, the Cerberus plains, or the MFF itself.

  13. Mapping Soil Properties of Africa at 250 m Resolution: Random Forests Significantly Improve Current Predictions

    PubMed Central

    Hengl, Tomislav; Heuvelink, Gerard B. M.; Kempen, Bas; Leenaars, Johan G. B.; Walsh, Markus G.; Shepherd, Keith D.; Sila, Andrew; MacMillan, Robert A.; Mendes de Jesus, Jorge; Tamene, Lulseged; Tondoh, Jérôme E.

    2015-01-01

    80% of arable land in Africa has low soil fertility and suffers from physical soil problems. Additionally, significant amounts of nutrients are lost every year due to unsustainable soil management practices. This is partially the result of insufficient use of soil management knowledge. To help bridge the soil information gap in Africa, the Africa Soil Information Service (AfSIS) project was established in 2008. Over the period 2008–2014, the AfSIS project compiled two point data sets: the Africa Soil Profiles (legacy) database and the AfSIS Sentinel Site database. These data sets contain over 28 thousand sampling locations and represent the most comprehensive soil sample data sets of the African continent to date. Utilizing these point data sets in combination with a large number of covariates, we have generated a series of spatial predictions of soil properties relevant to the agricultural management—organic carbon, pH, sand, silt and clay fractions, bulk density, cation-exchange capacity, total nitrogen, exchangeable acidity, Al content and exchangeable bases (Ca, K, Mg, Na). We specifically investigate differences between two predictive approaches: random forests and linear regression. Results of 5-fold cross-validation demonstrate that the random forests algorithm consistently outperforms the linear regression algorithm, with average decreases of 15–75% in Root Mean Squared Error (RMSE) across soil properties and depths. Fitting and running random forests models takes an order of magnitude more time and the modelling success is sensitive to artifacts in the input data, but as long as quality-controlled point data are provided, an increase in soil mapping accuracy can be expected. Results also indicate that globally predicted soil classes (USDA Soil Taxonomy, especially Alfisols and Mollisols) help improve continental scale soil property mapping, and are among the most important predictors. This indicates a promising potential for transferring pedological

  14. Mapping Soil Properties of Africa at 250 m Resolution: Random Forests Significantly Improve Current Predictions.

    PubMed

    Hengl, Tomislav; Heuvelink, Gerard B M; Kempen, Bas; Leenaars, Johan G B; Walsh, Markus G; Shepherd, Keith D; Sila, Andrew; MacMillan, Robert A; Mendes de Jesus, Jorge; Tamene, Lulseged; Tondoh, Jérôme E

    2015-01-01

    80% of arable land in Africa has low soil fertility and suffers from physical soil problems. Additionally, significant amounts of nutrients are lost every year due to unsustainable soil management practices. This is partially the result of insufficient use of soil management knowledge. To help bridge the soil information gap in Africa, the Africa Soil Information Service (AfSIS) project was established in 2008. Over the period 2008-2014, the AfSIS project compiled two point data sets: the Africa Soil Profiles (legacy) database and the AfSIS Sentinel Site database. These data sets contain over 28 thousand sampling locations and represent the most comprehensive soil sample data sets of the African continent to date. Utilizing these point data sets in combination with a large number of covariates, we have generated a series of spatial predictions of soil properties relevant to the agricultural management--organic carbon, pH, sand, silt and clay fractions, bulk density, cation-exchange capacity, total nitrogen, exchangeable acidity, Al content and exchangeable bases (Ca, K, Mg, Na). We specifically investigate differences between two predictive approaches: random forests and linear regression. Results of 5-fold cross-validation demonstrate that the random forests algorithm consistently outperforms the linear regression algorithm, with average decreases of 15-75% in Root Mean Squared Error (RMSE) across soil properties and depths. Fitting and running random forests models takes an order of magnitude more time and the modelling success is sensitive to artifacts in the input data, but as long as quality-controlled point data are provided, an increase in soil mapping accuracy can be expected. Results also indicate that globally predicted soil classes (USDA Soil Taxonomy, especially Alfisols and Mollisols) help improve continental scale soil property mapping, and are among the most important predictors. This indicates a promising potential for transferring pedological

  15. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks.

    PubMed

    Walsh, Ian; Baù, Davide; Martin, Alberto J M; Mooney, Catherine; Vullo, Alessandro; Pollastri, Gianluca

    2009-01-30

    Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3-4 A from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C alpha trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 A threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 A predictions on the CASP7 targets using a pre-CASP7 PDB

  16. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

    PubMed Central

    Walsh, Ian; Baù, Davide; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro; Pollastri, Gianluca

    2009-01-01

    Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets

  17. Predicting ambulance time of arrival to the emergency department using global positioning system and Google maps.

    PubMed

    Fleischman, Ross J; Lundquist, Mark; Jui, Jonathan; Newgard, Craig D; Warden, Craig

    2013-01-01

    To derive and validate a model that accurately predicts ambulance arrival time that could be implemented as a Google Maps web application. This was a retrospective study of all scene transports in Multnomah County, Oregon, from January 1 through December 31, 2008. Scene and destination hospital addresses were converted to coordinates. ArcGIS Network Analyst was used to estimate transport times based on street network speed limits. We then created a linear regression model to improve the accuracy of these street network estimates using weather, patient characteristics, use of lights and sirens, daylight, and rush-hour intervals. The model was derived from a 50% sample and validated on the remainder. Significance of the covariates was determined by p < 0.05 for a t-test of the model coefficients. Accuracy was quantified by the proportion of estimates that were within 5 minutes of the actual transport times recorded by computer-aided dispatch. We then built a Google Maps-based web application to demonstrate application in real-world EMS operations. There were 48,308 included transports. Street network estimates of transport time were accurate within 5 minutes of actual transport time less than 16% of the time. Actual transport times were longer during daylight and rush-hour intervals and shorter with use of lights and sirens. Age under 18 years, gender, wet weather, and trauma system entry were not significant predictors of transport time. Our model predicted arrival time within 5 minutes 73% of the time. For lights and sirens transports, accuracy was within 5 minutes 77% of the time. Accuracy was identical in the validation dataset. Lights and sirens saved an average of 3.1 minutes for transports under 8.8 minutes, and 5.3 minutes for longer transports. An estimate of transport time based only on a street network significantly underestimated transport times. A simple model incorporating few variables can predict ambulance time of arrival to the emergency department

  18. Predicting and mapping potential Whooping Crane stopover habitat to guide site selection for wind energy projects.

    PubMed

    Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily

    2014-04-01

    Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions. © 2013 Society for Conservation Biology.

  19. Predictive risk mapping of West Nile virus (WNV) infection in Saskatchewan horses.

    PubMed

    Epp, Tasha Y; Waldner, Cheryl; Berke, Olaf

    2011-07-01

    The objective of this study was to develop a model using equine data from geographically limited surveillance locations to predict risk categories for West Nile virus (WNV) infection in horses in all geographic locations across the province of Saskatchewan. The province was divided geographically into low-, medium-, or high-risk categories for WNV, based on available serology information from 923 horses obtained through 4 studies of WNV infection in horse populations in Saskatchewan. Discriminant analysis was used to build models using the observed risk of WNV in horses and geographic division-specific environmental data as well as to predict the risk category for all areas, including those beyond the surveillance zones. High-risk areas were indicated by relatively lower rainfall, higher temperatures, and a lower percentage of area covered in trees, water, and wetland. These conditions were most often identified in the southwest corner of the province. Environmental conditions can be used to identify those areas that are at highest risk for WNV. Public health managers could use prediction maps, which are based on animal or human information and developed from annual early season meteorological information, to guide ongoing decisions about when and where to focus intervention strategies for WNV.

  20. An algorithm to parse segment packing in predicted protein contact maps.

    PubMed

    Taylor, William R

    2016-01-01

    The analysis of correlation in alignments generates a matrix of predicted contacts between positions in the structure and while these can arise for many reasons, the simplest explanation is that the pair of residues are in contact in a three-dimensional structure and are affecting each others selection pressure. To analyse these data, A dynamic programming algorithm was developed for parsing secondary structure interactions in predicted contact maps. The non-local nature of the constraints required an iterated approach (using a "frozen approximation") but with good starting definitions, a single pass was usually sufficient. The method was shown to be effective when applied to the transmembrane class of protein and error tolerant even when the signal becomes degraded. In the globular class of protein, where the extent of interactions are more limited and more complex, the algorithm still behaved well, classifying most of the important interactions correctly in both a small and a large test case. For the larger protein, this involved examples of the algorithm apportioning parts of a single large secondary structure element between two different interactions. It is expected that the method will be useful as a pre-processor to coarse-grained modelling methods to extend the range of protein tertiary structure prediction to larger proteins or to data that is currently too 'noisy' to be used by current residue-based methods.

  1. Potentiometric-surface map of water in the Judith River Formation in the Northern Great Plains area of Montana

    USGS Publications Warehouse

    Levings, Gary W.

    1982-01-01

    The potentiometric surface of the Judith River Formation is mapped at a scale of 1:1,000,000. The map is one of a series produced as part of a regional study of aquifers of Cenozoic and Mesozoic age in the northern Great Plains of Montana. The contour interval is 200 feet. Water in the Judith River Formation occurs under water-table and artesian conditions. The direction of regional ground-water movement is from west to east. Water is discharged from the Judith River Formation to the Milk River from near Havre, Montana, to Malta and to the Missouri River south of the Bearpaw and Little Rocky Mountains. The average discharge from 236 wells is about 10 gallons per minute, and the specific capacity of 186 wells averages 0.66 gallon per minute per foot of drawdown. (USGS)

  2. A program for the conversion of The National Map data from proprietary format to resource description framework (RDF)

    USGS Publications Warehouse

    Bulen, Andrew; Carter, Jonathan J.; Varanka, Dalia E.

    2011-01-01

    To expand data functionality and capabilities for users of The National Map of the U.S. Geological Survey, data sets for six watersheds and three urban areas were converted from the Best Practices vector data model formats to Semantic Web data formats. This report describes and documents the conver-sion process. The report begins with an introduction to basic Semantic Web standards and the background of The National Map. Data were converted from a proprietary format to Geog-raphy Markup Language to capture the geometric footprint of topographic data features. Configuration files were designed to eliminate redundancy and make the conversion more efficient. A SPARQL endpoint was established for data validation and queries. The report concludes by describing the results of the conversion.

  3. Unsupervised and self-mapping category formation and semantic object recognition for mobile robot vision used in an actual environment

    NASA Astrophysics Data System (ADS)

    Madokoro, H.; Tsukada, M.; Sato, K.

    2013-07-01

    This paper presents an unsupervised learning-based object category formation and recognition method for mobile robot vision. Our method has the following features: detection of feature points and description of features using a scale-invariant feature transform (SIFT), selection of target feature points using one class support vector machines (OC-SVMs), generation of visual words using self-organizing maps (SOMs), formation of labels using adaptive resonance theory 2 (ART-2), and creation and classification of categories on a category map of counter propagation networks (CPNs) for visualizing spatial relations between categories. Classification results of dynamic images using time-series images obtained using two different-size robots and according to movements respectively demonstrate that our method can visualize spatial relations of categories while maintaining time-series characteristics. Moreover, we emphasize the effectiveness of our method for category formation of appearance changes of objects.

  4. Architecture design study and technology road map for the Planet Formation Imager (PFI)

    NASA Astrophysics Data System (ADS)

    Monnier, John D.; Ireland, Michael J.; Kraus, Stefan; Baron, Fabien; Creech-Eakman, Michelle; Dong, Ruobing; Isella, Andrea; Merand, Antoine; Michael, Ernest; Minardi, Stefano; Mozurkewich, David; Petrov, Romain; Rinehart, Stephen; ten Brummelaar, Theo; Vasisht, Gautam; Wishnow, Ed; Young, John; Zhu, Zhaohuan

    2016-08-01

    The Planet Formation Imager (PFI) Project has formed a Technical Working Group (TWG) to explore possible facility architectures to meet the primary PFI science goal of imaging planet formation in situ in nearby starforming regions. The goals of being sensitive to dust emission on solar system scales and resolving the Hill-sphere around forming giant planets can best be accomplished through sub-milliarcsecond imaging in the thermal infrared. Exploiting the 8-13 micron atmospheric window, a ground-based long-baseline interferometer with approximately 20 apertures including 10km baselines will have the necessary resolution to image structure down 0.1 milliarcseconds (0.014 AU) for T Tauri disks in Taurus. Even with large telescopes, this array will not have the sensitivity to directly track fringes in the mid-infrared for our prime targets and a fringe tracking system will be necessary in the near-infrared. While a heterodyne architecture using modern mid-IR laser comb technology remains a competitive option (especially for the intriguing 24 and 40μm atmospheric windows), the prioritization of 3-5μm observations of CO/H2O vibrotational levels by the PFI-Science Working Group (SWG) pushes the TWG to require vacuum pipe beam transport with potentially cooled optics. We present here a preliminary study of simulated L- and N-band PFI observations of a realistic 4-planet disk simulation, finding 21x2.5m PFI can easily detect the accreting protoplanets in both L and N-band but can see non-accreting planets only in L band. We also find that even an ambitious PFI will lack sufficient surface brightness sensitivity to image details of the fainter emission from dust structures beyond 5 AU, unless directly illuminated or heated by local energy sources. That said, the utility of PFI at N-band is highly dependent on the stage of planet formation in the disk and we require additional systematic studies in conjunction with the PFI-SWG to better understand the science capabilities

  5. Predicting Career Indecision in College Students: The Roles of Identity Formation and Parental Relationship Factors.

    ERIC Educational Resources Information Center

    Guerra, Antonia L.; Braungart-Rieker, Julia M.

    1999-01-01

    Investigates students' identity formation and perceptions of parental acceptance and encouragement of independence as predictors of career indecision. Four measurements were administered to 169 undergraduate students for the study. Results show career indecision was predicted by higher identity moratorium, less maternal acceptance, and fewer years…

  6. Mapping as a tool for predicting the risk of anthrax outbreaks in Northern Region of Ghana

    PubMed Central

    Nsoh, Ayamdooh Evans; Kenu, Ernest; Forson, Eric Kofi; Afari, Edwin; Sackey, Samuel; Nyarko, Kofi Mensah; Yebuah, Nathaniel

    2016-01-01

    Introduction Anthrax is a febrile soil-born infectious disease that can affect all warm-blooded animals including man. Outbreaks of anthrax have been reported in northern region of Ghana but no concerted effort has been made to implement risk-based surveillance systems to document outbreaks so as to implement policies to address the disease. We generated predictive maps using soil pH, temperature and rainfall as predictor variables to identify hotspot areas for the outbreaks. Methods A 10-year secondary data records on soil pH, temperature and rainfall were used to create climate-based risk maps using ArcGIS 10.2. The monthly mean values of rainfall and temperature for ten years were calculated and anthrax related evidence based constant raster values were created as weights for the three factors. All maps were generated using the Kriging interpolation method. Results There were 43 confirmed outbreaks. The deaths involved were 131 cattle, 44 sheep, 15 goats, 562 pigs with 6 human deaths and 22 developed cutaneous anthrax. We found three strata of well delineated distribution pattern indicating levels of risk due to suitability of area for anthrax spore survival. The likelihood of outbreaks occurrence and reoccurrence was higher in Strata I, Strata II and strata III respectively in descending order, due to the suitability of soil pH, temperature and rainfall for the survival and dispersal of B. anthracis spore. Conclusion The eastern corridor of Northern region is a Hots spot area. Policy makers can develop risk based surveillance system and focus on this area to mitigate anthrax outbreaks and reoccurrence. PMID:28149439

  7. Mapping as a tool for predicting the risk of anthrax outbreaks in Northern Region of Ghana.

    PubMed

    Nsoh, Ayamdooh Evans; Kenu, Ernest; Forson, Eric Kofi; Afari, Edwin; Sackey, Samuel; Nyarko, Kofi Mensah; Yebuah, Nathaniel

    2016-01-01

    Anthrax is a febrile soil-born infectious disease that can affect all warm-blooded animals including man. Outbreaks of anthrax have been reported in northern region of Ghana but no concerted effort has been made to implement risk-based surveillance systems to document outbreaks so as to implement policies to address the disease. We generated predictive maps using soil pH, temperature and rainfall as predictor variables to identify hotspot areas for the outbreaks. A 10-year secondary data records on soil pH, temperature and rainfall were used to create climate-based risk maps using ArcGIS 10.2. The monthly mean values of rainfall and temperature for ten years were calculated and anthrax related evidence based constant raster values were created as weights for the three factors. All maps were generated using the Kriging interpolation method. There were 43 confirmed outbreaks. The deaths involved were 131 cattle, 44 sheep, 15 goats, 562 pigs with 6 human deaths and 22 developed cutaneous anthrax. We found three strata of well delineated distribution pattern indicating levels of risk due to suitability of area for anthrax spore survival. The likelihood of outbreaks occurrence and reoccurrence was higher in Strata I, Strata II and strata III respectively in descending order, due to the suitability of soil pH, temperature and rainfall for the survival and dispersal of B. anthracis spore. The eastern corridor of Northern region is a Hots spot area. Policy makers can develop risk based surveillance system and focus on this area to mitigate anthrax outbreaks and reoccurrence.

  8. Large-scale mapping and predictive modeling of submerged aquatic vegetation in a shallow eutrophic lake.

    PubMed

    Havens, Karl E; Harwell, Matthew C; Brady, Mark A; Sharfstein, Bruce; East, Therese L; Rodusky, Andrew J; Anson, Daniel; Maki, Ryan P

    2002-04-09

    A spatially intensive sampling program was developed for mapping the submerged aquatic vegetation (SAV) over an area of approximately 20,000 ha in a large, shallow lake in Florida, U.S. The sampling program integrates Geographic Information System (GIS) technology with traditional field sampling of SAV and has the capability of producing robust vegetation maps under a wide range of conditions, including high turbidity, variable depth (0 to 2 m), and variable sediment types. Based on sampling carried out in August-September 2000, we measured 1,050 to 4,300 ha of vascular SAV species and approximately 14,000 ha of the macroalga Chara spp. The results were similar to those reported in the early 1990s, when the last large-scale SAV sampling occurred. Occurrence of Chara was strongly associated with peat sediments, and maximal depths of occurrence varied between sediment types (mud, sand, rock, and peat). A simple model of Chara occurrence, based only on water depth, had an accuracy of 55%. It predicted occurrence of Chara over large areas where the plant actually was not found. A model based on sediment type and depth had an accuracy of 75% and produced a spatial map very similar to that based on observations. While this approach needs to be validated with independent data in order to test its general utility, we believe it may have application elsewhere. The simple modeling approach could serve as a coarse-scale tool for evaluating effects of water level management on Chara populations.

  9. Maps showing formation temperatures and configurations of the tops of the Minnelusa Formation and the Madison Limestone, Powder River basin, Wyoming, Montana, and adjacent areas

    USGS Publications Warehouse

    Head, William J.; Kilty, Kevin Thomas; Knottek, Richard K.

    1978-01-01

    This report is part of a study to describe the hydrogeologic framework needed to evaluate the water resources of the Paleozoic age aquifers in the Northern Great Plains coal region. Preliminary studies by the U.S. Geological Survey and State agencies in Wyoming, Montana, and South Dakota have indicated that these aquifers might provide a significant percentage of the water requirements for coal development. Geologic and water-temperature data for the Minnelusa Formation of Permian and Pennsylvanian age and for the Madison Limestone (Group where it is subdivided) of Mississippian and locally late Devonian age , and their equivalents, were compiled and interpreted. Maps were produced showing the altitude and ground-water temperatures of the top of these formations. The altitude (configuration) maps show the depth and position of the formations throughout the area. Temperature maps can be used to calculate changes in the viscosity of water caused by large temperature differences. The viscosity differences will be useful in adjusting calculated transmissivity aquifer values (the rate at which water can be transmitted through an aquifer). (Woodard-USGS)

  10. The Functional Diffusion Map: An Imaging Biomarker for the Early Prediction of Cancer Treatment Outcome1

    PubMed Central

    Moffat, Bradford A; Chenevert, Thomas L; Meyer, Charles R; Mckeever, Paul E; Hall, Daniel E; Hoff, Benjamin A; Johnson, Timothy D; Rehemtulla, Alnawaz; Ross, Brian D

    2006-01-01

    Abstract Functional diffusion map (fDM) has been recently reported as an early and quantitative biomarker of clinical brain tumor treatment outcome. This MRI approach spatially maps and quantifies treatment-induced changes in tumor water diffusion values resulting from alterations in cell density/cell membrane function and microenvironment. This current study was designed to evaluate the capability of fDM for preclinical evaluation of dose escalation studies and to determine if these changes were correlated with outcome measures (cell kill and overall survival). Serial T2-weighted and diffusion MRI were carried out on rodents with orthotopically implanted 9L brain tumors receiving three doses of 1,3-bis(2-chloroethyl)-1-nitrosourea (6.65, 13.3, and 26.6 mg/kg, i.p.). All images were coregistered to baseline T2-weighted images for fDM analysis. Analysis of tumor fDM data on day 4 posttreatment detected dosedependent changes in tumor diffusion values, which were also found to be spatially dependent. Histologic analysis of treated tumors confirmed spatial changes in cellularity as observed by fDM. Early changes in tumor diffusion values were found to be highly correlative with drug dose and independent biologic outcome measures (cell kill and survival). Therefore, the fDM imaging biomarker for early prediction of treatment efficacy can be used in the drug development process. PMID:16756718

  11. Predictive Mapping of Human Risk for West Nile Virus (WNV) Based on Environmental and Socioeconomic Factors

    PubMed Central

    Rochlin, Ilia; Turbow, David; Gomez, Frank; Ninivaggi, Dominick V.; Campbell, Scott R.

    2011-01-01

    A West Nile virus (WNV) human risk map was developed for Suffolk County, New York utilizing a case-control approach to explore the association between the risk of vector-borne WNV and habitat, landscape, virus activity, and socioeconomic variables derived from publically available datasets. Results of logistic regression modeling for the time period between 2000 and 2004 revealed that higher proportion of population with college education, increased habitat fragmentation, and proximity to WNV positive mosquito pools were strongly associated with WNV human risk. Similar to previous investigations from north-central US, this study identified middle class suburban neighborhoods as the areas with the highest WNV human risk. These results contrast with similar studies from the southern and western US, where the highest WNV risk was associated with low income areas. This discrepancy may be due to regional differences in vector ecology, urban environment, or human behavior. Geographic Information Systems (GIS) analytical tools were used to integrate the risk factors in the 2000–2004 logistic regression model generating WNV human risk map. In 2005–2010, 41 out of 46 (89%) of WNV human cases occurred either inside of (30 cases) or in close proximity (11 cases) to the WNV high risk areas predicted by the 2000–2004 model. The novel approach employed by this study may be implemented by other municipal, local, or state public health agencies to improve geographic risk estimates for vector-borne diseases based on a small number of acute human cases. PMID:21853103

  12. Predictive Modeling and Mapping of Malayan Sun Bear (Helarctos malayanus) Distribution Using Maximum Entropy

    PubMed Central

    Nazeri, Mona; Jusoff, Kamaruzaman; Madani, Nima; Mahmud, Ahmad Rodzi; Bahman, Abdul Rani; Kumar, Lalit

    2012-01-01

    One of the available tools for mapping the geographical distribution and potential suitable habitats is species distribution models. These techniques are very helpful for finding poorly known distributions of species in poorly sampled areas, such as the tropics. Maximum Entropy (MaxEnt) is a recently developed modeling method that can be successfully calibrated using a relatively small number of records. In this research, the MaxEnt model was applied to describe the distribution and identify the key factors shaping the potential distribution of the vulnerable Malayan Sun Bear (Helarctos malayanus) in one of the main remaining habitats in Peninsular Malaysia. MaxEnt results showed that even though Malaysian sun bear habitat is tied with tropical evergreen forests, it lives in a marginal threshold of bio-climatic variables. On the other hand, current protected area networks within Peninsular Malaysia do not cover most of the sun bears potential suitable habitats. Assuming that the predicted suitability map covers sun bears actual distribution, future climate change, forest degradation and illegal hunting could potentially severely affect the sun bear’s population. PMID:23110182

  13. Predictive mapping of human risk for West Nile virus (WNV) based on environmental and socioeconomic factors.

    PubMed

    Rochlin, Ilia; Turbow, David; Gomez, Frank; Ninivaggi, Dominick V; Campbell, Scott R

    2011-01-01

    A West Nile virus (WNV) human risk map was developed for Suffolk County, New York utilizing a case-control approach to explore the association between the risk of vector-borne WNV and habitat, landscape, virus activity, and socioeconomic variables derived from publically available datasets. Results of logistic regression modeling for the time period between 2000 and 2004 revealed that higher proportion of population with college education, increased habitat fragmentation, and proximity to WNV positive mosquito pools were strongly associated with WNV human risk. Similar to previous investigations from north-central US, this study identified middle class suburban neighborhoods as the areas with the highest WNV human risk. These results contrast with similar studies from the southern and western US, where the highest WNV risk was associated with low income areas. This discrepancy may be due to regional differences in vector ecology, urban environment, or human behavior. Geographic Information Systems (GIS) analytical tools were used to integrate the risk factors in the 2000-2004 logistic regression model generating WNV human risk map. In 2005-2010, 41 out of 46 (89%) of WNV human cases occurred either inside of (30 cases) or in close proximity (11 cases) to the WNV high risk areas predicted by the 2000-2004 model. The novel approach employed by this study may be implemented by other municipal, local, or state public health agencies to improve geographic risk estimates for vector-borne diseases based on a small number of acute human cases.

  14. Geologic Mapping of the Medusae Fossae Formation on Mars (MC-8 SE and MC-23 NW) and the Northern Lowlands of Venus (V-16 and V-15)

    NASA Technical Reports Server (NTRS)

    Zimbelman, J. R.

    2008-01-01

    This report summarizes the status of a mapping project supported by NASA grant NNX07AP42G, funding for which became available on July 18, focusing on the mapping of the Medusae Fossae Formation (MFF) on Mars. The report also briefly discusses the status of maps of Venus and Ascraeus Mons, begun under previous NASA grants but which are still in progress.

  15. Widespread rocky reef occurrence in the central English Channel and the implications for predictive habitat mapping

    NASA Astrophysics Data System (ADS)

    Diesing, Markus; Coggan, Roger; Vanstaen, Koen

    2009-08-01

    Reefs are one of the marine habitats listed in Annex I of the European Union's Habitats Directive, which aims to establish a coherent European ecological network of Special Areas of Conservation. EU Member States are required to prepare and propose a national list of sites for evaluation under the scheme, but currently the occurrence of reefs in the United Kingdom's nearshore and offshore areas is not well documented. Here we report on our search for rocky reefs in the central English Channel, which unexpectedly revealed an extensive reef system covering an area of 1100 km 2. Prior to our work, it was generally perceived that the seabed in this area comprised mostly gravel, with a few isolated rock outcrops. Our approach to determining the location, extent and character of these reefs incorporated broad, medium and fine-scale analyses over a 3200 km 2 area of seabed, using single- and multi-beam acoustic data, ground-truthed by underwater video and stills imagery. A benthic terrain model was developed in ArcGIS to map topographic features at the broad and medium scales. Biotope assignments were made at the fine scale through detailed analysis of video footage obtained from 30 sampling stations. The study area has a complex geological history and lies at the centre of a major bedload-parting zone. Together, these strongly influence the seabed character and the distribution of biotopes. An integrated assessment of the physical and biological features was used to map the study area to level 4 of the EUNIS habitat classification system. Similar physical conditions exist in other areas of the UK continental shelf, raising the prospect of predicting where other rocky reef systems might occur. In the absence of a co-ordinated national seabed survey programme, such predictions, coupled with interpretation of existing single-beam bathymetry data, can help prioritise areas where limited survey resources could be most effectively deployed.

  16. Magnetic field inversions at 1 AU: Comparisons between mapping predictions and observations

    NASA Astrophysics Data System (ADS)

    Li, B.; Cairns, Iver H.; Owens, M. J.; Neudegg, D.; Lobzin, V. V.; Steward, G.

    2016-11-01

    Large-scale magnetic field configurations are important for the transport of solar wind strahl electrons, which are suprathermal and directed along the field outward from the Sun. Strahl electrons are routinely used to infer not only the field configurations between the Sun and Earth but also local field structures, i.e., field inversions, where the magnetic field is locally folded back or inverted. Using solar wind data from ACE observations and a 2-D data-driven solar wind model with nonzero azimuthal magnetic field at the solar wind source surface, magnetic field lines are mapped between the Sun and Earth and beyond, in the solar equatorial plane. Standard verification metrics are used to assess, for five solar rotations at different phases of solar cycle 23, the performance of the mapping predictions for observed inversions, which are inferred from solar wind suprathermal electrons and magnetic fields measured by ACE. The probability of detection is consistently ≈0.70 across the different phases. The success ratio, the Hanssen-Kuipers skill score, and the Heidke skill score are ≈0.55-0.70 for the four rotations in the rising, solar maximum, and declining phases, but ≈0.35-0.60 for the rotation near solar minimum, during which almost half of the samples have undetermined field configurations. Our analyses confirm the persistence of inversions throughout solar cycle 23, suggest for most observed inversions a solar/coronal origin at the wind's source surface or below, and predict that inversions should be less common for larger heliocentric distance r ˜> 3 AU than for smaller r.

  17. Predicting and mapping malaria under climate change scenarios: the potential redistribution of malaria vectors in Africa

    PubMed Central

    2010-01-01

    Background Malaria is rampant in Africa and causes untold mortality and morbidity. Vector-borne diseases are climate sensitive and this has raised considerable concern over the implications of climate change on future disease risk. The problem of malaria vectors (Anopheles mosquitoes) shifting from their traditional locations to invade new zones is an important concern. The vision of this study was to exploit the sets of information previously generated by entomologists, e.g. on geographical range of vectors and malaria distribution, to build models that will enable prediction and mapping the potential redistribution of Anopheles mosquitoes in Africa. Methods The development of the modelling tool was carried out through calibration of CLIMEX parameters. The model helped estimate the potential geographical distribution and seasonal abundance of the species in relation to climatic factors. These included temperature, rainfall and relative humidity, which characterized the living environment for Anopheles mosquitoes. The same parameters were used in determining the ecoclimatic index (EI). The EI values were exported to a GIS package for special analysis and proper mapping of the potential future distribution of Anopheles gambiae and Anophles arabiensis within the African continent under three climate change scenarios. Results These results have shown that shifts in these species boundaries southward and eastward of Africa may occur rather than jumps into quite different climatic environments. In the absence of adequate control, these predictions are crucial in understanding the possible future geographical range of the vectors and the disease, which could facilitate planning for various adaptation options. Conclusion Thus, the outputs from this study will be helpful at various levels of decision making, for example, in setting up of an early warning and sustainable strategies for climate change and climate change adaptation for malaria vectors control programmes in

  18. Miedema Calculator: A thermodynamic platform for predicting formation enthalpies of alloys within framework of Miedema's Theory

    NASA Astrophysics Data System (ADS)

    Zhang, R. F.; Zhang, S. H.; He, Z. J.; Jing, J.; Sheng, S. H.

    2016-12-01

    The theoretical background and implementation of "Miedema Calculator", a thermodynamic platform for predicting formation enthalpies of various alloys within framework of Miedema's theory, is summarized and presented. Several user-friendly interfaces are designed for the following major functional modules, i.e. the formation enthalpies of binary intermetallic compounds based on the original Miedema's model and two more improved ones, the chemical, elastic and structural enthalpies of solid solutions, the formation enthalpies of amorphous alloys, the volume corrections upon alloying, and the formation enthalpies of ternary alloys based on various geometrical models. Various models and methods have been justified and implemented into the platform together with the unified model parameters and properties for each element as a basic database. A set of critical tests and evaluations have been performed on each module, providing its efficiency and validation for a fast screening of thermodynamic properties of various alloys.

  19. A computational approach to predicting the formation of iron sulfide species using stability diagrams

    NASA Astrophysics Data System (ADS)

    Anderko, Andrzej; Shuler, Patrick J.

    1997-07-01

    A program has been developed for generating stability diagrams that combine the principles of the Pourbaix E-pH diagrams with a rigorous and predictive thermodynamic model for multicomponent, nonideal aqueous solutions. Since the diagrams are based on a realistic model for the aqueous phase, they are referred to as real-solution stability diagrams. They are valid for solutions ranging from dilute to concentrated (up to 30 mol kg -1) at temperatures up to 300 °C and pressures up to 1 kbar. The stability diagrams are used to predict the conditions that favor the stability of various iron sulfide species. For this purpose, the applicability of the diagrams is extended to include the prediction of both stable and metastable products. The diagrams indicate that the formation of iron monosulfide follows the FeHS + → amorphous FeS → mackinawite → pyrrhotite replacement sequence. It is predicted that a transformation of iron monosulfides to pyrite may occur through greigite and/or marcasite. Greigite is predicted to be absent in strictly reducing environments. The predictions are in agreement with experimental data on iron sulfide formation in solution and/or at the iron/solution interface.

  20. New method for prediction of shale gas content in continental shale formation using well logs

    NASA Astrophysics Data System (ADS)

    Li, Sheng-Jie; Cui, Zhe; Jiang, Zhen-Xue; Shao, Yu; Liao, Wei; Li, Li

    2016-06-01

    Shale needs to contain a sufficient amount of gas to make it viable for exploitation. The continental heterogeneous shale formation in the Yan-chang (YC) area is investigated by firstly measuring the shale gas content in a laboratory and then investigating use of a theoretical prediction model. Key factors controlling the shale gas content are determined, and a prediction model for free gas content is established according to the equation of gas state and a new petrophysical volume model. Application of the Langmuir volume constant and pressure constant obtained from results of adsorption isotherms is found to be limited because these constants are greatly affected by experimental temperature and pressures. Therefore, using measurements of adsorption isotherms and thermodynamic theory, the influence of temperature, total organic carbon (TOC), and mineralogy on Langmuir volume constants and pressure constants are investigated in detail. A prediction model for the Langmuir pressure constant with a correction of temperatures is then established, and a prediction model for the Langmuir volume constant with correction of temperature, TOC, and quartz contents is also proposed. Using these corrected Langmuir constants, application of the Langmuir model determined using experimental adsorption isotherms is extrapolated to reservoir temperature, pressure, and lithological conditions, and a method for the prediction of shale gas content using well logs is established. Finally, this method is successfully applied to predict the shale gas content of the continental shale formation in the YC area, and practical application is shown to deliver good results with high precision.

  1. Mapping Medusae Fossae Formation materials in the southern highlands of Mars

    NASA Astrophysics Data System (ADS)

    Harrison, S. K.; Balme, M. R.; Hagermann, A.; Murray, J. B.; Muller, J.-P.

    2010-10-01

    The Medusae Fossae Formation (MFF) is an extensive deposit (2.2 × 10 6 km 2, Bradley, B.A., Sakimoto, S.E.H., Frey, H., Zimbelman, J.R. [2002]. J. Geophys. Res. 107, 5058) of wind-eroded material of widely debated origin, which unconformably overlies a considerable area of the crustal dichotomy boundary on Mars. The MFF shows a variety of layering patterns, erosional styles and channel-like forms and has been mapped into five main outcrops and three geological members according to exposure and stratigraphy (Scott, D.H., Tanaka, K.L., 1986. USGS Map I-1802-A; Greeley, R., Guest, J.E., 1987. Map I-1802-B; Zimbelman, J.R., Crown, D., Jenson, D., 1996. Lunar Planet. Sci. XXVII. Abstract #1748.). Away from the three main lobes are numerous outliers of MFF materials. These have mainly been reported in the northern lowlands regions (Keszthelyi, L., Jaeger, W.L., and HiRISE team, 2008. Lunar Planet. Sci. XXXIX. Abstract #2420.) but few studies have examined the possibility of MFF outliers on high ground south of the dichotomy boundary. We have searched Mars Orbiter Camera Narrow Angle (MOC NA) images for outliers in this region. Our observations show that there are many MFF outliers on the southern highlands. The characteristics of the outliers indicate materials which overlie the underlying terrain for they appear widely in dips, craters and topographic lows. The surfaces are typified by yardang fields and have a similar patchy and discontinuous nature to materials of the upper member of the MFF. Most have consistent lineation orientations across the wider area which match the dominant orientation of yardangs in the main MFF outcrops. Furthermore, elevation data shows that the maximum, minimum and mean elevations of these newly discovered outliers are closest to those of the upper member of the MFF. We therefore conclude that these deposits are MFF outliers and that they probably represent remnant upper member material. We suggest that there might be two possible

  2. Tree structure-based bit-to-symbol mapping for multidimensional modulation format

    NASA Astrophysics Data System (ADS)

    Zhaoxi, Li; Yujuan, Si; Guijun, Hu

    2017-06-01

    Bit-to-symbol mapping is one of the key issues in multidimensional modulation. In an effort to resolve this issue, a tree structure based bit-to-symbol mapping scheme is proposed. By constructing a tree structure of constellation points, any neighboring constellation points become nearest-neighbor constellation points with minimum Euclidean distance, which in turn, changes the bit-to-symbol mapping problem in multidimensional signal modulation from random to orderly. Then, through the orderly distribution of labels, the minimum Hamming distance between the nearest neighboring constellation points is ensured, eventually achieving bit-to-symbol mapping optimization for multidimensional signals. Simulation analysis indicates that, compared with random search mapping, tree mapping can effectively improve the bit error rate performance of multidimensional signal modulation without multiple searching, reducing the computational cost.

  3. Genetic mapping and characterization of Pseudomonas aeruginosa mutants defective in the formation of extracellular proteins.

    PubMed Central

    Wretlind, B; Pavlovskis, O R

    1984-01-01

    We isolated 15 mutants of Pseudomonas aeruginosa PAO which were defective in the formation of certain extracellular proteins, such as elastase, staphylolytic enzyme, and lipase ( Xcp mutants). The mutations were mapped on the chromosome by conjugation and transduction. The locations were xcp -1 near 0', with the gene order cys-59- xcp -1- proB , and loci xcp -2, xcp -3, and xcp -31 at 35', with the gene order trpC , D- xcp -3/ xcp -31- xcp -2- argC . Loci xcp -4 and xcp -41 through xcp -44 were cotransducible with proA at 40'; loci xcp -5, xcp -51, xcp -52, and xcp53 were located at 55', with the gene order leu-10- trpF -met-9010- xcp -53- xcp -5/ xcp -51/ xcp+ ++-52, and xcp -6 was located at 65' to 70', between catA and mtu-9002. Nine mutations ( xcp -2, xcp -3, xcp -31, xcp -4, and xcp -41 through xcp -45) caused decreased production of extracellular enzymes. Six strains with mutations xcp -1, xcp -5, xcp -51, xcp -52, xcp -53, and xcp -6 produced cell-bound exoproteins and had defective release mechanisms. The regulation of production of alkaline phosphatase and phospholipase C is different from other exoproteins , such as elastase, but they all seem to share a common release mechanism. Alkaline protease had separate mechanisms for regulation and release, since this protease was found in culture supernatants of all but one of the mutants, and none of the strains had cell-bound enzyme. PMID:6427194

  4. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

    PubMed Central

    Lu, Zhi John; Turner, Douglas H.; Mathews, David H.

    2006-01-01

    A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. PMID:16982646

  5. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.

    PubMed

    Lu, Zhi John; Turner, Douglas H; Mathews, David H

    2006-01-01

    A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37 degrees C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60 degrees C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures.

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

    PubMed Central

    Li, Zhen; Zhang, Renyu

    2017-01-01

    -assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. Availability http://raptorx.uchicago.edu/ContactMap/ PMID:28056090

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

    PubMed

    Wang, Sheng; Sun, Siqi; Li, Zhen; Zhang, Renyu; Xu, Jinbo

    2017-01-01

    much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. http://raptorx.uchicago.edu/ContactMap/.

  8. Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity

    PubMed Central

    Hassan, Islam; Kotrotsou, Aikaterini; Bakhtiari, Ali Shojaee; Thomas, Ginu A.; Weinberg, Jeffrey S.; Kumar, Ashok J.; Sawaya, Raymond; Luedi, Markus M.; Zinn, Pascal O.; Colen, Rivka R.

    2016-01-01

    Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias. PMID:27151623

  9. Comparison of Northern Ireland radon maps based on indoor radon measurements and geology with maps derived by predictive modelling of airborne radiometric and ground permeability data.

    PubMed

    Appleton, J D; Miles, J C H; Young, M

    2011-03-15

    Publicly available information about radon potential in Northern Ireland is currently based on indoor radon results averaged over 1-km grid squares, an approach that does not take into account the geological origin of the radon. This study describes a spatially more accurate estimate of the radon potential of Northern Ireland using an integrated radon potential mapping method based on indoor radon measurements and geology that was originally developed for mapping radon potential in England and Wales. A refinement of this method was also investigated using linear regression analysis of a selection of relevant airborne and soil geochemical parameters from the Tellus Project. The most significant independent variables were found to be eU, a parameter derived from airborne gamma spectrometry measurements of radon decay products in the top layer of soil and exposed bedrock, and the permeability of the ground. The radon potential map generated from the Tellus data agrees in many respects with the map based on indoor radon data and geology but there are several areas where radon potential predicted from the airborne radiometric and permeability data is substantially lower. This under-prediction could be caused by the radon concentration being lower in the top 30 cm of the soil than at greater depth, because of the loss of radon from the surface rocks and soils to air. Copyright © 2011. Published by Elsevier B.V.

  10. Predictive Mapping of Topsoil Organic Carbon in an Alpine Environment Aided by Landsat TM.

    PubMed

    Yang, Renmin; Rossiter, David G; Liu, Feng; Lu, Yuanyuan; Yang, Fan; Yang, Fei; Zhao, Yuguo; Li, Decheng; Zhang, Ganlin

    2015-01-01

    The objective of this study was to examine the reflectance of Landsat TM imagery for mapping soil organic Carbon (SOC) content in an Alpine environment. The studied area (ca. 3*104 km2) is the upper reaches of the Heihe River at the northeast edge of the Tibetan plateau, China. A set (105) of topsoil samples were analyzed for SOC. Boosted regression tree (BRT) models using Landsat TM imagery were built to predict SOC content, alone or with topography and climate covariates (temperature and precipitation). The best model, combining all covariates, was only marginally better than using only imagery. Imagery alone was sufficient to build a reasonable model; this was a bit better than only using topography and climate covariates. The Lin's concordance correlation coefficient values of the imagery only model and the full model are very close, larger than the topography and climate variables based model. In the full model, SOC was mainly explained by Landsat TM imagery (65% relative importance), followed by climate variables (20%) and topography (15% of relative importance). The good results from imagery are likely due to (1) the strong dependence of SOC on native vegetation intensity in this Alpine environment; (2) the strong correlation in this environment between imagery and environmental covariables, especially elevation (corresponding to temperature), precipitation, and slope aspect. We conclude that multispectral satellite data from Landsat TM images may be used to predict topsoil SOC with reasonable accuracy in Alpine regions, and perhaps other regions covered with natural vegetation, and that adding topography and climate covariables to the satellite data can improve the predictive accuracy.

  11. Predictive Mapping of Topsoil Organic Carbon in an Alpine Environment Aided by Landsat TM

    PubMed Central

    Yang, Renmin; Rossiter, David G.; Liu, Feng; Lu, Yuanyuan; Yang, Fan; Yang, Fei; Zhao, Yuguo; Li, Decheng; Zhang, Ganlin

    2015-01-01

    The objective of this study was to examine the reflectance of Landsat TM imagery for mapping soil organic Carbon (SOC) content in an Alpine environment. The studied area (ca. 3*104 km2) is the upper reaches of the Heihe River at the northeast edge of the Tibetan plateau, China. A set (105) of topsoil samples were analyzed for SOC. Boosted regression tree (BRT) models using Landsat TM imagery were built to predict SOC content, alone or with topography and climate covariates (temperature and precipitation). The best model, combining all covariates, was only marginally better than using only imagery. Imagery alone was sufficient to build a reasonable model; this was a bit better than only using topography and climate covariates. The Lin’s concordance correlation coefficient values of the imagery only model and the full model are very close, larger than the topography and climate variables based model. In the full model, SOC was mainly explained by Landsat TM imagery (65% relative importance), followed by climate variables (20%) and topography (15% of relative importance). The good results from imagery are likely due to (1) the strong dependence of SOC on native vegetation intensity in this Alpine environment; (2) the strong correlation in this environment between imagery and environmental covariables, especially elevation (corresponding to temperature), precipitation, and slope aspect. We conclude that multispectral satellite data from Landsat TM images may be used to predict topsoil SOC with reasonable accuracy in Alpine regions, and perhaps other regions covered with natural vegetation, and that adding topography and climate covariables to the satellite data can improve the predictive accuracy. PMID:26473739

  12. Multispectral Thermal Imagery and Its Application to the Geologic Mapping of the Koobi Fora Formation, Northwestern Kenya

    SciTech Connect

    Green, Mary K.

    2005-12-01

    The Koobi Fora Formation in northwestern Kenya has yielded more hominin fossils dated between 2.1 and 1.2 Ma than any other location on Earth. This research was undertaken to discover the spectral signatures of a portion of the Koobi Fora Formation using imagery from the DOE's Multispectral Thermal Imager (MTI) satellite. Creation of a digital geologic map from MTI imagery was a secondary goal of this research. MTI is unique amongst multispectral satellites in that it co-collects data from 15 spectral bands ranging from the visible to the thermal infrared with a ground sample distance of 5 meters per pixel in the visible and 20 meters in the infrared. The map was created in two stages. The first was to correct the base MTI image using spatial accuracy assessment points collected in the field. The second was to mosaic various MTI images together to create the final Koobi Fora map. Absolute spatial accuracy of the final map product is 73 meters. The geologic classification of the Koobi Fora MTI map also took place in two stages. The field work stage involved location of outcrops of different lithologies within the Koobi Fora Formation. Field descriptions of these outcrops were made and their locations recorded. During the second stage, a linear spectral unmixing algorithm was applied to the MTI mosaic. In order to train the linear spectra unmixing algorithm, regions of interest representing four different classes of geologic material (tuff, alluvium, carbonate, and basalt), as well as a vegetation class were defined within the MTI mosaic. The regions of interest were based upon the aforementioned field data as well as overlays of geologic maps from the 1976 Iowa State mapping project. Pure spectra were generated for each class from the regions of interest, and then the unmixing algorithm classified each pixel according to relative percentage of classes found within the pixel based upon the pure spectra values. A total of four unique combinations of geologic classes

  13. MAPping the Ndc80 loop in cancer: A possible link between Ndc80/Hec1 overproduction and cancer formation.

    PubMed

    Tang, Ngang Heok; Toda, Takashi

    2015-03-01

    Mis-regulation (e.g. overproduction) of the human Ndc80/Hec1 outer kinetochore protein has been associated with aneuploidy and tumourigenesis, but the genetic basis and underlying mechanisms of this phenomenon remain poorly understood. Recent studies have identified the ubiquitous Ndc80 internal loop as a protein-protein interaction platform. Binding partners include the Ska complex, the replication licensing factor Cdt1, the Dam1 complex, TACC-TOG microtubule-associated proteins (MAPs) and kinesin motors. We review the field and propose that the overproduction of Ndc80 may unfavourably absorb these interactors through the internal loop domain and lead to a change in the equilibrium of MAPs and motors in the cells. This sequestration will disrupt microtubule dynamics and the proper segregation of chromosomes in mitosis, leading to aneuploid formation. Further investigation of Ndc80 internal loop-MAPs interactions will bring new insights into their roles in kinetochore-microtubule attachment and tumourigenesis.

  14. Galaxy Formation At Extreme Redshifts: Semi-Analytic Model Predictions And Challenges For Observations

    NASA Astrophysics Data System (ADS)

    Yung, L. Y. Aaron; Somerville, Rachel S.

    2017-06-01

    The well-established Santa Cruz semi-analytic galaxy formation framework has been shown to be quite successful at explaining observations in the local Universe, as well as making predictions for low-redshift observations. Recently, metallicity-based gas partitioning and H2-based star formation recipes have been implemented in our model, replacing the legacy cold-gas based recipe. We then use our revised model to explore the high-redshift Universe and make predictions up to z = 15. Although our model is only calibrated to observations from the local universe, our predictions seem to match incredibly well with mid- to high-redshift observational constraints available-to-date, including rest-frame UV luminosity functions and the reionization history as constrained by CMB and IGM observations. We provide predictions for individual and statistical galaxy properties at a wide range of redshifts (z = 4 - 15), including objects that are too far or too faint to be detected with current facilities. And using our model predictions, we also provide forecasted luminosity functions and other observables for upcoming studies with JWST.

  15. The Art of Teaching Map and Compass: Instructional Techniques, Curricular Formats and Practical Field Exercises.

    ERIC Educational Resources Information Center

    Watters, Ron

    This paper discusses the value of teaching map and compass skills in the classroom or an outdoor situation. Navigation is the most basic of all outdoor skills. A map and compass curriculum can be taught to anyone, is inexpensive, and is easily incorporated in a variety of educational situations. General teaching principles are outlined: (1) start…

  16. Structural Bioinformatics-Based Prediction of Exceptional Selectivity of p38 MAP Kinase Inhibitor PH-797804

    SciTech Connect

    Xing, Li; Shieh, Huey S.; Selness, Shaun R.; Devraj, Rajesh V.; Walker, John K.; Devadas, Balekudru; Hope, Heidi R.; Compton, Robert P.; Schindler, John F.; Hirsch, Jeffrey L.; Benson, Alan G.; Kurumbail, Ravi G.; Stegeman, Roderick A.; Williams, Jennifer M.; Broadus, Richard M.; Walden, Zara; Monahan, Joseph B.; Pfizer

    2009-07-24

    PH-797804 is a diarylpyridinone inhibitor of p38{alpha} mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. On the basis of structural comparison with a different biaryl pyrazole template and supported by dozens of high-resolution crystal structures of p38{alpha} inhibitor complexes, PH-797804 is predicted to possess a high level of specificity across the broad human kinase genome. We used a structural bioinformatics approach to identify two selectivity elements encoded by the TXXXG sequence motif on the p38{alpha} kinase hinge: (i) Thr106 that serves as the gatekeeper to the buried hydrophobic pocket occupied by 2,4-difluorophenyl of PH-797804 and (ii) the bidentate hydrogen bonds formed by the pyridinone moiety with the kinase hinge requiring an induced 180{sup o} rotation of the Met109-Gly110 peptide bond. The peptide flip occurs in p38{alpha} kinase due to the critical glycine residue marked by its conformational flexibility. Kinome-wide sequence mining revealed rare presentation of the selectivity motif. Corroboratively, PH-797804 exhibited exceptionally high specificity against MAP kinases and the related kinases. No cross-reactivity was observed in large panels of kinase screens (selectivity ratio of >500-fold). In cellular assays, PH-797804 demonstrated superior potency and selectivity consistent with the biochemical measurements. PH-797804 has met safety criteria in human phase I studies and is under clinical development for several inflammatory conditions. Understanding the rationale for selectivity at the molecular level helps elucidate the biological function and design of specific p38{alpha} kinase inhibitors.

  17. Formative use of select-and-fill-in concept maps in online instruction: Implications for students of different learning styles

    NASA Astrophysics Data System (ADS)

    Kaminski, Charles William

    The purpose of this research was to investigate the formative use of Select and Fill-In (SAFI) maps in online instruction and the cognitive, metacognitive, and affective responses of students to their use. In particular, the implications of their use with students of different learning styles was considered. The research question investigated in this qualitative study was: How do students of different learning styles respond to online instruction in which SAFI maps are utilized? This question was explored by using an emergent, collective case study. Each case consisted of community college students who shared a dominant learning style and were enrolled in an online course in environmental studies. Cases in the study were determined using Kolb's Learning Style Inventory (LSI). Seven forms of data were collected during the study. During the first phase of data collection, dominant learning style and background information on student experience with concept mapping and online instruction was determined. In the second phase of data collection, participants completed SAFI maps and quiz items that corresponded to the content of the maps. Achievement data on the map activities and quiz and student responses to a post-SAFI survey and questionnaire were recorded to identify learner cognitive, metacognitive, and affective responses to the tasks. Upon completion of data collection, cases were constructed and compared across learning styles. Cases are presented using the trends, across participants sharing the same dominant learning style, in achievement, behaviors and attitudes as seen in the evidence present in the data. Triangulation of multiple data sources increased reliability and validity, through cross-case analyses, and produced a thick description of the relationship between the cases for each learning style. Evidence suggesting a cognitive response to the SAFI tasks was inconsistent across cases. However, learners with an affinity towards reflective learning

  18. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

    DTIC Science & Technology

    2016-03-15

    RESEARCH ARTICLE Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism Francisco G...we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosametabolic network and gene expression...synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we

  19. Simple Computation of the Heat of Formation and Density from Theoretically Predicted Values

    DTIC Science & Technology

    2012-09-01

    or the Gutowski model (20), which is applicable only for 1:1 salts . Both the Jenkins and Gutowski models correlate the molecular volume to the...can be obtained for non-1:1 salts , assuming one had knowledge of the crystal structure, the Jenkins methodology allows for a completely predictive...tool for the determination of solid-phase heats of formation of molecular energetic salts without requiring this information. Surprisingly, the

  20. Fuzzy Cognitive Maps for Glacier Hazards Assessment: Application to Predicting the Potential for Glacier Lake Outbursts

    NASA Astrophysics Data System (ADS)

    Furfaro, R.; Kargel, J. S.; Fink, W.; Bishop, M. P.

    2010-12-01

    Glaciers and ice sheets are among the largest unstable parts of the solid Earth. Generally, glaciers are devoid of resources (other than water), are dangerous, are unstable and no infrastructure is normally built directly on their surfaces. Areas down valley from large alpine glaciers are also commonly unstable due to landslide potential of moraines, debris flows, snow avalanches, outburst floods from glacier lakes, and other dynamical alpine processes; yet there exists much development and human occupation of some disaster-prone areas. Satellite remote sensing can be extremely effective in providing cost-effective and time- critical information. Space-based imagery can be used to monitor glacier outlines and their lakes, including processes such as iceberg calving and debris accumulation, as well as changing thicknesses and flow speeds. Such images can also be used to make preliminary identifications of specific hazardous spots and allows preliminary assessment of possible modes of future disaster occurrence. Autonomous assessment of glacier conditions and their potential for hazards would present a major advance and permit systematized analysis of more data than humans can assess. This technical leap will require the design and implementation of Artificial Intelligence (AI) algorithms specifically designed to mimic glacier experts’ reasoning. Here, we introduce the theory of Fuzzy Cognitive Maps (FCM) as an AI tool for predicting and assessing natural hazards in alpine glacier environments. FCM techniques are employed to represent expert knowledge of glaciers physical processes. A cognitive model embedded in a fuzzy logic framework is constructed via the synergistic interaction between glaciologists and AI experts. To verify the effectiveness of the proposed AI methodology as applied to predicting hazards in glacier environments, we designed and implemented a FCM that addresses the challenging problem of autonomously assessing the Glacier Lake Outburst Flow

  1. Thalamic theta phase alignment predicts human memory formation and anterior thalamic cross-frequency coupling.

    PubMed

    Sweeney-Reed, Catherine M; Zaehle, Tino; Voges, Jürgen; Schmitt, Friedhelm C; Buentjen, Lars; Kopitzki, Klaus; Hinrichs, Hermann; Heinze, Hans-Jochen; Rugg, Michael D; Knight, Robert T; Richardson-Klavehn, Alan

    2015-05-20

    Previously we reported electrophysiological evidence for a role for the anterior thalamic nucleus (ATN) in human memory formation (Sweeney-Reed et al., 2014). Theta-gamma cross-frequency coupling (CFC) predicted successful memory formation, with the involvement of gamma oscillations suggesting memory-relevant local processing in the ATN. The importance of the theta frequency range in memory processing is well-established, and phase alignment of oscillations is considered to be necessary for synaptic plasticity. We hypothesized that theta phase alignment in the ATN would be necessary for memory encoding. Further analysis of the electrophysiological data reveal that phase alignment in the theta rhythm was greater during successful compared with unsuccessful encoding, and that this alignment was correlated with the CFC. These findings support an active processing role for the ATN during memory formation.

  2. Thermochemistry for silicic acid formation reaction: Prediction of new reaction pathway

    NASA Astrophysics Data System (ADS)

    Mondal, Bhaskar; Ghosh, Deepanwita; Das, Abhijit K.

    2009-08-01

    Reaction between SiO 2 and water has been studied extensively using ab initio methods. The mechanism for formation of metasilicic acid SiO(OH) 2 and orthosilicic acid Si(OH) 4 has been explored and a new pathway for formation of Si(OH) 4 is predicted. Heats of reaction ( ΔrH298∘) and heats of formation ( ΔfH298∘) at 298 K for the related reactions and species calculated at two different theoretical levels G3B3 and G3MP2B3 agree well with the literature values. It is found that when SiO 2 reacts simultaneously with two water molecules, the thermodynamic as well as kinetic feasibility of the process is much greater than that when SiO 2 reacts with one molecule of water.

  3. Thalamic theta phase alignment predicts human memory formation and anterior thalamic cross-frequency coupling

    PubMed Central

    Sweeney-Reed, Catherine M; Zaehle, Tino; Voges, Jürgen; Schmitt, Friedhelm C; Buentjen, Lars; Kopitzki, Klaus; Hinrichs, Hermann; Heinze, Hans-Jochen; Rugg, Michael D; Knight, Robert T; Richardson-Klavehn, Alan

    2015-01-01

    Previously we reported electrophysiological evidence for a role for the anterior thalamic nucleus (ATN) in human memory formation (Sweeney-Reed et al., 2014). Theta-gamma cross-frequency coupling (CFC) predicted successful memory formation, with the involvement of gamma oscillations suggesting memory-relevant local processing in the ATN. The importance of the theta frequency range in memory processing is well-established, and phase alignment of oscillations is considered to be necessary for synaptic plasticity. We hypothesized that theta phase alignment in the ATN would be necessary for memory encoding. Further analysis of the electrophysiological data reveal that phase alignment in the theta rhythm was greater during successful compared with unsuccessful encoding, and that this alignment was correlated with the CFC. These findings support an active processing role for the ATN during memory formation. DOI: http://dx.doi.org/10.7554/eLife.07578.001 PMID:25993559

  4. Factors affecting paddy soil arsenic concentration in Bangladesh: prediction and uncertainty of geostatistical risk mapping.

    PubMed

    Ahmed, Zia U; Panaullah, Golam M; DeGloria, Stephen D; Duxbury, John M

    2011-12-15

    Knowledge of the spatial correlation of soil arsenic (As) concentrations with environmental variables is needed to assess the nature and extent of the risk of As contamination from irrigation water in Bangladesh. We analyzed 263 paired groundwater and paddy soil samples covering highland (HL) and medium highland-1 (MHL-1) land types for geostatistical mapping of soil As and delineation of As contaminated areas in Tala Upazilla, Satkhira district. We also collected 74 non-rice soil samples to assess the baseline concentration of soil As for this area. The mean soil As concentrations (mg/kg) for different land types under rice and non-rice crops were: rice-MHL-1 (21.2)>rice-HL (14.1)>non-rice-MHL-1 (11.9)>non-rice-HL (7.2). Multiple regression analyses showed that irrigation water As, Fe, land elevation and years of tubewell operation are the important factors affecting the concentrations of As in HL paddy soils. Only years of tubewell operation affected As concentration in the MHL-1 paddy soils. Quantitatively similar increases in soil As above the estimated baseline-As concentration were observed for rice soils on HL and MHL-1 after 6-8 years of groundwater irrigation, implying strong retention of As added in irrigation water in both land types. Application of single geostatistical methods with secondary variables such as regression kriging (RK) and ordinary co-kriging (OCK) gave little improvement in prediction of soil As over ordinary kriging (OK). Comparing single prediction methods, kriging within strata (KWS), the combination of RK for HL and OCK for MHL-1, gave more accurate soil As predictions and showed the lowest misclassification of declaring a location "contaminated" with respect to 14.8 mg As/kg, the highest value obtained for the baseline soil As concentration. Prediction of soil As buildup over time indicated that 75% or the soils cropped to rice would contain at least 30 mg/L As by the year 2020. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Using dose-surface maps to predict radiation-induced rectal bleeding: a neural network approach

    NASA Astrophysics Data System (ADS)

    Buettner, Florian; Gulliford, Sarah L.; Webb, Steve; Partridge, Mike

    2009-09-01

    The incidence of late-toxicities after radiotherapy can be modelled based on the dose delivered to the organ under consideration. Most predictive models reduce the dose distribution to a set of dose-volume parameters and do not take the spatial distribution of the dose into account. The aim of this study was to develop a classifier predicting radiation-induced rectal bleeding using all available information on the dose to the rectal wall. The dose was projected on a two-dimensional dose-surface map (DSM) by virtual rectum-unfolding. These DSMs were used as inputs for a classification method based on locally connected neural networks. In contrast to fully connected conventional neural nets, locally connected nets take the topology of the input into account. In order to train the nets, data from 329 patients from the RT01 trial (ISRCTN 47772397) were split into ten roughly equal parts. By using nine of these parts as a training set and the remaining part as an independent test set, a ten-fold cross-validation was performed. Ensemble learning was used and 250 nets were built from randomly selected patients from the training set. Out of these 250 nets, an ensemble of expert nets was chosen. The performances of the full ensemble and of the expert ensemble were quantified by using receiver-operator-characteristic (ROC) curves. In order to quantify the predictive power of the shape, ensembles of fully connected conventional neural nets based on dose-surface histograms (DSHs) were generated and their performances were quantified. The expert ensembles performed better than or equally as well as the full ensembles. The area under the ROC curve for the DSM-based expert ensemble was 0.64. The area under the ROC curve for the DSH-based expert ensemble equalled 0.59. This difference in performance indicates that not only volumetric, but also morphological aspects of the dose distribution are correlated to rectal bleeding after radiotherapy. Thus, the shape of the dose

  6. Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

    PubMed

    Strohm, S; Tyson, R C; Powell, J A

    2013-10-01

    Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

  7. Predicting secondary organic aerosol formation from terpenoid ozonolysis with varying yields in indoor environments.

    PubMed

    Youssefi, S; Waring, M S

    2012-10-01

    The ozonolysis of terpenoids generates secondary organic aerosol (SOA) indoors. Models of varying complexity have been used to predict indoor SOA formation, and many models use the SOA yield, which is the ratio of the mass of produced SOA and the mass of consumed reactive organic gas. For indoor simulations, the SOA yield has been assumed as a constant, even though it depends on the concentration of organic particles in the air, including any formed SOA. We developed two indoor SOA formation models for single terpenoid ozonolysis, with yields that vary with the organic particle concentration. The models have their own strengths and were in agreement with published experiments for d-limonene ozonolysis. Monte Carlo analyses were performed, which simulated different residential and office environments to estimate ranges of SOA concentrations and yields for d-limonene and α-pinene ozonolysis occurring indoors. Results indicate that yields are highly variable indoors and are most influenced by background organic particles for steady-state formation and indoor ozone concentration for transient peak formation. Additionally, a review of ozonolysis yields for indoor-relevant terpenoids in the literature revealed much uncertainty in their values at low concentrations typical of indoors. The results in this study suggest important factors that govern indoor secondary organic aerosol (SOA) formation and yields, in typical residential and office spaces. This knowledge informs the development and comparison of control strategies to reduce indoor-generated SOA. The ranges of SOA concentrations predicted indoors allow the quantification of the effects of sorptive interactions of semi-volatile organic compounds or reactive oxygen species with SOA, filter loading owing to SOA formation, and impacts of SOA on health, if links are established. © 2012 John Wiley & Sons A/S.

  8. Predicting total organic halide formation from drinking water chlorination using quantitative structure-property relationships.

    PubMed

    Luilo, G B; Cabaniss, S E

    2011-10-01

    Chlorinating water which contains dissolved organic matter (DOM) produces disinfection byproducts, the majority of unknown structure. Hence, the total organic halide (TOX) measurement is used as a surrogate for toxic disinfection byproducts. This work derives a robust quantitative structure-property relationship (QSPR) for predicting the TOX formation potential of model compounds. Literature data for 49 compounds were used to train the QSPR in moles of chlorine per mole of compound (Cp) (mol-Cl/mol-Cp). The resulting QSPR has four descriptors, calibration [Formula: see text] of 0.72 and standard deviation of estimation of 0.43 mol-Cl/mol-Cp. Internal and external validation indicate that the QSPR has good predictive power and low bias (‰<‰1%). Applying this QSPR to predict TOX formation by DOM surrogates - tannic acid, two model fulvic acids and two agent-based model assemblages - gave a predicted TOX range of 136-184 µg-Cl/mg-C, consistent with experimental data for DOM, which ranged from 78 to 192 µg-Cl/mg-C. However, the limited structural variation in the training data may limit QSPR applicability; studies of more sulfur-containing compounds, heterocyclic compounds and high molecular weight compounds could lead to a more widely applicable QSPR.

  9. A Principle for the Formation of the Spatial Structure of Cortical Feature Maps

    NASA Astrophysics Data System (ADS)

    Obermayer, K.; Ritter, H.; Schulten, K.

    1990-11-01

    Orientation-selective cells in the striate cortex of higher animals are organized as a hierarchical topographic map of two stimulus features: (i) position in visual space and (ii) orientation. We show that the observed structure of the topographic map can arise from a principle of continuous mapping. For the realization of this principle we use a mathematical model that can be interpreted as an adaptive process changing a set of synaptic weights, or synaptic connection strengths, between two layers of cells. The patterns of orientation preference and selectivity generated by the model are similar to the patterns seen in the visual cortex of macaque monkey and cat and correspond to a neural projection that maps a more than two-dimensional feature space onto a two-dimensional cortical surface under the constraint that shape and position of the receptive fields of the neurons vary smoothly over the cortical surface.

  10. A New Thermodynamic Parameter to Predict Formation of Solid Solution or Intermetallic Phases in High Entropy Alloys (Postprint)

    DTIC Science & Technology

    2015-11-02

    AFRL-RX-WP-JA-2016-0345 A NEW THERMODYNAMIC PARAMETER TO PREDICT FORMATION OF SOLID SOLUTION OR INTERMETALLIC PHASES IN HIGH ENTROPY...Interim 22 September 2014 – 21 September 2015 4. TITLE AND SUBTITLE A NEW THERMODYNAMIC PARAMETER TO PREDICT FORMATION OF SOLID SOLUTION OR...simple thermodynamic criterion is proposed to predict the presence or absence of equilibrium intermetallic phases in a high entropy alloy at a given

  11. Comparing the efficiency of digital and conventional soil mapping to predict soil types in a semi-arid region in Iran

    NASA Astrophysics Data System (ADS)

    Zeraatpisheh, Mojtaba; Ayoubi, Shamsollah; Jafari, Azam; Finke, Peter

    2017-05-01

    The efficiency of different digital and conventional soil mapping approaches to produce categorical maps of soil types is determined by cost, sample size, accuracy and the selected taxonomic level. The efficiency of digital and conventional soil mapping approaches was examined in the semi-arid region of Borujen, central Iran. This research aimed to (i) compare two digital soil mapping approaches including Multinomial logistic regression and random forest, with the conventional soil mapping approach at four soil taxonomic levels (order, suborder, great group and subgroup levels), (ii) validate the predicted soil maps by the same validation data set to determine the best method for producing the soil maps, and (iii) select the best soil taxonomic level by different approaches at three sample sizes (100, 80, and 60 point observations), in two scenarios with and without a geomorphology map as a spatial covariate. In most predicted maps, using both digital soil mapping approaches, the best results were obtained using the combination of terrain attributes and the geomorphology map, although differences between the scenarios with and without the geomorphology map were not significant. Employing the geomorphology map increased map purity and the Kappa index, and led to a decrease in the 'noisiness' of soil maps. Multinomial logistic regression had better performance at higher taxonomic levels (order and suborder levels); however, random forest showed better performance at lower taxonomic levels (great group and subgroup levels). Multinomial logistic regression was less sensitive than random forest to a decrease in the number of training observations. The conventional soil mapping method produced a map with larger minimum polygon size because of traditional cartographic criteria used to make the geological map 1:100,000 (on which the conventional soil mapping map was largely based). Likewise, conventional soil mapping map had also a larger average polygon size that resulted

  12. Event-related potentials during word mapping to object shape predict toddlers' vocabulary size

    PubMed Central

    Borgström, Kristina; Torkildsen, Janne von Koss; Lindgren, Magnus

    2015-01-01

    What role does attention to different object properties play in early vocabulary development? This longitudinal study using event-related potentials in combination with behavioral measures investigated 20- and 24-month-olds' (n = 38; n = 34; overlapping n = 24) ability to use object shape and object part information in word-object mapping. The N400 component was used to measure semantic priming by images containing shape or detail information. At 20 months, the N400 to words primed by object shape varied in topography and amplitude depending on vocabulary size, and these differences predicted productive vocabulary size at 24 months. At 24 months, when most of the children had vocabularies of several hundred words, the relation between vocabulary size and the N400 effect in a shape context was weaker. Detached object parts did not function as word primes regardless of age or vocabulary size, although the part-objects were identified behaviorally. The behavioral measure, however, also showed relatively poor recognition of the part-objects compared to the shape-objects. These three findings provide new support for the link between shape recognition and early vocabulary development. PMID:25762957

  13. Applying Kohonen self-organizing map as a software sensor to predict biochemical oxygen demand.

    PubMed

    Rustum, Rabee; Adeloye, Adebayo J; Scholz, Miklas

    2008-01-01

    The 5 days at 20 degrees C biochemical oxygen demand (BOD5) is an important parameter for monitoring organic pollution in water and assessing the biotreatability of wastewater. Moreover, BOD5 is used for wastewater treatment plant discharge consents and other water pollution control purposes. However, the traditional bioassay method for estimating the BOD5 involves the incubation of sample water for 5 days. It follows that BOD5 is not available for real-time decisionmaking and process control purposes. On the other hand, previous efforts to solve this problem by developing more rapid biosensors had limited success. This paper reports on the development of Kohonen self-organizing map (KSOM)-based software sensors for the rapid prediction of BOD5. The findings indicate that the KSOM-based BOD5 estimates were in good agreement with those measured using the conventional bioassay method. This offers significant potential for more timely intervention and cost savings during problem diagnosis in water and wastewater treatment processes.

  14. Mapping and prediction of Coal Workers' Pneumoconiosis with bioavailable iron content in the bituminous coals

    USGS Publications Warehouse

    Huang, X.; Li, W.; Attfield, M.D.; Nadas, A.; Frenkel, K.; Finkelman, R.B.

    2005-01-01

    Based on the first National Study of Coal Workers' Pneumoconiosis (CWP) and the U.S. Geological Survey database of coal quality, we show that the prevalence of CWP in seven coal mine regions correlates with levels of bioavailable iron (BAI) in the coals from that particular region (correlation coefficient r = 0.94, p < 0.0015). CWP prevalence is also correlated with contents of pyritic sulfur (r = 0.91, p < 0.0048) or total iron (r = 0.85, p < 0.016) but not with coal rank (r = 0.59, p < 0.16) or silica (r = 0.28, p < 0.54). BAI was calculated using our model, taking into account chemical interactions of pyrite, sulfuric acid, calcite, and total iron. That is, iron present in coals can become bioavailable by pyrite oxidation, which produces ferrous sulfate and sulfuric acid. Calcite is the major component in coals that neutralizes the available acid and inhibits iron's bioavailabiity. Therefore, levels of BAI in the coals are determined by the available amounts of acid after neutralization of calcite and the amount of total iron in the coals. Using the linear fit of CWP prevalence and the calculated BAI in the seven coal mine regions, we have derived and mapped the pneumoconiotic potencies of 7,000 coal samples. Our studies indicate that levels of BAI in the coals may be used to predict coal's toxicity, even before large-scalen mining.

  15. Mapping and prediction of coal workers' pneumoconiosis with bioavailable iron content in the bituminous coals

    SciTech Connect

    Huang, X.; Li, W.H.; Attfield, M.D.; Nadas, A.; Frenkel, K.; Finkelman, R.B.

    2005-08-01

    Based on the first National Study of Coal Workers' Pneumoconiosis (CWP) and the U.S. Geological Survey database of coal quality, we show that the prevalence of CXXT in seven coal mine regions correlates with levels of bioavailable iron (BAI) in the coals from that particular region (correlation coefficient r = 0.94, p {lt} 0.0015). CWP prevalence is also correlated with contents of pyritic sulfur (r = 0.91, p {lt} 0.0048) or total iron (r = 0.85, p {lt} 0.016) but not with coal rank (r = 0.59, p {lt} 0.16) or silica (r = 0.28, p {lt} 0.54). BAI was calculated using our model, taking into account chemical interactions of pyrite, sulfuric acid, calcite, and total iron. That is, iron present in coals can become bioavailable by pyrite oxidation, which produces ferrous sulfate and sulfuric acid. Calcite is the major component in coals that neutralizes the available acid and inhibits iron's bioavailability. Therefore, levels of BAI in the coals are determined by the available amounts of acid after neutralization of calcite and the amount of total iron in the coals. Using the linear fit of CWP prevalence and the calculated BAI in the seven coal mine regions, we have derived and mapped the pneumoconiotic potencies of 7,000 coal samples. Our studies indicate that levels of BAI in the coals may be used to predict coal's toxicity, even before large-scale mining.

  16. Using self-organizing maps to determine observation threshold limit predictions in highly variant data

    USGS Publications Warehouse

    Paganoni, C.A.; Chang, K.C.; Robblee, M.B.

    2006-01-01

    A significant data quality challenge for highly variant systems surrounds the limited ability to quantify operationally reasonable limits on the data elements being collected and provide reasonable threshold predictions. In many instances, the number of influences that drive a resulting value or operational range is too large to enable physical sampling for each influencer, or is too complicated to accurately model in an explicit simulation. An alternative method to determine reasonable observation thresholds is to employ an automation algorithm that would emulate a human analyst visually inspecting data for limits. Using the visualization technique of self-organizing maps (SOM) on data having poorly understood relationships, a methodology for determining threshold limits was developed. To illustrate this approach, analysis of environmental influences that drive the abundance of a target indicator species (the pink shrimp, Farfantepenaeus duorarum) provided a real example of applicability. The relationship between salinity and temperature and abundance of F. duorarum is well documented, but the effect of changes in water quality upstream on pink shrimp abundance is not well understood. The highly variant nature surrounding catch of a specific number of organisms in the wild, and the data available from up-stream hydrology measures for salinity and temperature, made this an ideal candidate for the approach to provide a determination about the influence of changes in hydrology on populations of organisms.

  17. Mapping and Prediction of Coal Workers’ Pneumoconiosis with Bioavailable Iron Content in the Bituminous Coals

    PubMed Central

    Huang, Xi; Li, Weihong; Attfield, Michael D.; Nádas, Arthur; Frenkel, Krystyna; Finkelman, Robert B.

    2005-01-01

    Based on the first National Study of Coal Workers’ Pneumoconiosis (CWP) and the U.S. Geological Survey database of coal quality, we show that the prevalence of CWP in seven coal mine regions correlates with levels of bioavailable iron (BAI) in the coals from that particular region (correlation coefficient r = 0.94, p < 0.0015). CWP prevalence is also correlated with contents of pyritic sulfur (r = 0.91, p < 0.0048) or total iron (r = 0.85, p < 0.016) but not with coal rank (r = 0.59, p < 0.16) or silica (r = 0.28, p < 0.54). BAI was calculated using our model, taking into account chemical interactions of pyrite, sulfuric acid, calcite, and total iron. That is, iron present in coals can become bioavailable by pyrite oxidation, which produces ferrous sulfate and sulfuric acid. Calcite is the major component in coals that neutralizes the available acid and inhibits iron’s bioavailability. Therefore, levels of BAI in the coals are determined by the available amounts of acid after neutralization of calcite and the amount of total iron in the coals. Using the linear fit of CWP prevalence and the calculated BAI in the seven coal mine regions, we have derived and mapped the pneumoconiotic potencies of 7,000 coal samples. Our studies indicate that levels of BAI in the coals may be used to predict coal’s toxicity, even before large-scale mining. PMID:16079064

  18. Using self-organizing maps to determine observation threshold limit predictions in highly variant data

    NASA Astrophysics Data System (ADS)

    Paganoni, Christopher A.; Chang, K. C.; Robblee, Michael B.

    2006-05-01

    A significant data quality challenge for highly variant systems surrounds the limited ability to quantify operationally reasonable limits on the data elements being collected and provide reasonable threshold predictions. In many instances, the number of influences that drive a resulting value or operational range is too large to enable physical sampling for each influencer, or is too complicated to accurately model in an explicit simulation. An alternative method to determine reasonable observation thresholds is to employ an automation algorithm that would emulate a human analyst visually inspecting data for limits. Using the visualization technique of self-organizing maps (SOM) on data having poorly understood relationships, a methodology for determining threshold limits was developed. To illustrate this approach, analysis of environmental influences that drive the abundance of a target indicator species (the pink shrimp, Farfantepenaeus duorarum) provided a real example of applicability. The relationship between salinity and temperature and abundance of F. duorarum is well documented, but the effect of changes in water quality upstream on pink shrimp abundance is not well understood. The highly variant nature surrounding catch of a specific number of organisms in the wild, and the data available from up-stream hydrology measures for salinity and temperature, made this an ideal candidate for the approach to provide a determination about the influence of changes in hydrology on populations of organisms.

  19. Improved predictive mapping of indoor radon concentrations using ensemble regression trees based on automatic clustering of geological units.

    PubMed

    Kropat, Georg; Bochud, Francois; Jaboyedoff, Michel; Laedermann, Jean-Pascal; Murith, Christophe; Palacios Gruson, Martha; Baechler, Sébastien

    2015-09-01

    According to estimations around 230 people die as a result of radon exposure in Switzerland. This public health concern makes reliable indoor radon prediction and mapping methods necessary in order to improve risk communication to the public. The aim of this study was to develop an automated method to classify lithological units according to their radon characteristics and to develop mapping and predictive tools in order to improve local radon prediction. About 240 000 indoor radon concentration (IRC) measurements in about 150 000 buildings were available for our analysis. The automated classification of lithological units was based on k-medoids clustering via pair-wise Kolmogorov distances between IRC distributions of lithological units. For IRC mapping and prediction we used random forests and Bayesian additive regression trees (BART). The automated classification groups lithological units well in terms of their IRC characteristics. Especially the IRC differences in metamorphic rocks like gneiss are well revealed by this method. The maps produced by random forests soundly represent the regional difference of IRCs in Switzerland and improve the spatial detail compared to existing approaches. We could explain 33% of the variations in IRC data with random forests. Additionally, the influence of a variable evaluated by random forests shows that building characteristics are less important predictors for IRCs than spatial/geological influences. BART could explain 29% of IRC variability and produced maps that indicate the prediction uncertainty. Ensemble regression trees are a powerful tool to model and understand the multidimensional influences on IRCs. Automatic clustering of lithological units complements this method by facilitating the interpretation of radon properties of rock types. This study provides an important element for radon risk communication. Future approaches should consider taking into account further variables like soil gas radon measurements as

  20. First USGS urban seismic hazard maps predict the effects of soils

    USGS Publications Warehouse

    Cramer, C.H.; Gomberg, J.S.; Schweig, E.S.; Waldron, B.A.; Tucker, K.

    2006-01-01

    Probabilistic and scenario urban seismic hazard maps have been produced for Memphis, Shelby County, Tennessee covering a six-quadrangle area of the city. The nine probabilistic maps are for peak ground acceleration and 0.2 s and 1.0 s spectral acceleration and for 10%, 5%, and 2% probability of being exceeded in 50 years. Six scenario maps for these three ground motions have also been generated for both an M7.7 and M6.2 on the southwest arm of the New Madrid seismic zone ending at Marked Tree, Arkansas. All maps include the effect of local geology. Relative to the national seismic hazard maps, the effect of the thick sediments beneath Memphis is to decrease 0.2 s probabilistic ground motions by 0-30% and increase 1.0 s probabilistic ground motions by ???100%. Probabilistic peak ground accelerations remain at levels similar to the national maps, although the ground motion gradient across Shelby County is reduced and ground motions are more uniform within the county. The M7.7 scenario maps show ground motions similar to the 5%-in-50-year probabilistic maps. As an effect of local geology, both M7.7 and M6.2 scenario maps show a more uniform seismic ground-motion hazard across Shelby County than scenario maps with constant site conditions (i.e., NEHRP B/C boundary).

  1. The GIS layers of the "International Hydrogeological Map of Europe 1:1,500,000" in a vector format

    NASA Astrophysics Data System (ADS)

    Duscher, Klaus; Günther, Andreas; Richts, Andrea; Clos, Patrick; Philipp, Uta; Struckmeier, Wilhelm

    2015-12-01

    The map series of the International Hydrogeological Map of Europe at a scale of 1:1,500,000 (IHME1500) has been completed by the publication of the last two map sheets in August 2013. Altogether, the 25 sheets of the IHME1500 provide the first coherent overview of groundwater resources in Europe. The map displays productivity and lithology of potential aquifer systems. Some of the additional map contents relating to groundwater are presented only regionally. The most relevant features of IHME1500 are compiled in two seamless geographic information system (GIS) layers in shapefile format: (1) showing groundwater resources characterised by a basic aquifer typology, including a lithological description and areas of seawater intrusion, and (2) reproducing major tectonic fractures. The superficial lithology information was harmonised by implementing a lithological taxonomy and a multi-step aggregation. An enhancement of the GIS layers is envisaged through the release of updates, which will be distinguished by consecutive version numbers. The continent-wide harmonised presentation of contents constitutes the main feature of the IHME1500 GIS layers. This qualifies the spatial dataset as a basic tool for hydrogeological assessments aiming primarily at transboundary issues. Map scale and the manufacture date of the analogue base impose restrictions on the application of the IHME1500 vector data. A set of examples describes the initial use of the GIS layers in research projects and illustrates potential fields of application. The IHME1500 lithology layer establishes a spatial dataset suitable for the continent-wide evaluation of geological surface processes like the susceptibility to landslides.

  2. Predictive Malaria Risk and Uncertainty Mapping in Nchelenge District, Zambia: Evidence of Widespread, Persistent Risk and Implications for Targeted Interventions

    PubMed Central

    Pinchoff, Jessie; Chaponda, Mike; Shields, Timothy; Lupiya, James; Kobayashi, Tamaki; Mulenga, Modest; Moss, William J.; Curriero, Frank C.

    2015-01-01

    Malaria risk maps may be used to guide policy decisions on whether vector control interventions should be targeted and, if so, where. Active surveillance for malaria was conducted through household surveys in Nchelenge District, Zambia from April 2012 through December 2014. Households were enumerated based on satellite imagery and randomly selected for study enrollment. At each visit, participants were administered a questionnaire and a malaria rapid diagnostic test (RDT). Logistic regression models were used to construct spatial prediction risk maps and maps of risk uncertainty. A total of 461 households were visited, comprising 1,725 participants, of whom 48% were RDT positive. Several environmental features were associated with increased household malaria risk in a multivariable logistic regression model adjusting for seasonal variation. The model was validated using both internal and external evaluation measures to generate and assess root mean square error, as well as sensitivity and specificity for predicted risk. The final, validated model was used to predict and map malaria risk including a measure of risk uncertainty. Malaria risk in a high, perennial transmission setting is widespread but heterogeneous at a local scale, with seasonal variation. Targeting malaria control interventions may not be appropriate in this epidemiological setting. PMID:26416106

  3. Predictive Malaria Risk and Uncertainty Mapping in Nchelenge District, Zambia: Evidence of Widespread, Persistent Risk and Implications for Targeted Interventions.

    PubMed

    Pinchoff, Jessie; Chaponda, Mike; Shields, Timothy; Lupiya, James; Kobayashi, Tamaki; Mulenga, Modest; Moss, William J; Curriero, Frank C

    2015-12-01

    Malaria risk maps may be used to guide policy decisions on whether vector control interventions should be targeted and, if so, where. Active surveillance for malaria was conducted through household surveys in Nchelenge District, Zambia from April 2012 through December 2014. Households were enumerated based on satellite imagery and randomly selected for study enrollment. At each visit, participants were administered a questionnaire and a malaria rapid diagnostic test (RDT). Logistic regression models were used to construct spatial prediction risk maps and maps of risk uncertainty. A total of 461 households were visited, comprising 1,725 participants, of whom 48% were RDT positive. Several environmental features were associated with increased household malaria risk in a multivariable logistic regression model adjusting for seasonal variation. The model was validated using both internal and external evaluation measures to generate and assess root mean square error, as well as sensitivity and specificity for predicted risk. The final, validated model was used to predict and map malaria risk including a measure of risk uncertainty. Malaria risk in a high, perennial transmission setting is widespread but heterogeneous at a local scale, with seasonal variation. Targeting malaria control interventions may not be appropriate in this epidemiological setting. © The American Society of Tropical Medicine and Hygiene.

  4. Subpixel mapping on remote sensing imagery using a prediction model combining wavelet transform and radial basis function neural network

    NASA Astrophysics Data System (ADS)

    Dai, Xiaoyan; Guo, Zhongyang; Zhang, Liquan; Xu, Wencheng

    2009-12-01

    Soft classification methods can be used for mixed-pixel classification on remote sensing imagery by estimating different land cover class fractions of every pixel. However, the spatial distribution and location of these class components within the pixel remain unknown. To map land cover at subpixel scale and increase the spatial resolution of land cover classification maps, in this paper, a prediction model combining wavelet transform and Radial Basis Functions (RBF) neural network, abbreviated as Wavelet-RBFNN, is constructed by predicting high-frequency wavelet coefficients from low-frequency coefficients at the same resolution with RBF network and taking wavelet coefficients at coarser resolution as training samples. According to different land cover class fraction images obtained from mixed-pixel classification, based on the assumption of neighborhood dependence of wavelet coefficients, subpixel mapping on remote sensing imagery can be accomplished through two steps, i.e., prediction of land cover class compositions within subpixels and hard classification. The experimental results obtained with artificial images, QuickBird image and Landsat 7 ETM+ image indicate that the subpixel mapping method proposed in this paper can successfully produce super-resolution land cover classification maps from remote sensing imagery, outperforming cubic B-spline and Kriging interpolation method in visual effect and prediction accuracy. The Wavelet-RBFNN model can also be applied to simulate higher spatial resolution image, and automatically identify and locate land cover targets at the subpixel scales, when the cost and availability of high resolution imagery prohibit its use in many areas of work.

  5. Prediction of Optimal Folding Routes of Proteins That Satisfy the Principle of Lowest Entropy Loss: Dynamic Contact Maps and Optimal Control

    PubMed Central

    Arkun, Yaman; Erman, Burak

    2010-01-01

    An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of events during folding. We assume that the native state is available. As the protein folds, it makes different set of contacts at different folding steps. The dynamic contact map is constructed from these contacts. The topology of the dynamic contact map changes during the course of folding and this information is utilized in the dynamic optimization model. The solution is obtained using the optimal control theory. We show that the optimal solution can be cast into the form of a Gaussian Network that governs the optimal folding dynamics. Simulation results on three examples (CI2, Sso7d and Villin) show that folding starts by the formation of local clusters. Non-local clusters generally require the formation of several local clusters. Non-local clusters form cooperatively and not sequentially. We also observe that the optimal controller prefers “zipping” or small loop closure steps during folding. The folding routes predicted by the proposed method bear strong resemblance to the results in the literature. PMID:20967269

  6. Prediction of optimal folding routes of proteins that satisfy the principle of lowest entropy loss: dynamic contact maps and optimal control.

    PubMed

    Arkun, Yaman; Erman, Burak

    2010-10-12

    An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of events during folding. We assume that the native state is available. As the protein folds, it makes different set of contacts at different folding steps. The dynamic contact map is constructed from these contacts. The topology of the dynamic contact map changes during the course of folding and this information is utilized in the dynamic optimization model. The solution is obtained using the optimal control theory. We show that the optimal solution can be cast into the form of a Gaussian Network that governs the optimal folding dynamics. Simulation results on three examples (CI2, Sso7d and Villin) show that folding starts by the formation of local clusters. Non-local clusters generally require the formation of several local clusters. Non-local clusters form cooperatively and not sequentially. We also observe that the optimal controller prefers "zipping" or small loop closure steps during folding. The folding routes predicted by the proposed method bear strong resemblance to the results in the literature.

  7. Predicting brittle zones in the Bakken Formation using well logs and seismic data

    NASA Astrophysics Data System (ADS)

    Beecher, Michael E.

    The oil-in-place estimate for the Bakken Formation has varied from 10 billion barrels in 1974 to 503 billion barrels in 1999. However, only a small fraction of this estimate is recoverable due to the formation having very low porosity and permeability. Implementation of hydraulic fracture stages along horizontal wells in the Bakken has been productive. Recently, identification of zones where the formation is brittle has been used to improve hydraulic fracture stimulation efficiency in an effort to improve production. The first goal for this thesis is to identify a correlation between brittleness and production data by using elastic moduli and normalized production values. The hypothesis for this study is that rock with a low Poisson's ratio and high Young's modulus will be more brittle and will ultimately produce a higher amount of oil than more ductile rock. The next goal was to create and test a method to identify brittle zones with high normalized production in a 3D seismic data set without well control using producing wells from outside the survey with dipole sonic logs from the Bakken Formation. Correlations between normalized production values and elastic moduli were subsequently identified. Cumulative first-four-months' production was found to have the best correlation to the elastic moduli. Correlations of normalized production values and Poisson's ratio showed that sections of the middle Bakken with low Poisson's ratio yield higher normalized production values. Correlations of Young's modulus and normalized production showed that middle Bakken zones with low Young's modulus have higher normalized production values. However, when using additional wells that were not used for well-to-3D seismic correlations, the correlation shows that higher Young's modulus yield higher normalized production. The correlation with additional wells best represented the data and agrees with the initial hypothesis. Brittle zones were mapped in a 3D seismic data set by

  8. The Use of Learning Map Systems to Support the Formative Assessment in Mathematics

    ERIC Educational Resources Information Center

    Kingston, Neal M.; Broaddus, Angela

    2017-01-01

    Despite much theoretical support, meta-analysis of the efficacy of formative assessment does not provide empirical evidence commensurate with expectations. This theoretical study suggests that teachers need a better organizing structure to allow a formative assessment process to live up to its promise. We propose that the use of learning map…

  9. Isopach map of the interval from surface elevation to the top of the Pennsylvanian and Permian Minnelusa Formation and equivalents, Powder River basin, Wyoming and Montana

    USGS Publications Warehouse

    Crysdale, B.L.

    1990-01-01

    This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 1,480 of these wells that penetrate the Minnelusa Formation and equivalents.

  10. Map showing contours on the top of the Pennsylvanian and Permian Minnelusa Formation and equivalents, Powder River basin, Wyoming and Montana

    USGS Publications Warehouse

    Crysdale, B.L.

    1990-01-01

    This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 1,480 of these wells that penetrate the Minnelusa Formation and equivalents.

  11. Theoretical predictions of hydrolysis and complex formation of the heaviest elements

    NASA Astrophysics Data System (ADS)

    Pershina, V.

    2000-07-01

    In the presentation, investigations of hydrolysis and complex formation of group 4, 5 and 6 elements, including the transactinide elements 104, 105 and 106 are described. They were carried out on the basis of results of relativistic calculations of the electronic structure of various hydrated, hydrolyzed and complex compounds of these elements using the fully relativistic ab initio density functional method with the GGA approximation for the exchange-correlation potential. Predictions of equilibria of hydrolysis or complex formation reactions have been made using a model which enables determination of free energy changes of the reactions as changes in the ionic and covalent contributions to the binding molecular energy separately. Those contributions were calculated using the Mulliken analysis of the electronic density distribution.

  12. Prediction of subsidence: Relationship between lowering of formation pressure and subsidence due to fluid withdrawal

    SciTech Connect

    Serebryakov, V.A.; Chilingar, G.V.

    2000-06-01

    Abnormally low formation pressures develop in petroleum reservoirs during intensive oil and gas production or in aquifers as a result of water extraction. A simple method is presented for calculating (predicting) the amount of compaction (and resulting subsidence) from the pressure drop in formation due to production, i.e., the increase in the effective pressure p{sub e} (p{sub e} = p{sub t} {minus} p{sub p}, where p{sub t} is the total overburden pressure and p{sub p} is the fluid or pore pressure). This work is based on extensive data collected in Russia. For example, large petroliferous areas in Western Siberia became marshlands as a result of fluid withdrawal. One should remember that sophisticated methods, such as FSMT (direct measurement of rock compaction by wireline tools in situ) and GPS (measurement of surface subsidence by satellite microwave Doppler techniques), are not yet available in many areas of the world.

  13. Predictions on the application of the Hanle effect to map the surface magnetic field of Jupiter

    NASA Astrophysics Data System (ADS)

    Ben-Jaffel, L.; Harris, W.; Bommier, V.; Roesler, F.; Ballester, G. E.; Jossang, J.

    2005-11-01

    In this paper we evaluate the possibility of detecting, for the first time, the surface magnetic field of Jupiter (˜1 bar level) by observing the change of linear polarization induced by the Hanle effect on the H Lyman-alpha (Ly α) emission line of the planet. We find that, indeed, the Hanle effect, which results from the interaction between a local magnetic field and the atomic polarization induced by absorption of anisotropic radiation, is sensitive to relatively weak values of the strength of the magnetic fields expected on planets. First, we show that for the Ly α emission backscattered by atomic H in the presence of a magnetic field, the Hanle effect is polarizing. This new result is in total contrast to the depolarizing effect predicted and observed for emission lines scattered at right angles in solar prominences. Additionally, to estimate the polarization rate for the case of Jupiter, we have considered three magnetic field models: a dipole field for reference, an O based model [Connerney, J.E.P., 1981. The magnetic field of Jupiter—A generalized inverse approach. J. Geophys. Res. 86, 7679-7693], and finally, an O based model [Khurana, K.K., 1997. Euler potential models of Jupiter's magnetospheric field. J. Geophys. Res. 102, 11295-11306]. In all models, we show that for the jovian backscattered Ly α line, the Hanle effect does enhance the Ly α linear polarization; the polarization rate may exceed 2% at specific regions of the jovian disc, making detection possible either remotely or from an orbiter around Jupiter. In general, depending on the instrumental sensitivity and the observing strategy used, we show that accurate mapping of the linear polarization rate at the planetary surface (thermosphere) or off-disc (corona) may provide a rather accurate estimate of the jovian total magnetic field strength on large area scales.

  14. Spatial epidemiological techniques in cholera mapping and analysis towards a local scale predictive modelling

    NASA Astrophysics Data System (ADS)

    Rasam, A. R. A.; Ghazali, R.; Noor, A. M. M.; Mohd, W. M. N. W.; Hamid, J. R. A.; Bazlan, M. J.; Ahmad, N.

    2014-02-01

    Cholera spatial epidemiology is the study of the spread and control of the disease spatial pattern and epidemics. Previous studies have shown that multi-factorial causation such as human behaviour, ecology and other infectious risk factors influence the disease outbreaks. Thus, understanding spatial pattern and possible interrelationship factors of the outbreaks are crucial to be explored an in-depth study. This study focuses on the integration of geographical information system (GIS) and epidemiological techniques in exploratory analyzing the cholera spatial pattern and distribution in the selected district of Sabah. Spatial Statistic and Pattern tools in ArcGIS and Microsoft Excel software were utilized to map and analyze the reported cholera cases and other data used. Meanwhile, cohort study in epidemiological technique was applied to investigate multiple outcomes of the disease exposure. The general spatial pattern of cholera was highly clustered showed the disease spread easily at a place or person to others especially 1500 meters from the infected person and locations. Although the cholera outbreaks in the districts are not critical, it could be endemic at the crowded areas, unhygienic environment, and close to contaminated water. It was also strongly believed that the coastal water of the study areas has possible relationship with the cholera transmission and phytoplankton bloom since the areas recorded higher cases. GIS demonstrates a vital spatial epidemiological technique in determining the distribution pattern and elucidating the hypotheses generating of the disease. The next research would be applying some advanced geo-analysis methods and other disease risk factors for producing a significant a local scale predictive risk model of the disease in Malaysia.

  15. Predictive maps for stochastic nonaffine stiffening and damage in fibrous networks.

    PubMed

    Abhilash, A S; Zhang, Liang; Stiefel, Judah; Purohit, Prashant K; Joshi, Shailendra P

    2014-02-01

    The macroscopic responses of synthetic and natural filamentous networks are determined by a combination of microstructure and filament properties. Biofilament networks such as those of actin and fibrin have become vehicles for studying important concepts in mechanics such as rigidity percolation, linearity and nonlinearity, isotropy and anisotropy, affinity and nonaffinity, hardening and softening, bending and stretching transitions, etc. In this work, we consider generic fibrous network architectures to map out their mechanical responses over a wide range of filament properties. Using the finite element method, we perform two-dimensional simulations of discrete networks subjected to shear deformation. These simulations encompass stochastic effects arising from network topology (filament arrangement, orientation, and length distribution) and the thermally activated crosslink scission. We study the mechanics of these random networks up to a strain of 10%, including damage that is induced by crosslink scission. The response is nonlinear and the initial elastic modulus alone is not sufficient to give an understanding about the overall response. We show that the nonlinear elastic response of the network can be captured using a few parameters that depend on some well known length scales in network mechanics. For networks with filament density above the rigidity percolation threshold, by increasing filament density and bending stiffness, we observe a crossover from the bending dominated elastically compliant stiffening regime to a stretching dominated rigid nonstiffening regime. We show that in the bending dominated regime there are large deviations from the predictions of affine continuum theories. We also give a simple qualitative model for describing the contours of the incubation strain which marks the onset of damage in networks.

  16. A thermodynamic prediction for microporosity formation in aluminum-rich Al-Cu alloys

    NASA Technical Reports Server (NTRS)

    Poirier, D. R.; Yeum, K.; Maples, A. L.

    1987-01-01

    A computer model is used to predict the formation and degree of microporosity in a directionally solidified Al-4.5 wt pct Cu alloy, considering the interplay between solidification shrinkage and gas porosity. Macrosegregation theory is used to determine the local pressure within the interdendritic liquid. Results show interdendritic porosity for initial hydrogen contents in the 0.03-1 ppm range, and none below contents of 0.03. An increase in either the thermal gradient or the solidification rate is show to decrease the amount of interdendritic porosity.

  17. Novel methods for predicting gas-particle partitioning during the formation of secondary organic aerosol

    NASA Astrophysics Data System (ADS)

    Wania, F.; Lei, Y. D.; Wang, C.; Abbatt, J. P. D.; Goss, K.-U.

    2014-12-01

    Several methods have been presented in the literature to predict an organic chemical's equilibrium partitioning between the water insoluble organic matter (WIOM) component of aerosol and the gas phase, Ki,WIOM, as a function of temperature. They include (i) polyparameter linear free energy relationships calibrated with empirical aerosol sorption data, as well as (ii) the solvation models implemented in SPARC and (iii) the quantum-chemical software COSMOtherm, which predict solvation equilibria from molecular structure alone. We demonstrate that these methods can be used to predict Ki,WIOM for large numbers of individual molecules implicated in secondary organic aerosol (SOA) formation, including those with multiple functional groups. Although very different in their theoretical foundations, these methods give remarkably consistent results for the products of the reaction of normal alkanes with OH, i.e. their partition coefficients Ki,WIOM generally agree within one order of magnitude over a range of more than ten orders of magnitude. This level of agreement is much better than that achieved by different vapour pressure estimation methods that are more commonly used in the SOA community. Also, in contrast to the agreement between vapour pressure estimates, the agreement between the Ki,WIOM estimates does not deteriorate with increasing number of functional groups. Furthermore, these partitioning coefficients Ki,WIOM predicted SOA mass yields in agreement with those measured in chamber experiments of the oxidation of normal alkanes. If a Ki,WIOM prediction method was based on one or more surrogate molecules representing the solvation properties of the mixed OM phase of SOA, the choice of those molecule(s) was found to have a relatively minor effect on the predicted Ki,WIOM, as long as the molecule(s) are not very polar. This suggests that a single surrogate molecule, such as 1-octanol or a hypothetical SOA structure proposed by Kalberer et al. (2004), may often be

  18. Novel methods for predicting gas-particle partitioning during the formation of secondary organic aerosol

    NASA Astrophysics Data System (ADS)

    Wania, F.; Lei, Y. D.; Wang, C.; Abbatt, J. P. D.; Goss, K.-U.

    2014-08-01

    Several methods have been presented in the literature to predict an organic chemical's equilibrium partitioning between the water insoluble organic matter (WIOM) component of aerosol and the gas phase, Ki, WIOM as a function of temperature. They include (i) polyparameter linear free energy relationships calibrated with empirical aerosol sorption data, as well as (ii) the solvation models implemented in SPARC and (iii) the quantum-chemical software Cosmotherm, which predict solvation equilibria from molecular structure alone. We demonstrate that these methods can be used to predict Ki, WIOM for large numbers of individual molecules implicated in secondary organic aerosol (SOA) formation, including those with multiple functional groups. Although very different in their theoretical foundations, these methods give remarkably consistent results for the products of the reaction of normal alkanes with OH, i.e. their partition coefficients Ki, WIOM generally agree within one order of magnitude over a range of more than ten orders of magnitude. This level of agreement is much better than that achieved by different vapour pressure estimation methods that are more commonly used in the SOA community. Also, in contrast to the agreement between vapour pressure estimates, that between the Ki, WIOM estimates does not deteriorate with increasing number of functional groups. Furthermore, these partitioning coefficients Ki, WIOM are found to predict the SOA mass yield in chamber experiments of the oxidation of normal alkanes as good or better than a vapour pressure based method. If a Ki, WIOM prediction method was based on one or more surrogate molecules representing the solvation properties of the mixed OM phase of SOA, the choice of those molecule(s) was found to have a relatively minor effect on the predicted Ki, WIOM, as long as the molecule(s) are not very polar. This suggests that a single surrogate molecule, such as 1-octanol or a hypothetical SOA structure proposed by

  19. Prediction of the Shear Wave Velocity from Compressional Wave Velocity for Gachsaran Formation

    NASA Astrophysics Data System (ADS)

    Parvizi, Saeed; Kharrat, Riyaz; Asef, Mohammad R.; Jahangiry, Bijan; Hashemi, Abdolnabi

    2015-10-01

    Shear and compressional wave velocities, coupled with other petrophysical data, are very important for hydrocarbon reservoir characterization. In situ shear wave velocity ( Vs) is measured by some sonic logging tools. Shear velocity coupled with compressional velocity is vitally important in determining geomechanical parameters, identifying the lithology, mud weight design, hydraulic fracturing, geophysical studies such as VSP, etc. In this paper, a correlation between compressional and shear wave velocity is obtained for Gachsaran formation in Maroon oil field. Real data were used to examine the accuracy of the prediction equation. Moreover, the genetic algorithm was used to obtain the optimal value for constants of the suggested equation. Furthermore, artificial neural network was used to inspect the reliability of this method. These investigations verify the notion that the suggested equation could be considered as an efficient, fast, and cost-effective method for predicting Vs from Vp.

  20. Criteria for predicting the formation of single-phase high-entropy alloys

    DOE PAGES

    Troparevsky, M Claudia; Morris, James R..; Kent, Paul R.; ...

    2015-03-15

    High entropy alloys constitute a new class of materials whose very existence poses fundamental questions. Originally thought to be stabilized by the large entropy of mixing, these alloys have attracted attention due to their potential applications, yet no model capable of robustly predicting which combinations of elements will form a single-phase currently exists. Here we propose a model that, through the use of high-throughput computation of the enthalpies of formation of binary compounds, is able to confirm all known high-entropy alloys while rejecting similar alloys that are known to form multiple phases. Despite the increasing entropy, our model predicts thatmore » the number of potential single-phase multicomponent alloys decreases with an increasing number of components: out of more than two million possible 7-component alloys considered, fewer than twenty single-phase alloys are likely.« less

  1. A bridge-functional-based classical mapping method for predicting the correlation functions of uniform electron gases at finite temperature

    SciTech Connect

    Liu, Yu; Wu, Jianzhong

    2014-02-28

    Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.

  2. Prediction of Vehicle Mobility on Large-Scale Soft-Soil Terrain Maps Using Physics-Based Simulation

    DTIC Science & Technology

    2016-08-04

    SOFT-SOIL TERRAIN MAPS USING PHYSICS -BASED SIMULATION Tamer Wasfy*, Paramsothy Jayakumar**, Dave Mechergui**, and Srinivas Sanikommu** *Advanced...relations used in NRMM. The objective of this paper is to present a high-fidelity physics -based approach to accurately and reliably predict the vehicle...suitable for mud and snow type materials. Then the governing equations of motion of both the vehicle and the soil particles are solved along with joint

  3. Keratometry obtained by corneal mapping versus the IOLMaster in the prediction of postoperative refraction in routine cataract surgery.

    PubMed

    Dulku, Simon; Smith, Henry B; Antcliff, Richard J

    2013-01-01

    To establish whether simulated keratometry values obtained by corneal mapping (videokeratography) would provide a superior refractive outcome to those obtained by Zeiss IOLMaster (partial coherence interferometry) in routine cataract surgery. Prospective, non-randomized, single-surgeon study set at the The Royal United Hospital, Bath, UK, District General Hospital. Thirty-three patients undergoing routine cataract surgery in the absence of significant ocular comorbidity. Conventional biometry was recorded using the Zeiss IOLMaster. Postoperative refraction was calculated using the SRK/T formula and the most appropriate power of lens implanted. Preoperative keratometry values were also obtained using Humphrey Instruments Atlas Version A6 corneal mapping. Achieved refraction was compared with predicted refraction for the two methods of keratometry after the A-constants were optimized to obtain a mean arithmetic error of zero dioptres for each device. The mean absolute prediction error was 0.39 dioptres (standard deviation 0.29) for IOLMaster and 0.48 dioptres (standard deviation 0.31) for corneal mapping (P = 0.0015). Keratometry readings between the devices were highly correlated by Spearman correlation (0.97). The Bland-Altman plot demonstrated close agreement between keratometers, with a bias of 0.0079 dioptres and 95% limits of agreement of -0.48-0.49 dioptres. The IOLMaster was superior to Humphrey Atlas A6 corneal mapping in the prediction of postoperative refraction. This difference could not have been predicted from the keratometry readings alone. When comparing biometry devices, close agreement between readings should not be considered a substitute for actual postoperative refraction data. © 2012 The Authors. Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.

  4. Role of Excessive Autophagy Induced by Mechanical Overload in Vein Graft Neointima Formation: Prediction and Prevention

    NASA Astrophysics Data System (ADS)

    Chang, Ya-Ju; Huang, Hui-Chun; Hsueh, Yuan-Yu; Wang, Shao-Wei; Su, Fong-Chin; Chang, Chih-Han; Tang, Ming-Jer; Li, Yi-Shuan; Wang, Shyh-Hau; Shung, Kirk K.; Chien, Shu; Wu, Chia-Ching

    2016-02-01

    Little is known regarding the interplays between the mechanical and molecular bases for vein graft restenosis. We elucidated the stenosis initiation using a high-frequency ultrasonic (HFU) echogenicity platform and estimated the endothelium yield stress from von-Mises stress computation to predict the damage locations in living rats over time. The venous-arterial transition induced the molecular cascades for autophagy and apoptosis in venous endothelial cells (ECs) to cause neointimal hyperplasia, which correlated with the high echogenicity in HFU images and the large mechanical stress that exceeded the yield strength. The ex vivo perfusion of arterial laminar shear stress to isolated veins further confirmed the correlation. EC damage can be rescued by inhibiting autophagy formation using 3-methyladenine (3-MA). Pretreatment of veins with 3-MA prior to grafting reduced the pathological increases of echogenicity and neointima formation in rats. Therefore, this platform provides non-invasive temporal spatial measurement and prediction of restenosis after venous-arterial transition as well as monitoring the progression of the treatments.

  5. Role of Excessive Autophagy Induced by Mechanical Overload in Vein Graft Neointima Formation: Prediction and Prevention.

    PubMed

    Chang, Ya-Ju; Huang, Hui-Chun; Hsueh, Yuan-Yu; Wang, Shao-Wei; Su, Fong-Chin; Chang, Chih-Han; Tang, Ming-Jer; Li, Yi-Shuan; Wang, Shyh-Hau; Shung, Kirk K; Chien, Shu; Wu, Chia-Ching

    2016-02-26

    Little is known regarding the interplays between the mechanical and molecular bases for vein graft restenosis. We elucidated the stenosis initiation using a high-frequency ultrasonic (HFU) echogenicity platform and estimated the endothelium yield stress from von-Mises stress computation to predict the damage locations in living rats over time. The venous-arterial transition induced the molecular cascades for autophagy and apoptosis in venous endothelial cells (ECs) to cause neointimal hyperplasia, which correlated with the high echogenicity in HFU images and the large mechanical stress that exceeded the yield strength. The ex vivo perfusion of arterial laminar shear stress to isolated veins further confirmed the correlation. EC damage can be rescued by inhibiting autophagy formation using 3-methyladenine (3-MA). Pretreatment of veins with 3-MA prior to grafting reduced the pathological increases of echogenicity and neointima formation in rats. Therefore, this platform provides non-invasive temporal spatial measurement and prediction of restenosis after venous-arterial transition as well as monitoring the progression of the treatments.

  6. Role of Excessive Autophagy Induced by Mechanical Overload in Vein Graft Neointima Formation: Prediction and Prevention

    PubMed Central

    Chang, Ya-Ju; Huang, Hui-Chun; Hsueh, Yuan-Yu; Wang, Shao-Wei; Su, Fong-Chin; Chang, Chih-Han; Tang, Ming-Jer; Li, Yi-Shuan; Wang, Shyh-Hau; Shung, Kirk K.; Chien, Shu; Wu, Chia-Ching

    2016-01-01

    Little is known regarding the interplays between the mechanical and molecular bases for vein graft restenosis. We elucidated the stenosis initiation using a high-frequency ultrasonic (HFU) echogenicity platform and estimated the endothelium yield stress from von-Mises stress computation to predict the damage locations in living rats over time. The venous-arterial transition induced the molecular cascades for autophagy and apoptosis in venous endothelial cells (ECs) to cause neointimal hyperplasia, which correlated with the high echogenicity in HFU images and the large mechanical stress that exceeded the yield strength. The ex vivo perfusion of arterial laminar shear stress to isolated veins further confirmed the correlation. EC damage can be rescued by inhibiting autophagy formation using 3-methyladenine (3-MA). Pretreatment of veins with 3-MA prior to grafting reduced the pathological increases of echogenicity and neointima formation in rats. Therefore, this platform provides non-invasive temporal spatial measurement and prediction of restenosis after venous-arterial transition as well as monitoring the progression of the treatments. PMID:26915560

  7. A global model of thunderstorm electricity and the prediction of whistler duct formation

    SciTech Connect

    Stansbery, E.K.

    1989-01-01

    A two-dimensional numerical model is created to calculate the electric field and current that flow from a thunderstorm source into the global electrical circuit. The model includes a hemisphere in which the thunderstorm is located, an equalization layer, and a passive magnetic conjugate hemisphere. To maintain the fair weather electric field, the output current from the thunderstorm is allowed to spread out in the ionosphere or flow along the magnetic field lines into the conjugate hemisphere. The vertical current is constant up to approximately 65 km, decays and is redirected horizontally in the ionosphere. Approximately half of the current that reaches the ionosphere flows along magnetic field lines into the conjugate hemisphere while the rest is spread out in the ionosphere and redirected to the fair weather portion of the storm hemisphere. Our results show that it is important to include a realistic model of the equalization layer to evaluate the role of thunderstorm charging of the global circuit. The mapping of thunderstorm electric fields at middle and subauroral latitudes into the magnetic equatorial plane is studied. The geomagnetic field lines are assumed to be dipolar above approximately 150 km. The horizontal electric field computed in the ionosphere by our model is of sufficient size and shape for the formation of electron density irregularities in the magnetosphere. The mechanism involves a localized convection of ionization tubes by ExB drift. It is shown that the horizontal range of the electric field disturbance in the ionosphere must be within approximately 160 km to produce density irregularities necessary for the formation of whistler ducts. Although the electric field strength at ionospheric heights depends sensitively on the conductivity profile, the results presented show that whistler duct formation is possible by thunderstorm generated electric fields.*

  8. Modeling and predicting the biofilm formation of Salmonella Virchow with respect to temperature and pH.

    PubMed

    Ariafar, M Nima; Buzrul, Sencer; Akçelik, Nefise

    2016-03-01

    Biofilm formation of Salmonella Virchow was monitored with respect to time at three different temperature (20, 25 and 27.5 °C) and pH (5.2, 5.9 and 6.6) values. As the temperature increased at a constant pH level, biofilm formation decreased while as the pH level increased at a constant temperature, biofilm formation increased. Modified Gompertz equation with high adjusted determination coefficient (Radj(2)) and low mean square error (MSE) values produced reasonable fits for the biofilm formation under all conditions. Parameters of the modified Gompertz equation could be described in terms of temperature and pH by use of a second order polynomial function. In general, as temperature increased maximum biofilm quantity, maximum biofilm formation rate and time of acceleration of biofilm formation decreased; whereas, as pH increased; maximum biofilm quantity, maximum biofilm formation rate and time of acceleration of biofilm formation increased. Two temperature (23 and 26 °C) and pH (5.3 and 6.3) values were used up to 24 h to predict the biofilm formation of S. Virchow. Although the predictions did not perfectly match with the data, reasonable estimates were obtained. In principle, modeling and predicting the biofilm formation of different microorganisms on different surfaces under various conditions could be possible.

  9. The precision of mapping between number words and the approximate number system predicts children's formal math abilities.

    PubMed

    Libertus, Melissa E; Odic, Darko; Feigenson, Lisa; Halberda, Justin

    2016-10-01

    Children can represent number in at least two ways: by using their non-verbal, intuitive approximate number system (ANS) and by using words and symbols to count and represent numbers exactly. Furthermore, by the time they are 5years old, children can map between the ANS and number words, as evidenced by their ability to verbally estimate numbers of items without counting. How does the quality of the mapping between approximate and exact numbers relate to children's math abilities? The role of the ANS-number word mapping in math competence remains controversial for at least two reasons. First, previous work has not examined the relation between verbal estimation and distinct subtypes of math abilities. Second, previous work has not addressed how distinct components of verbal estimation-mapping accuracy and variability-might each relate to math performance. Here, we addressed these gaps by measuring individual differences in ANS precision, verbal number estimation, and formal and informal math abilities in 5- to 7-year-old children. We found that verbal estimation variability, but not estimation accuracy, predicted formal math abilities, even when controlling for age, expressive vocabulary, and ANS precision, and that it mediated the link between ANS precision and overall math ability. These findings suggest that variability in the ANS-number word mapping may be especially important for formal math abilities. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Apolipoprotein M predicts pre-beta-HDL formation: studies in type 2 diabetic and nondiabetic subjects.

    PubMed

    Plomgaard, P; Dullaart, R P F; de Vries, R; Groen, A K; Dahlbäck, B; Nielsen, L B

    2009-09-01

    Studies in mice suggest that plasma apoM is lowered in hyperinsulinaemic diabetes and that apoM stimulates formation of pre-beta-HDL. Pre-beta-HDL is an acceptor of cellular cholesterol and may be critical for reverse cholesterol transport. Herein, we examined whether patients with type 2 diabetes have reduced plasma apoM and whether apoM is associated with pre-beta-HDL formation and cellular cholesterol efflux. In 78 patients with type 2 diabetes and 89 control subjects, we measured plasma apoM with ELISA, pre-beta-HDL and pre-beta-HDL formation, phospholipid transfer protein (PLTP) activity and the ability of plasma to promote cholesterol efflux from cultured fibroblasts. ApoM was approximately 9% lower in patients with type 2 diabetes compared to controls (0.025 +/- 0.006 vs. 0.027 +/- 0.007 g L(-1), P = 0.01). The difference in apoM was largely attributable to diabetes-associated obesity. ApoM was positively related to both HDL (r = 0.16; P = 0.04) and LDL cholesterol (r = 0.28; P = 0.0003). Pre-beta-HDL and pre-beta-HDL formation were not different between diabetic and control subjects. ApoM predicted pre-beta-HDL (r = 0.16; P = 0.04) and pre-beta-HDL formation (r = 0.19; P = 0.02), even independently of positive relationships with apoA-I, HDL-cholesterol and PLTP activity. Cellular cholesterol efflux to plasma was positively related to pre-beta-HDL and PLTP activity but not significantly to apoM. Plasma apoM is modestly reduced in type 2 diabetes. Pre-beta-HDL and pre-beta-HDL formation are positively associated with apoM, supporting the hypothesis that apoM plays a role in HDL remodelling in humans. Lower apoM may provide a mechanism to explain why pre-beta-HDL formation is not increased in type 2 diabetes despite elevated PLTP activity.

  11. A distributed model predictive control (MPC) fault reconfiguration strategy for formation flying satellites

    NASA Astrophysics Data System (ADS)

    Esfahani, N. R.; Khorasani, K.

    2016-05-01

    In this paper, an active distributed (also referred to as semi-decentralised) fault recovery control scheme is proposed that employs inaccurate and unreliable fault information into a model-predictive-control-based design. The objective is to compensate for the identified actuator faults that are subject to uncertainties and detection time delays, in the attitude control subsystems of formation flying satellites. The proposed distributed fault recovery scheme is developed through a two-level hierarchical framework. In the first level, or the agent level, the fault is recovered locally to maintain as much as possible the design specifications, feasibility, and tracking performance of all the agents. In the second level, or the formation level, the recovery is carried out by enhancing the entire team performance. The fault recovery performance of our proposed distributed (semi-decentralised) scheme is compared with two other alternative schemes, namely the centralised and the decentralised fault recovery schemes. It is shown that the distributed (semi-decentralised) fault recovery scheme satisfies the recovery design specifications and also imposes lower fault compensation control effort cost and communication bandwidth requirements as compared to the centralised scheme. Our proposed distributed (semi-decentralised) scheme also outperforms the achievable performance capabilities of the decentralised scheme. Simulation results corresponding to a network of four precision formation flight satellites are also provided to demonstrate and illustrate the advantages of our proposed distributed (semi-decentralised) fault recovery strategy.

  12. Pore pressure prediction and well bore stability analysis in Lower Paleozoic shale formation, N Poland

    NASA Astrophysics Data System (ADS)

    Słota-Valim, Małgorzata

    2017-04-01

    Pore pressure and wellbore stability sometimes pose a serious challenge while drilling, especially through rock formations of reduced strength or through intervals where abnormally high pore pressure was formed. Lack of prediction of pore pressure and lack of wellbore stability analysis introduce an element of uncertainty in selection of drilling fluid density. Too low density of drilling fluid can lead to uncontrolled flow of the reservoir fluid to the wellbore (kicks), washouts and occurrence of cavern like structures called breakouts. On the other hand too high density can lead to formation fracturing and further fluid loss. Therefore wellbore stability loss frequently prolongs the operating time, rising the costs of the drilling and in severe cases may end up well abandons loss. The above mentioned complications can be avoided or greatly reduced by reliable analysis of drilling conditions with the aspects to geomechanical characteristics of drilled rock formations. This study presents the results of analysis of pore pressure performed with the use of commonly used in oil industry methods. The analysis of pore pressure was carried out in almost entire profile of four boreholes drilled through lower Paleozoic shales, deposited in the southern part of the Baltic Basin. In addition wellbore stability analysis was performed in the well with most complete geomechanical input data base. Obtained results helped identifying intervals with elevated pore pressure could pose a risk during drilling operation. Elaborated 1D geomechanical model provides safe mud weight window helping to reduce the instabilities risk and constitute a great tool for geomechanical model validation.

  13. Numerical Model Predictions for Autogenic Fluvial Terrace Formation and Comparison to Natural River Valleys

    NASA Astrophysics Data System (ADS)

    Limaye, A. B. S.; Lamb, M. P.

    2015-12-01

    Terraces cut into bedrock (strath) and sediment (fill-cut) offer key constraints on river evolution over millennial timescales, and are often interpreted to form during phases of increased river vertical incision driven by changes in climate or tectonics. Yet all actively meandering channels evolve their shapes through spatial and temporal changes in lateral erosion rates. Therefore, the sparsest requirement for a meandering river to generate terraces is that the intrinsically unsteady lateral erosion rate be coupled with relief generation by vertical incision, which need not be unsteady. In principle, this basic mechanism for terrace formation by meandering rivers should be possible in all fluvial environments, including for valleys with strath or fill-cut terraces, and may overprint signals from external drivers. We have used a numerical model of a vertically incising, meandering river to identify the age and geometric properties of autogenic terraces. Simulations indicate that autogenic terraces form with a recurrence timescale, set by the rate of relief generation, which may overlap with timescales for climate change. The autogenic terraces also have predictable geometries that can include slope proportional to the ratio of vertical incision rate to lateral erosion rate, pairing, and continuous along-valley extent. We compare these simulation results to data for terrace age and geometry from several well studied natural river valleys that span a wide range in terrace sizes and geometries, rock types, tectonic settings, incision rates, and hypothesized formation mechanisms. In cases, terrace age and geometric properties are consistent with formation by meandering with constant vertical incision rates. These similarities suggest that efforts to distinguish terraces that record signals from climatic and tectonic drivers are best focused on environments where terrace ages and geometries are far different than would be predicted by a constant vertical incision model.

  14. Mapping of independent V3 envelope determinants of human immunodeficiency virus type 1 macrophage tropism and syncytium formation in lymphocytes.

    PubMed Central

    Chesebro, B; Wehrly, K; Nishio, J; Perryman, S

    1996-01-01

    The V3 region of the human immunodeficiency virus type 1 (HIV-1) envelope protein is known to have a major influence on macrophage tropism as well as the ability to cause syncytium formation or fusion in CD4-positive lymphocyte cultures. Using infectious molecular HIV-1 clones, a series of mutant clones was created which allowed detailed mapping of V3 amino acid positions involved in these properties. In these experiments the non-syncytium-inducing phenotype in T cells did not always correlate with macrophage tropism. Macrophage tropism appeared to depend on the presence of certain combinations of amino acids at five specific positions within and just outside of the V3 loop itself, whereas syncytium formation in lymphocytes was influenced by substitution of particular residues at two to four positions within V3. In most cases, different V3 amino acid positions were found to independently influence macrophage tropism and syncytium formation in T cells and position 13 was the only V3 location which appeared to simultaneously influence both macrophage tropism and syncytium formation in lymphocytes. PMID:8971043

  15. Predicting Galaxy Star Formation Rates via the Co-evolution of Galaxies and Halos

    DOE PAGES

    Watson, Douglas F.; Hearin, Andrew P.; Berlind, Andreas A.; ...

    2014-03-06

    In this paper, we test the age matching hypothesis that the star formation rate (SFR) of a galaxy is determined by its dark matter halo formation history, and as such, that more quiescent galaxies reside in older halos. This simple model has been remarkably successful at predicting color-based galaxy statistics at low redshift as measured in the Sloan Digital Sky Survey (SDSS). To further test this method with observations, we present new SDSS measurements of the galaxy two-point correlation function and galaxy-galaxy lensing as a function of stellar mass and SFR, separated into quenched and star forming galaxy samples. Wemore » find that our age matching model is in excellent agreement with these new measurements. We also employ a galaxy group finder and show that our model is able to predict: (1) the relative SFRs of central and satellite galaxies, (2) the SFR-dependence of the radial distribution of satellite galaxy populations within galaxy groups, rich groups, and clusters and their surrounding larger scale environments, and (3) the interesting feature that the satellite quenched fraction as a function of projected radial distance from the central galaxy exhibits an approx r-.15 slope, independent of environment. The accurate prediction for the spatial distribution of satellites is intriguing given the fact that we do not explicitly model satellite-specific processes after infall, and that in our model the virial radius does not mark a special transition region in the evolution of a satellite, contrary to most galaxy evolution models. The success of the model suggests that present-day galaxy SFR is strongly correlated with halo mass assembly history.« less

  16. Predicting Galaxy Star Formation Rates via the Co-evolution of Galaxies and Halos

    SciTech Connect

    Watson, Douglas F.; Hearin, Andrew P.; Berlind, Andreas A.; Becker, Matthew R.; Behroozi, Peter S.; Skibba, Ramin A.; Reyes, Reinabelle; Zentner, Andrew R.

    2014-03-06

    In this paper, we test the age matching hypothesis that the star formation rate (SFR) of a galaxy is determined by its dark matter halo formation history, and as such, that more quiescent galaxies reside in older halos. This simple model has been remarkably successful at predicting color-based galaxy statistics at low redshift as measured in the Sloan Digital Sky Survey (SDSS). To further test this method with observations, we present new SDSS measurements of the galaxy two-point correlation function and galaxy-galaxy lensing as a function of stellar mass and SFR, separated into quenched and star forming galaxy samples. We find that our age matching model is in excellent agreement with these new measurements. We also employ a galaxy group finder and show that our model is able to predict: (1) the relative SFRs of central and satellite galaxies, (2) the SFR-dependence of the radial distribution of satellite galaxy populations within galaxy groups, rich groups, and clusters and their surrounding larger scale environments, and (3) the interesting feature that the satellite quenched fraction as a function of projected radial distance from the central galaxy exhibits an approx r-.15 slope, independent of environment. The accurate prediction for the spatial distribution of satellites is intriguing given the fact that we do not explicitly model satellite-specific processes after infall, and that in our model the virial radius does not mark a special transition region in the evolution of a satellite, contrary to most galaxy evolution models. The success of the model suggests that present-day galaxy SFR is strongly correlated with halo mass assembly history.

  17. Hepatitis B virus HBx protein activates Ras-GTP complex formation and establishes a Ras, Raf, MAP kinase signaling cascade.

    PubMed Central

    Benn, J; Schneider, R J

    1994-01-01

    Hepatitis B virus produces a small (154-amino acid) transcriptional transactivating protein, HBx, which is required for viral infection and has been implicated in virus-mediated liver oncogenesis. However, the molecular mechanism for HBx activity and its possible influence on cell proliferation have remained obscure. A number of studies suggest that HBx may stimulate transcription by indirectly activating transcription factors, possibly by influencing cell signaling pathways. We now present biochemical evidence that HBx activates Ras and rapidly induces a cytoplasmic signaling cascade linking Ras, Raf, and mitogen-activated protein kinase (MAP kinase), leading to transcriptional transactivation. HBx strongly elevates levels of GTP-bound Ras, activated and phosphorylated Raf, and tyrosine-phosphorylated and activated MAP kinase. Transactivation of transcription factor AP-1 by HBx is blocked by inhibition of Ras or Raf activities but not by inhibition of Ca(2+)- and diacylglycerol-dependent protein kinase C. HBx was also found to stimulate DNA synthesis in serum-starved cells. The hepatitis B virus HBx protein therefore stimulates Ras-GTP complex formation and promotes downstream signaling through Raf and MAP kinases, and may influence cell proliferation. Images PMID:7937954

  18. Mapping Physical Formats to Logical Models to Extract Data and Metadata: The Defuddle Parsing Engine

    SciTech Connect

    Talbott, Tara D.; Schuchardt, Karen L.; Stephan, Eric G.; Myers, James D.

    2006-07-25

    Scientists, fueled by the desire for systems-level understanding of phenomena, increasingly need to share their results across multiple disciplines. Accomplishing this requires data to be annotated, contextualized, and readily searchable and translated into other formats. While these requirements can be addressed by custom programming or obviated by community standardization, neither approach has ‘solved’ the problem. In this paper, we describe a complementary approach – a general capability for articulating the format of arbitrary textual and binary data using a logical data model, expressed in XML-Schema, which can be used to provide annotation and context, extract metadata, and enable translation. This work is based on the draft specification for the Data Format Description Language and our open source “Defuddle” parser. We present an overview of the specification, detail the design of Defuddle, and discuss the benefits and challenges of this general approach to enabling discovery and sharing of diverse data sets.

  19. A priori performance prediction in pharmaceutical wet granulation: testing the applicability of the nucleation regime map to a formulation with a broad size distribution and dry binder addition.

    PubMed

    Kayrak-Talay, Defne; Litster, James D

    2011-10-14

    In this study, Hapgood's nucleation regime map (Hapgood et al., 2003) was tested for a formulation that consists of an active pharmaceutical ingredient (API) of broad size distribution and a fine dry binder. Gabapentin was used as the API and hydroxypropyl cellulose (HPC) as the dry binder with deionized water as the liquid binder. The formulation was granulated in a 6l Diosna high shear granulator. The effect of liquid addition method (spray, dripping), liquid addition rate (29-245 g/min), total liquid content (2, 4 and 10%), and impeller speed (250 and 500 rpm) on the granule size distribution and lump formation were investigated. Standard methods were successfully used to characterize the process parameters (spray drop size, spray geometry and powder surface velocity) for calculating the dimensionless spray flux. However, the addition of dry binder had a very strong effect on drop penetration time that could not be predicted from simple capillary flow considerations. This is most likely due to preferential liquid penetration into the fine pores related to the dry binder particles and subsequent partial softening and dissolution of the binder. For systems containing a dry binder or other amorphous powders, it is recommended that drop penetration time be measured directly for the blended formulation and then scaled to the drop size during spraying. Using these approaches to characterize the key dimensionless groups (dimensionless spray flux and drop penetration time), Hapgood's nucleation regime map was successfully used to predict a priori the effect of process conditions on the quality of the granule size distribution as measured by lump formation and the span of the size distribution, both before and after wet massing for range of conditions studied. Wider granule size distributions and higher amount of lumps were obtained moving from intermediate to mechanical dispersion regime. Addition of the liquid in the dripping mode gave the broadest size distribution

  20. Numerical shake prediction for Earthquake Early Warning: data assimilation, real-time shake-mapping, and simulation of wave propagation

    NASA Astrophysics Data System (ADS)

    Hoshiba, M.; Aoki, S.

    2014-12-01

    In many methods of the present Earthquake Early Warning (EEW) systems, hypocenter and magnitude are determined quickly and then strengths of ground motions are predicted. The 2011 Tohoku Earthquake (MW9.0), however, revealed some technical issues with the conventional methods: under-prediction due to the large extent of the fault rupture, and over-prediction due to confusion of the system by multiple aftershocks occurred simultaneously. To address these issues, a new concept is proposed for EEW: applying data assimilation technique, present wavefield is estimated precisely in real time (real-time shake mapping) and then future wavefield is predicted time-evolutionally using physical process of seismic wave propagation. Information of hypocenter location and magnitude are not required, which is basically different from the conventional method. In the proposed method, data assimilation technique is applied to estimate the current spatial distribution of wavefield, in which not only actual observation but also anticipated wavefield predicted from one time-step before are used. Real-time application of the data assimilation technique enables us to estimate wavefield in real time, which corresponds to real-time shake mapping. Once present situation is estimated precisely, we go forward to the prediction of future situation using simulation of wave propagation. The proposed method is applied to the 2011 Tohoku Earthquake (MW9.0) and the 2004 Mid-Niigata earthquake (Mw6.7). Future wavefield is precisely predicted, and the prediction is improved with shortening the lead time: for example, the error of 10 s prediction is smaller than that of 20 s, and that of 5 s is much smaller. By introducing this method, it becomes possible to predict ground motion precisely even for cases of the large extent of fault rupture and the multiple simultaneous earthquakes. The proposed method is based on a simulation of physical process from the precisely estimated present condition. This

  1. The effect of shyness on children's formation and retention of novel word-object mappings.

    PubMed

    Hilton, Matt; Westermann, Gert

    2016-12-05

    This study set out to examine whether shyness, an aversion to novelty and unfamiliar social situations, can affect the processes that underlie early word learning. Twenty-four-month-old children (n =32) were presented with sets of one novel and two familiar objects, and it was found that shyer children were less likely to select a novel object as the referent of a novel label. Furthermore, not-shy children then showed evidence of retaining these novel mappings, but shy children did not. These findings suggest that shy children's aversion to novelty and to the unfamiliar context can impact on their word learning.

  2. Cell Based Associations: A procedure for considering scarce and mixed mineral occurrences in predictive mapping

    NASA Astrophysics Data System (ADS)

    Tourlière, Bruno; Pakyuz-Charrier, Evren; Cassard, Daniel; Barbanson, Luc; Gumiaux, Charles

    2015-05-01

    Cell Based Association is an innovative mineral favorability procedure designed to answer special needs of the mining industry in data wise critical situations where usual favorability methods may not yield satisfactory results. Those situations relate to input data quality (e.g. clustered points, mixed and scarce data, approximate location) or some assumptions that are considered unreasonable (e.g. map areas relevance, conditional independence). The principle of CBA consists in replacing polygons of geological units with a square cell grid (hence the 'cell-based'). Each cell contains a range of units ('association') that are binary coded in terms of their presence (1) or absence (0) within study area. The loss of resolution inherent to this procedure is compensated by the enriched information contained in each cell owing to the notion of (lithological) association. Lithological associations are considered as binary spectra and as such are classified using Ascendant Hierarchical Clustering (AHC) thus obtaining a synthetic map of lithological associations. The prospectivity map shows as favourable the cells of the same AHC classes that the ones including mineral occurrences. It was observed that CBA can distinguish between different ore deposit varieties from a blended mineral occurrences data set. CBA can theoretically include any spatialized data (e.g. geophysics, structural data) as an extra variable to specify classification and narrow favourable areas. Doing so would make it an independent favorability mapping procedure and is still under development. Cell size in a grid is a critical parameter of the procedure; it must be compatible with the looked-for phenomena and should have a sufficient lithological variability. In addition to its use for producing favorability maps, a CBA-derived map could help in understanding the background information contained in geological maps. CBA can also be applied to other fields, such as agriculture and urban planning

  3. Rice crop mapping and change prediction using multi-temporal satellite images in the Mekong Delta, Vietnam

    NASA Astrophysics Data System (ADS)

    Chen, C. R.; Chen, C. F.; Nguyen, S. T.

    2014-12-01

    The rice cropping systems in the Vietnamese Mekong Delta (VMD) has been undergoing major changes to cope with developing agro-economics, increasing population and changing climate. Information on rice cropping practices and changes in cropping systems is critical for policymakers to devise successful strategies to ensure food security and rice grain exports for the country. The primary objective of this research is to map rice cropping systems and predict future dynamics of rice cropping systems using the MODIS time-series data of 2002, 2006, and 2010. First, a phenology-based classification approach was applied for the classification and assessment of rice cropping systems in study region. Second, the Cellular Automata-Markov (CA-Markov) models was used to simulate the rice-cropping system map of VMD for 2010. The comparisons between the classification maps and the ground reference data indicated satisfactory results with overall accuracies and Kappa coefficients, respectively, of 81.4% and 0.75 for 2002, 80.6% and 0.74 for 2006 and 85.5% and 0.81 for 2010. The simulated map of rice cropping system for 2010 was extrapolated by CA-Markov model based on the trend of rice cropping systems during 2002~2006. The comparison between predicted scenario and classification map for 2010 presents a reasonably closer agreement. In conclusion, the CA-Markov model performs a powerful tool for the dynamic modeling of changes in rice cropping systems, and the results obtained demonstrate that the approach produces satisfactory results in terms of accuracy, quantitative forecast and spatial pattern changes. Meanwhile, the projections of the future changes would provide useful inputs to the agricultural policy for effective management of the rice cropping practices in VMD.

  4. Geologic map of the Peach Orchard Flat quadrangle, Carbon County, Wyoming, and descriptions of new stratigraphic units in the Upper Cretaceous Lance Formation and Paleocene Fort Union Formation, eastern Greater Green River Basin, Wyoming-Colorado

    USGS Publications Warehouse

    Honey, J.D.; Hettinger, R.D.

    2004-01-01

    This report provides a geologic map of the Peach Orchard Flat 7.5-minute quadrangle, located along the eastern flank of the Washakie Basin, Wyo. Geologic formations and individual coal beds were mapped at a scale of 1:24,000; surface stratigraphic sections were measured and described; and well logs were examined to determine coal correlations and thicknesses in the subsurface. In addition, four lithostratigraphic units were named: the Red Rim Member of the Upper Cretaceous Lance Formation, and the China Butte, Blue Gap, and Overland Members of the Paleocene Fort Union Formation.

  5. Prediction of CT Substitutes from MR Images Based on Local Diffeomorphic Mapping for Brain PET Attenuation Correction.

    PubMed

    Wu, Yao; Yang, Wei; Lu, Lijun; Lu, Zhentai; Zhong, Liming; Huang, Meiyan; Feng, Yanqiu; Feng, Qianjin; Chen, Wufan

    2016-10-01

    Attenuation correction is important for PET reconstruction. In PET/MR, MR intensities are not directly related to attenuation coefficients that are needed in PET imaging. The attenuation coefficient map can be derived from CT images. Therefore, prediction of CT substitutes from MR images is desired for attenuation correction in PET/MR. This study presents a patch-based method for CT prediction from MR images, generating attenuation maps for PET reconstruction. Because no global relation exists between MR and CT intensities, we propose local diffeomorphic mapping (LDM) for CT prediction. In LDM, we assume that MR and CT patches are located on 2 nonlinear manifolds, and the mapping from the MR manifold to the CT manifold approximates a diffeomorphism under a local constraint. Locality is important in LDM and is constrained by the following techniques. The first is local dictionary construction, wherein, for each patch in the testing MR image, a local search window is used to extract patches from training MR/CT pairs to construct MR and CT dictionaries. The k-nearest neighbors and an outlier detection strategy are then used to constrain the locality in MR and CT dictionaries. Second is local linear representation, wherein, local anchor embedding is used to solve MR dictionary coefficients when representing the MR testing sample. Under these local constraints, dictionary coefficients are linearly transferred from the MR manifold to the CT manifold and used to combine CT training samples to generate CT predictions. Our dataset contains 13 healthy subjects, each with T1- and T2-weighted MR and CT brain images. This method provides CT predictions with a mean absolute error of 110.1 Hounsfield units, Pearson linear correlation of 0.82, peak signal-to-noise ratio of 24.81 dB, and Dice in bone regions of 0.84 as compared with real CTs. CT substitute-based PET reconstruction has a regression slope of 1.0084 and R(2) of 0.9903 compared with real CT-based PET. In this method

  6. Mapping agricultural fields with GPR and EMI to predict offsite movement of agrochemicals

    NASA Astrophysics Data System (ADS)

    Yoder, Ronald E.; Freeland, Robert S.; Ammons, J. T.; Leonard, L. L.

    2000-04-01

    Offsite movement of waterborne agrochemicals is increasingly targeted as a nonpoint source of water quality degradation. Our research has indicated that subsurface water movement is variable and site-specific, and that a small soil volume frequently conducts a large volume of flow. This concentrated flow is usually caused by soil morphology, and it often results in water moving rapidly offsite from certain areas of fields; little or no lateral subsurface flow may occur in other areas. Identifying these subsurface regions is difficult using conventional soil survey and vadose zone sampling techniques. In this study, traditional surveying is combined with electromagnetic induction (EMI) and ground penetrating radar (GPR) mapping to identify areas with high potential for subsurface offsite movement of agrochemicals, optimizing these identification techniques, and expanding the mapping procedures to make them useful at the field-scale for agricultural production practices. Conclusions from this research are: (1) EMI mapping provides rapid identification of areas of soil with a high potential for offsite movement of subsurface water, (2) GPR mapping of areas identified by EMI mapping provides a means to identify features that are known to conduct concentrated lateral flow of water, and (3) combining the capabilities of EMI and GPR instrumentation make possible the surveys of large areas that would otherwise be impossible or unfeasible to characterize.

  7. Providing access to risk prediction tools via the HL7 XML-formatted risk web service.

    PubMed

    Chipman, Jonathan; Drohan, Brian; Blackford, Amanda; Parmigiani, Giovanni; Hughes, Kevin; Bosinoff, Phil

    2013-07-01

    Cancer risk prediction tools provide valuable information to clinicians but remain computationally challenging. Many clinics find that CaGene or HughesRiskApps fit their needs for easy- and ready-to-use software to obtain cancer risks; however, these resources may not fit all clinics' needs. The HughesRiskApps Group and BayesMendel Lab therefore developed a web service, called "Risk Service", which may be integrated into any client software to quickly obtain standardized and up-to-date risk predictions for BayesMendel tools (BRCAPRO, MMRpro, PancPRO, and MelaPRO), the Tyrer-Cuzick IBIS Breast Cancer Risk Evaluation Tool, and the Colorectal Cancer Risk Assessment Tool. Software clients that can convert their local structured data into the HL7 XML-formatted family and clinical patient history (Pedigree model) may integrate with the Risk Service. The Risk Service uses Apache Tomcat and Apache Axis2 technologies to provide an all Java web service. The software client sends HL7 XML information containing anonymized family and clinical history to a Dana-Farber Cancer Institute (DFCI) server, where it is parsed, interpreted, and processed by multiple risk tools. The Risk Service then formats the results into an HL7 style message and returns the risk predictions to the originating software client. Upon consent, users may allow DFCI to maintain the data for future research. The Risk Service implementation is exemplified through HughesRiskApps. The Risk Service broadens the availability of valuable, up-to-date cancer risk tools and allows clinics and researchers to integrate risk prediction tools into their own software interface designed for their needs. Each software package can collect risk data using its own interface, and display the results using its own interface, while using a central, up-to-date risk calculator. This allows users to choose from multiple interfaces while always getting the latest risk calculations. Consenting users contribute their data for future

  8. Berkeley Prize: Mapping the Fuel for Star Formation in Early Universe Galaxies

    NASA Astrophysics Data System (ADS)

    Tacconi, Linda

    2012-01-01

    Stars form from cold molecular interstellar gas, which is relatively rare in galaxies like the Milky Way, which form only a few new stars per year. Massive galaxies in the distant universe formed stars much more rapidly. Was star formation more efficient in the past, and/or were early galaxies richer in molecular gas? The answer was elusive when our instruments could probe molecules only in the most luminous and rare objects such as mergers and quasars. But a new survey of molecular gas in typical massive star-forming galaxies at redshifts from about 1.2 to 2.3 (corresponding to when the universe was 24% to 40% of its current age) reveals that distant star-forming galaxies were indeed molecular-gas rich and that the star-formation efficiency is not strongly dependent on cosmic epoch.

  9. Selected data for wells and test holes used in structure-contour maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation in the Black Hills area, South Dakota

    USGS Publications Warehouse

    Carter, J.M.

    1999-01-01

    This report presents selected data on wells and test holes that were used in the construction of structure-contour maps of selected formations that contain major aquifers in the Black Hills area of western South Dakota. Altitudes of the top of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation are presented for the wells and test holes presented in this report.

  10. Corticothalamic phase synchrony and cross-frequency coupling predict human memory formation.

    PubMed

    Sweeney-Reed, Catherine M; Zaehle, Tino; Voges, Juergen; Schmitt, Friedhelm C; Buentjen, Lars; Kopitzki, Klaus; Esslinger, Christine; Hinrichs, Hermann; Heinze, Hans-Jochen; Knight, Robert T; Richardson-Klavehn, Alan

    2014-12-23

    The anterior thalamic nucleus (ATN) is thought to play an important role in a brain network involving the hippocampus and neocortex, which enables human memories to be formed. However, its small size and location deep within the brain have impeded direct investigation in humans with non-invasive techniques. Here we provide direct evidence for a functional role for the ATN in memory formation from rare simultaneous human intrathalamic and scalp electroencephalogram (EEG) recordings from eight volunteering patients receiving intrathalamic electrodes implanted for the treatment of epilepsy, demonstrating real-time communication between neocortex and ATN during successful memory encoding. Neocortical-ATN theta oscillatory phase synchrony of local field potentials and neocortical-theta-to-ATN-gamma cross-frequency coupling during presentation of complex photographic scenes predicted later memory for the scenes, demonstrating a key role for the ATN in human memory encoding.

  11. Predicted formation of superconducting platinum-hydride crystals under pressure in the presence of molecular hydrogen.

    PubMed

    Kim, Duck Young; Scheicher, Ralph H; Pickard, Chris J; Needs, R J; Ahuja, R

    2011-09-09

    Noble metals adopt close-packed structures at ambient pressure and rarely undergo structural transformation at high pressures. Platinum (Pt) is normally considered to be unreactive and is therefore not expected to form hydrides under pressure. We predict that platinum hydride (PtH) has a lower enthalpy than its constituents solid Pt and molecular hydrogen at pressures above 21.5 GPa. PtH transforms to a hexagonal close-packed or face-centered cubic (fcc) structure between 70 and 80 GPa. Linear response calculations indicate that PtH is a superconductor at these pressures with a critical temperature of about 10-25 K. These findings help to shed light on recent observations of pressure-induced metallization and superconductivity in hydrogen-rich materials. We show that the formation of fcc noble metal hydrides under pressure is common and examine the possibility of superconductivity in these materials.

  12. Corticothalamic phase synchrony and cross-frequency coupling predict human memory formation

    PubMed Central

    Sweeney-Reed, Catherine M; Zaehle, Tino; Voges, Juergen; Schmitt, Friedhelm C; Buentjen, Lars; Kopitzki, Klaus; Esslinger, Christine; Hinrichs, Hermann; Heinze, Hans-Jochen; Knight, Robert T; Richardson-Klavehn, Alan

    2014-01-01

    The anterior thalamic nucleus (ATN) is thought to play an important role in a brain network involving the hippocampus and neocortex, which enables human memories to be formed. However, its small size and location deep within the brain have impeded direct investigation in humans with non-invasive techniques. Here we provide direct evidence for a functional role for the ATN in memory formation from rare simultaneous human intrathalamic and scalp electroencephalogram (EEG) recordings from eight volunteering patients receiving intrathalamic electrodes implanted for the treatment of epilepsy, demonstrating real-time communication between neocortex and ATN during successful memory encoding. Neocortical-ATN theta oscillatory phase synchrony of local field potentials and neocortical-theta-to-ATN-gamma cross-frequency coupling during presentation of complex photographic scenes predicted later memory for the scenes, demonstrating a key role for the ATN in human memory encoding. DOI: http://dx.doi.org/10.7554/eLife.05352.001 PMID:25535839

  13. MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula

    PubMed Central

    Ryu, Hojin; Laffont, Carole; Frugier, Florian; Hwang, Ildoo

    2017-01-01

    Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula. The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN. We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors. PMID:28152300

  14. Assessing "economic value": symbolic-number mappings predict risky and riskless valuations.

    PubMed

    Schley, Dan R; Peters, Ellen

    2014-03-01

    Diminishing marginal utility (DMU) is a basic tenet of economic and psychological models of judgment and choice, but its determinants are little understood. In the research reported here, we tested whether insensitivities in valuations of dollar amounts (e.g., $40, $100) may be due to inexact mappings of symbolic numbers (i.e., "40," "100") onto mental magnitudes. In three studies, we demonstrated that inexact mappings appear to guide valuation and mediate numeracy's relations with riskless valuations (Studies 1 and 1a) and risky choices (Study 2). The results highlight the fundamental notion that individuals' valuations of $100 depend critically on how individuals perceive and map the symbolic quantity "100." This notion has implications for conceptualizations of value, risk aversion, intertemporal choice, and dual-process theories of decision making. Normative implications are also briefly discussed.

  15. Brief Report: Fast Mapping Predicts Differences in Concurrent and Later Language Abilities Among Children with ASD.

    PubMed

    Venker, Courtney E; Kover, Sara T; Ellis Weismer, Susan

    2016-03-01

    This study investigated whether the ability to learn word-object associations following minimal exposure (i.e., fast mapping) was associated with concurrent and later language abilities in children with ASD. Children who were poor learners at age 3½ had significantly lower receptive language abilities than children who successfully learned the new words, both concurrently (n = 59) and 2 years later (n = 53), lending ecological validity to experimental fast-mapping tasks. Fast mapping comprehension at age 3½ was associated with better language outcomes regardless of whether children had produced the new words. These findings highlight the importance of investigating processes of language learning in children with ASD. Understanding these processes will enable the development of maximally effective strategies for supporting word learning.

  16. Spatial risk prediction and mapping of Schistosoma mansoni infections among schoolchildren living in western Côte d'Ivoire.

    PubMed

    Raso, G; Matthys, B; N'Goran, E K; Tanner, M; Vounatsou, P; Utzinger, J

    2005-07-01

    The objectives of this study were (1) to examine risk factors for Schistosoma mansoni infection among schoolchildren living in western Côte d'Ivoire, and (2) to carry forward spatial risk prediction and mapping at non-sampled locations. First, demographic and socio-economic data were obtained from 3818 children, aged 6-16 years, from 55 schools. Second, a single stool sample was examined from each child by the Kato-Katz technique to assess infection status of S. mansoni and its intensity. Third, remotely sensed environmental data were derived from satellite imagery and digitized ground maps. With these databases a comprehensive geographical information system was established. Bayesian variogram models were applied for spatial risk modelling and prediction. The infection prevalence of S. mansoni was 38.9%, ranging from 0% to 89.3% among schools. Results showed that age, sex, the richest wealth quintile, elevation and rainfall explained the geographical variation of the school prevalences of S. mansoni infection. The goodness of fit of different spatial models revealed that age, sex and socio-economic status had a stronger influence on infection prevalence than environmental covariates. The generated risk map can be used by decision-makers for the design and implementation of schistosomiasis control in this setting. If successfully validated elsewhere, this approach can guide control programmes quite generally.

  17. A-DROP: A predictive model for the formation of oil particle aggregates (OPAs)

    USGS Publications Warehouse

    Zhao, Lin; Boufadel, Michel C.; Geng, Xiaolong; Lee, Kenneth; King, Thomas; Robinson, Brian; Fitzpatrick, Faith A.

    2016-01-01

    Oil–particle interactions play a major role in removal of free oil from the water column. We present a new conceptual–numerical model, A-DROP, to predict oil amount trapped in oil–particle aggregates. A new conceptual formulation of oil–particle coagulation efficiency is introduced to account for the effects of oil stabilization by particles, particle hydrophobicity, and oil–particle size ratio on OPA formation. A-DROP was able to closely reproduce the oil trapping efficiency reported in experimental studies. The model was then used to simulate the OPA formation in a typical nearshore environment. Modeling results indicate that the increase of particle concentration in the swash zone would speed up the oil–particle interaction process; but the oil amount trapped in OPAs did not correspond to the increase of particle concentration. The developed A-DROP model could become an important tool in understanding the natural removal of oil and developing oil spill countermeasures by means of oil–particle aggregation.

  18. H₂S-Mediated Protein S-Sulfhydration: A Prediction for Its Formation and Regulation.

    PubMed

    Ju, Youngjun; Fu, Ming; Stokes, Eric; Wu, Lingyun; Yang, Guangdong

    2017-08-11

    Protein S-sulfhydration is a newly discovered post-translational modification of specific cysteine residue(s) in target proteins, which is involved in a broad range of cellular functions and metabolic pathways. By changing local conformation and the final activity of target proteins, S-sulfhydration is believed to mediate most cellular responses initiated by H₂S, a novel gasotransmitter. In comparison to protein S-sulfhydration, nitric oxide-mediated protein S-nitrosylation has been extensively investigated, including its formation, regulation, transfer and metabolism. Although the investigation on the regulatory mechanisms associated with protein S-sulfhydration is still in its infancy, accumulated evidence suggested that protein S-sulfhydration may share similar chemical features with protein S-nitrosylation. Glutathione persulfide acts as a major donor for protein S-sulfhydration. Here, we review the present knowledge on protein S-sulfhydration, and also predict its formation and regulation mechanisms based on the knowledge from protein S-nitrosylation.

  19. A-DROP: A predictive model for the formation of oil particle aggregates (OPAs).

    PubMed

    Zhao, Lin; Boufadel, Michel C; Geng, Xiaolong; Lee, Kenneth; King, Thomas; Robinson, Brian; Fitzpatrick, Faith

    2016-05-15

    Oil-particle interactions play a major role in removal of free oil from the water column. We present a new conceptual-numerical model, A-DROP, to predict oil amount trapped in oil-particle aggregates. A new conceptual formulation of oil-particle coagulation efficiency is introduced to account for the effects of oil stabilization by particles, particle hydrophobicity, and oil-particle size ratio on OPA formation. A-DROP was able to closely reproduce the oil trapping efficiency reported in experimental studies. The model was then used to simulate the OPA formation in a typical nearshore environment. Modeling results indicate that the increase of particle concentration in the swash zone would speed up the oil-particle interaction process; but the oil amount trapped in OPAs did not correspond to the increase of particle concentration. The developed A-DROP model could become an important tool in understanding the natural removal of oil and developing oil spill countermeasures by means of oil-particle aggregation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Dynamics and predictability of secondary eyewall formation in sheared tropical cyclones

    NASA Astrophysics Data System (ADS)

    Zhang, Fuqing; Tao, Dandan; Sun, Y. Qiang; Kepert, Jeffrey D.

    2017-03-01

    This study examines the predictability and dynamics of tropical cyclone (TC) secondary eyewall formation (SEF), eyewall replacement cycles (ERC), and intensity changes under moderate environmental shear through convection-permitting ensemble simulations. Even with the same environmental shear, the TC intensity changes during formation, rapid intensification, and SEF/ERC can be extremely sensitive to small, unobservable, random initial condition uncertainties, or computer's truncation error due to the chaotic nature of moist convection. Through composite analysis of five ensemble members with similar clear SEF/ERC and diagnostics with a nonlinear boundary layer (BL) model, we identify several key factors in the SEF/ERC process: (1) fast expansion of outer wind fields and changing inertial stability through shear-induced peripheral convection outside of the primary eyewall, (2) downward building and axisymmetrization of the primary (outer) rainband due to enhanced inertial stability and positive feedback between BL and outer convection, (3) establishment of the secondary eyewall along with moat formation that is facilitated by compensating subsidence from the primary eyewall, and (4) weakening and eventual replacement of the original primary eyewall by the strengthening secondary eyewall. It is also seen from the partial ERC cases that the preexisting rainband can be of great importance to the later development of SEF. Diagnosis with the nonlinear BL model shows that the location and relative strengths of the diagnosed frictional updrafts closely match those in the ensemble simulation of the ERC case, suggesting that the boundary layer convergence substantially influences the location of the convection in both eyewalls there.

  1. Becoming popular: interpersonal emotion regulation predicts relationship formation in real life social networks

    PubMed Central

    Niven, Karen; Garcia, David; van der Löwe, Ilmo; Holman, David; Mansell, Warren

    2015-01-01

    Building relationships is crucial for satisfaction and success, especially when entering new social contexts. In the present paper, we investigate whether attempting to improve others’ feelings helps people to make connections in new networks. In Study 1, a social network study following new networks of people for a 12-week period indicated that use of interpersonal emotion regulation (IER) strategies predicted growth in popularity, as indicated by other network members’ reports of spending time with the person, in work and non-work interactions. In Study 2, linguistic analysis of the tweets from over 8000 Twitter users from formation of their accounts revealed that use of IER predicted greater popularity in terms of the number of followers gained. However, not all types of IER had positive effects. Behavioral IER strategies (which use behavior to reassure or comfort in order to regulate affect) were associated with greater popularity, while cognitive strategies (which change a person’s thoughts about his or her situation or feelings in order to regulate affect) were negatively associated with popularity. Our findings have implications for our understanding of how new relationships are formed, highlighting the important the role played by intentional emotion regulatory processes. PMID:26483718

  2. Becoming popular: interpersonal emotion regulation predicts relationship formation in real life social networks.

    PubMed

    Niven, Karen; Garcia, David; van der Löwe, Ilmo; Holman, David; Mansell, Warren

    2015-01-01

    Building relationships is crucial for satisfaction and success, especially when entering new social contexts. In the present paper, we investigate whether attempting to improve others' feelings helps people to make connections in new networks. In Study 1, a social network study following new networks of people for a 12-week period indicated that use of interpersonal emotion regulation (IER) strategies predicted growth in popularity, as indicated by other network members' reports of spending time with the person, in work and non-work interactions. In Study 2, linguistic analysis of the tweets from over 8000 Twitter users from formation of their accounts revealed that use of IER predicted greater popularity in terms of the number of followers gained. However, not all types of IER had positive effects. Behavioral IER strategies (which use behavior to reassure or comfort in order to regulate affect) were associated with greater popularity, while cognitive strategies (which change a person's thoughts about his or her situation or feelings in order to regulate affect) were negatively associated with popularity. Our findings have implications for our understanding of how new relationships are formed, highlighting the important the role played by intentional emotion regulatory processes.

  3. Protein pheromone expression levels predict and respond to the formation of social dominance networks

    PubMed Central

    Nelson, Adam C.; Cunningham, Christopher B.; Ruff, James S.; Potts, Wayne K.

    2015-01-01

    Communication signals are key regulators of social networks, and are thought to be under selective pressure to honestly reflect social status, including dominance status. The odors of dominants and nondominants differentially influence behavior, and identification of the specific pheromones associated with, and predictive of, dominance status is essential for understanding the mechanisms of network formation and maintenance. In mice, major urinary proteins (MUPs) are excreted in extraordinary large quantities and expression level has been hypothesized to provide an honest signal of dominance status. Here, we evaluate whether MUPs are associated with dominance in wild-derived mice by analyzing expression levels before, during, and after competition for reproductive resources over three days. During competition, dominant males have 24% greater urinary MUP expression than nondominants. The MUP darcin, a pheromone that stimulates female attraction, is predictive of dominance status: dominant males have higher darcin expression before competition. Dominants also have a higher ratio of darcin to other MUPs before and during competition. These differences appear transient, because there are no differences in MUPs or darcin after competition. We also find MUP expression is affected by sire dominance status: socially naive sons of dominant males have lower MUP expression, but this apparent repression is released during competition. A requisite condition for the evolution of communication signals is honesty, and we provide novel insight into pheromones and social networks by showing that MUP and darcin expression is a reliable signal of dominance status, a primary determinant of male fitness in many species. PMID:25867293

  4. Haplotype mapping and sequence analysis of the mouse Nramp gene predict susceptibility to infection with intracellular parasites

    SciTech Connect

    Malo, D.; Hu, Jinxin; Schurr, E.

    1994-09-01

    The mouse chromosome 1 locus Bcg (Ity, Lsh) controls the capacity of the tissue macrophage to restrict the replication of antigenically unrelated intracellular parasites and therefore determines the natural resistance (BCG-R, dominant) or susceptibility (BCG-S, recessive) of inbred mouse strains to infection with diverse pathogens. We have used a positional cloning strategy based on genetic and physical mapping, YAC cloning, and exon trapping to isolate a candidate gene for Beg (Nramp) that encodes a predicted macrophage-specific transport protein. We have analyzed a total of 27 inbred mouse strains of BCG-R and BCG-S phenotypes for the presence of nucleotide sequence variations within the coding portion of Nramp and have carried out haplotype typing of the corresponding chromosome 1 region in these mice, using 11 additional polymorphic markers mapping in the immediate vicinity of Nramp. cDNA cloning and nucleotide sequencing identified 5 nucleotide sequence variations within Nramp in the inbred strains.

  5. Modeling Career Counselor Decisions with Artificial Neural Networks: Predictions of Fit across a Comprehensive Occupational Map.

    ERIC Educational Resources Information Center

    Carson, Andrew D.; Bizot, Elizabeth B.; Hendershot, Peggy E.; Barton, Margaret G.; Garvin, Mary K.; Kraemer, Barbara

    1999-01-01

    Career recommendations were made based on aptitude scores of 335 high school freshmen. Artificial neural networks were used to map recommendations to 12 occupational clusters. Overall accuracy of neural networks (.80) approached that of discriminant function analysis (.84). The two methods had different strengths and weaknesses. (SK)

  6. Brief Report: Fast Mapping Predicts Differences in Concurrent and Later Language Abilities among Children with ASD

    ERIC Educational Resources Information Center

    Venker, Courtney E.; Kover, Sara T.; Weismer, Susan Ellis

    2016-01-01

    This study investigated whether the ability to learn word-object associations following minimal exposure (i.e., fast mapping) was associated with concurrent and later language abilities in children with ASD. Children who were poor learners at age 3½ had significantly lower receptive language abilities than children who successfully learned the new…

  7. Modeling Career Counselor Decisions with Artificial Neural Networks: Predictions of Fit across a Comprehensive Occupational Map.

    ERIC Educational Resources Information Center

    Carson, Andrew D.; Bizot, Elizabeth B.; Hendershot, Peggy E.; Barton, Margaret G.; Garvin, Mary K.; Kraemer, Barbara

    1999-01-01

    Career recommendations were made based on aptitude scores of 335 high school freshmen. Artificial neural networks were used to map recommendations to 12 occupational clusters. Overall accuracy of neural networks (.80) approached that of discriminant function analysis (.84). The two methods had different strengths and weaknesses. (SK)

  8. Brief Report: Fast Mapping Predicts Differences in Concurrent and Later Language Abilities among Children with ASD

    ERIC Educational Resources Information Center

    Venker, Courtney E.; Kover, Sara T.; Weismer, Susan Ellis

    2016-01-01

    This study investigated whether the ability to learn word-object associations following minimal exposure (i.e., fast mapping) was associated with concurrent and later language abilities in children with ASD. Children who were poor learners at age 3½ had significantly lower receptive language abilities than children who successfully learned the new…

  9. Potential of EnMAP spaceborne imaging spectroscopy for the prediction of common surface soil properties and expected accuracy

    NASA Astrophysics Data System (ADS)

    Chabrillat, Sabine; Foerster, Saskia; Steinberg, Andreas; Stevens, Antoine; Segl, Karl

    2016-04-01

    There is a renewed awareness of the finite nature of the world's soil resources, growing concern about soil security, and significant uncertainties about the carrying capacity of the planet. As a consequence, soil scientists are being challenged to provide regular assessments of soil conditions from local through to global scales. However, only a few countries have the necessary survey and monitoring programs to meet these new needs and existing global data sets are out-of-date. A particular issue is the clear demand for a new area-wide regional to global coverage with accurate, up-to-date, and spatially referenced soil information as expressed by the modeling scientific community, farmers and land users, and policy and decision makers. Soil spectroscopy from remote sensing observations based on studies from the laboratory scale to the airborne scale has been shown to be a proven method for the quantitative prediction of key soil surface properties in local areas for exposed soils in appropriate surface conditions such as low vegetation cover and low water content. With the upcoming launch of the next generation of hyperspectral satellite sensors in the next 3 to 5 years (EnMAP, HISUI, PRISMA, SHALOM), a great potential for the global mapping and monitoring of soil properties is appearing. Nevertheless, the capabilities to extend the soil properties current spectral modeling from local to regional scales are still to be demonstrated using robust methods. In particular, three central questions are at the forefront of research nowadays: a) methodological developments toward improved algorithms and operational tools for the extraction of soil properties, b) up scaling from the laboratory into space domain, and c) demonstration of the potential of upcoming satellite systems and expected accuracy of soil maps. In this study, airborne imaging spectroscopy data from several test sites are used to simulate EnMAP satellite images at 30 m scale. Then, different soil

  10. The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

    PubMed Central

    Klie, Sebastian; Nikoloski, Zoran

    2012-01-01

    Since the introduction of the Gene Ontology (GO), the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis) with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of co-expression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies. PMID:22754563

  11. Mapping the star formation history of Mrk 86. II. Stellar populations and global interpretation

    NASA Astrophysics Data System (ADS)

    Gil de Paz, A.; Zamorano, J.; Gallego, J.

    2000-09-01

    In this paper, continuation of Gil de Paz et al. (Paper I), we derive the main properties of the stellar populations in the Blue Compact Dwarf galaxy Mrk 86. Ages, stellar masses, metallicites and burst strengths have been obtained using the combination of Monte Carlo simulations, a maximum likelihood estimator and Cluster and Principal Component Analysis. The three stellar populations detected show well defined properties. We have studied the underlying stellar population, which shows an age between 5-13 Gyr and no significant color gradients. The intermediate aged (30 Myr old) central starburst show a very low dust extinction with high burst strength and high stellar mass content ( ~ 9x106 Msun). Finally, the properties of 46 low-metallicity ( ~ 1/10 Zsun ) star-forming regions were also studied. The properties derived suggest that the most recent star-forming activity in Mrk 86 was triggered by the evolution of a superbubble originated at the central starburst by the energy deposition of stellar winds and supernova explosions. This superbubble produced the blowout of a fraction of the interstellar medium at distances of about 1 kpc with high gas surface densities, leading to the activation of the star formation. Finally, different mechanisms for the star formation triggering in this massive central starburst are studied, including the merging with a low mass companion and the interaction with UGC 4278. We have assumed a distance to Mrk 86 of 6.9 Mpc.

  12. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population

    USDA-ARS?s Scientific Manuscript database

    Quantitative trait loci (QTL) mapping has been used to dissect the genetic architecture of a trait and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an ...

  13. Graded functional diffusion map-defined characteristics of apparent diffusion coefficients predict overall survival in recurrent glioblastoma treated with bevacizumab.

    PubMed

    Ellingson, Benjamin M; Cloughesy, Timothy F; Lai, Albert; Mischel, Paul S; Nghiemphu, Phioanh L; Lalezari, Shadi; Schmainda, Kathleen M; Pope, Whitney B

    2011-10-01

    Diffusion imaging has shown promise as a predictive and prognostic biomarker in glioma. We assessed the ability of graded functional diffusion maps (fDMs) and apparent diffusion coefficient (ADC) characteristics to predict overall survival (OS) in recurrent glioblastoma multiforme (GBM) patients treated with bevacizumab. Seventy-seven patients with recurrent GBMs were retrospectively examined. MRI scans were obtained before and approximately 6 weeks after treatment with bevacizumab. Graded fDMs were created by registering datasets to each patient's pretreatment scan and then performing voxel-wise subtraction between post- and pretreatment ADC maps. Voxels were categorized according to the degree of change in ADC within pretreatment fluid-attenuated inversion recovery (FLAIR) and contrast-enhancing regions of interest (ROIs). We found that the volume of tissue showing decreased ADC within both FLAIR and contrast-enhancing regions stratified OS (log-rank, P < .05). fDMs applied to contrast-enhancing ROIs more accurately predicted OS compared with fDMs applied to FLAIR ROIs. Graded fDMs (showing voxels with decreased ADC between 0.25 and 0.4 µm(2)/ms) were more predictive of OS than traditional (single threshold) fDMs, and the predictive ability of graded fDMs could be enhanced even further by adding the ADC characteristics from the fDM-classified voxels to the analysis (log-rank, P < .001). These results demonstrate that spatially resolved diffusion-based tumor metrics are a powerful imaging biomarker of survival in patients with recurrent GBM treated with bevacizumab.

  14. SAR prediction in adults and children by combining measured B1+ maps and simulations at 7.0 Tesla.

    PubMed

    Tiberi, Gianluigi; Costagli, Mauro; Biagi, Laura; Ciantis, Alessio De; Fontana, Nunzia; Stara, Riccardo; Symms, Mark Roger; Cosottini, Mirco; Guerrini, Renzo; Tosetti, Michela

    2016-10-01

    To predict local and global specific absorption rate (SAR) in individual subjects. SAR was simulated for a head volume coil for two imaging sequences: axial T1-weighted "zero" time-of-echo (ZTE) sequence, sagittal T2-weighted fluid attenuated inversion recovery (FLAIR). Two head models (one adult, one child) were simulated inside the coil. For 19 adults and 27 children, measured B1 (+) maps were acquired, and global (head) SAR estimated by the system was recorded. We performed t-test between the B1 (+) in models and human subjects. The B1 (+) maps of individual subjects were used to scale the SAR simulated on the models, to predict local and global (head) SAR. A phantom experiment was performed to validate SAR prediction, using a fiberoptic temperature probe to measure the temperature rise due to ZTE scanning. The normalized B1 (+) standard deviation in subjects was not significantly different from that of the models (P > 0.68 and P > 0.54). The rise in temperature generated in the phantom by ZTE was 0.3°C; from the heat equation it followed that the temperature-based measured SAR was 2.74 W/kg, while the predicted value was 3.1 W/kg. For ZTE and FLAIR, limits on maximum local and global SAR were met in all subjects, both adults and children. To enhance safety in adults and children with 7.0 Tesla MR systems, we suggest the possibility of using SAR prediction. J. MAGN. RESON. IMAGING 2016;44:1048-1055. © 2016 International Society for Magnetic Resonance in Medicine.

  15. Formation Mechanisms, Structure, and Properties of HVOF-Sprayed WC-CoCr Coatings: An Approach Toward Process Maps

    NASA Astrophysics Data System (ADS)

    Varis, T.; Suhonen, T.; Ghabchi, A.; Valarezo, A.; Sampath, S.; Liu, X.; Hannula, S.-P.

    2014-08-01

    Our study focuses on understanding the damage tolerance and performance reliability of WC-CoCr coatings. In this paper, the formation of HVOF-sprayed tungsten carbide-based cermet coatings is studied through an integrated strategy: First-order process maps are created by using online-diagnostics to assess particle states in relation to process conditions. Coating properties such as hardness, wear resistance, elastic modulus, residual stress, and fracture toughness are discussed with a goal to establish a linkage between properties and particle characteristics via second-order process maps. A strong influence of particle state on the mechanical properties, wear resistance, and residual stress stage of the coating was observed. Within the used processing window (particle temperature ranged from 1687 to 1831 °C and particle velocity from 577 to 621 m/s), the coating hardness varied from 1021 to 1507 HV and modulus from 257 to 322 GPa. The variation in coating mechanical state is suggested to relate to the microstructural changes arising from carbide dissolution, which affects the properties of the matrix and, on the other hand, cohesive properties of the lamella. The complete tracking of the coating particle state and its linking to mechanical properties and residual stresses enables coating design with desired properties.

  16. CSO Bolocam 1.1 mm Continuum Mapping of the Braid Nebula Star Formation Region in Cygnus OB7

    NASA Astrophysics Data System (ADS)

    Aspin, Colin; Beck, Tracy L.; Davis, Chris J.; Froebrich, Dirk; Khanzadyan, Tigran; Magakian, Tigran Yu.; Moriarty-Schieven, Gerald H.; Movsessian, Tigran A.; Mitchison, Sharon; Nikogossian, Elena G.; Pyo, Tae-Soo; Smith, Michael D.

    2011-04-01

    We present a 1.1 mm map of the Braid Nebula star formation region in Cygnus OB7 taken using Bolocam on the Caltech Submillimeter Observatory. Within the 1 deg2 covered by the map, we have detected 55 cold dust clumps all of which are new detections. A number of these clumps are coincident with IRAS point sources although the majority are not. Some of the previously studied optical/near-IR sources are detected at 1.1 mm. We estimate total dust/gas masses for the 55 clumps together with peak visual extinctions. We conclude that over the whole region, approximately 20% of the clumps are associated with IRAS sources suggesting that these are protostellar objects. The remaining 80% are classed as starless clumps. In addition, both FU Orionis (FUor) like objects in the field, the Braid Star and HH 381 IRS, are associated with strong millimeter emission. This implies that FUor eruptions can occur at very early stages of pre-main-sequence life. Finally, we determine that the cumulative clump mass function for the region is very similar to that found in both the Perseus and ρ Ophiuchus star-forming regions.

  17. A brain region-specific predictive gene map for autism derived by profiling a reference gene set.

    PubMed

    Kumar, Ajay; Swanwick, Catherine Croft; Johnson, Nicole; Menashe, Idan; Basu, Saumyendra N; Bales, Michael E; Banerjee-Basu, Sharmila

    2011-01-01

    Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) remain largely unresolved. Increasingly, structural variations in discrete chromosomal loci are implicated in ASD, expanding the search space for its disease etiology. We exploited the high genetic heterogeneity of ASD to derive a predictive map of candidate genes by an integrated bioinformatics approach. Using a reference set of 84 Rare and Syndromic candidate ASD genes (AutRef84), we built a composite reference profile based on both functional and expression analyses. First, we created a functional profile of AutRef84 by performing Gene Ontology (GO) enrichment analysis which encompassed three main areas: 1) neurogenesis/projection, 2) cell adhesion, and 3) ion channel activity. Second, we constructed an expression profile of AutRef84 by conducting DAVID analysis which found enrichment in brain regions critical for sensory information processing (olfactory bulb, occipital lobe), executive function (prefrontal cortex), and hormone secretion (pituitary). Disease specificity of this dual AutRef84 profile was demonstrated by comparative analysis with control, diabetes, and non-specific gene sets. We then screened the human genome with the dual AutRef84 profile to derive a set of 460 potential ASD candidate genes. Importantly, the power of our predictive gene map was demonstrated by capturing 18 existing ASD-associated genes which were not part of the AutRef84 input dataset. The remaining 442 genes are entirely novel putative ASD risk genes. Together, we used a composite ASD reference profile to generate a predictive map of novel ASD candidate genes which should be prioritized for future research.

  18. A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

    PubMed

    Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

    2015-01-15

    Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  19. Predictable nonwandering localization of covariant Lyapunov vectors and cluster synchronization in scale-free networks of chaotic maps.

    PubMed

    Kuptsov, Pavel V; Kuptsova, Anna V

    2014-09-01

    Covariant Lyapunov vectors for scale-free networks of Hénon maps are highly localized. We revealed two mechanisms of the localization related to full and phase cluster synchronization of network nodes. In both cases the localization nodes remain unaltered in the course of the dynamics, i.e., the localization is nonwandering. Moreover, this is predictable: The localization nodes are found to have specific dynamical and topological properties and they can be found without computing of the covariant vectors. This is an example of explicit relations between the system topology, its phase-space dynamics, and the associated tangent-space dynamics of covariant Lyapunov vectors.

  20. MAPPING THE SHORES OF THE BROWN DWARF DESERT. II. MULTIPLE STAR FORMATION IN TAURUS-AURIGA

    SciTech Connect

    Kraus, Adam L.; Ireland, Michael J.; Martinache, Frantz; Hillenbrand, Lynne A.

    2011-04-10

    We have conducted a high-resolution imaging study of the Taurus-Auriga star-forming region in order to characterize the primordial outcome of multiple star formation and the extent of the brown dwarf desert. Our survey identified 16 new binary companions to primary stars with masses of 0.25-2.5 M{sub sun}, raising the total number of binary pairs (including components of high-order multiples) with separations of 3-5000 AU to 90. We find that {approx}2/3-3/4 of all Taurus members are multiple systems of two or more stars, while the other {approx}1/4-1/3 appear to have formed as single stars; the distribution of high-order multiplicity suggests that fragmentation into a wide binary has no impact on the subsequent probability that either component will fragment again. The separation distribution for solar-type stars (0.7-2.5 M{sub sun}) is nearly log-flat over separations of 3-5000 AU, but lower-mass stars (0.25-0.7 M{sub sun}) show a paucity of binary companions with separations of {approx}>200 AU. Across this full mass range, companion masses are well described with a linear-flat function; all system mass ratios (q = M{sub B} /M{sub A} ) are equally probable, apparently including substellar companions. Our results are broadly consistent with the two expected modes of binary formation (free-fall fragmentation on large scales and disk fragmentation on small scales), but the distributions provide some clues as to the epochs at which the companions are likely to form.

  1. Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data

    PubMed Central

    Zhaoping, Li; Zhe, Li

    2015-01-01

    It has been hypothesized that neural activities in the primary visual cortex (V1) represent a saliency map of the visual field to exogenously guide attention. This hypothesis has so far provided only qualitative predictions and their confirmations. We report this hypothesis’ first quantitative prediction, derived without free parameters, and its confirmation by human behavioral data. The hypothesis provides a direct link between V1 neural responses to a visual location and the saliency of that location to guide attention exogenously. In a visual input containing many bars, one of them saliently different from all the other bars which are identical to each other, saliency at the singleton’s location can be measured by the shortness of the reaction time in a visual search for singletons. The hypothesis predicts quantitatively the whole distribution of the reaction times to find a singleton unique in color, orientation, and motion direction from the reaction times to find other types of singletons. The prediction matches human reaction time data. A requirement for this successful prediction is a data-motivated assumption that V1 lacks neurons tuned simultaneously to color, orientation, and motion direction of visual inputs. Since evidence suggests that extrastriate cortices do have such neurons, we discuss the possibility that the extrastriate cortices play no role in guiding exogenous attention so that they can be devoted to other functions like visual decoding and endogenous attention. PMID:26441341

  2. Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data.

    PubMed

    Zhaoping, Li; Zhe, Li

    2015-10-01

    It has been hypothesized that neural activities in the primary visual cortex (V1) represent a saliency map of the visual field to exogenously guide attention. This hypothesis has so far provided only qualitative predictions and their confirmations. We report this hypothesis' first quantitative prediction, derived without free parameters, and its confirmation by human behavioral data. The hypothesis provides a direct link between V1 neural responses to a visual location and the saliency of that location to guide attention exogenously. In a visual input containing many bars, one of them saliently different from all the other bars which are identical to each other, saliency at the singleton's location can be measured by the shortness of the reaction time in a visual search for singletons. The hypothesis predicts quantitatively the whole distribution of the reaction times to find a singleton unique in color, orientation, and motion direction from the reaction times to find other types of singletons. The prediction matches human reaction time data. A requirement for this successful prediction is a data-motivated assumption that V1 lacks neurons tuned simultaneously to color, orientation, and motion direction of visual inputs. Since evidence suggests that extrastriate cortices do have such neurons, we discuss the possibility that the extrastriate cortices play no role in guiding exogenous attention so that they can be devoted to other functions like visual decoding and endogenous attention.

  3. Geologic Map of Upper Cretaceous and Tertiary Strata and Coal Stratigraphy of the Paleocene Fort Union Formation, Rawlins-Little Snake River Area, South-Central Wyoming

    USGS Publications Warehouse

    Hettinger, R.D.; Honey, J.G.; Ellis, M.S.; Barclay, C.S.V.; East, J.A.

    2008-01-01

    This report provides a map and detailed descriptions of geologic formations for a 1,250 square mile region in the Rawlins-Little Snake River coal field in the eastern part of the Washakie and Great Divide Basins of south-central Wyoming. Mapping of geologic formations and coal beds was conducted at a scale of 1:24,000 and compiled at a scale of 1:100,000. Emphasis was placed on coal-bearing strata of the China Butte and Overland Members of the Paleocene Fort Union Formation. Surface stratigraphic sections were measured and described and well logs were examined to determine the lateral continuity of individual coal beds; the coal-bed stratigraphy is shown on correlation diagrams. A structure contour and overburden map constructed on the uppermost coal bed in the China Butte Member is also provided.

  4. Analysis and prediction of lightning strike distributions associated with synoptic map types over Florida

    SciTech Connect

    Reap, R.M.

    1994-08-01

    The temporal and spatial distributions of lightning activity associated with specific synoptic regimes of low-level wind flow were analyzed as part of an experiment to develop improved statistical thunderstorm forecasts for Florida. The synoptic regimes were identified by means of a linear correlation technique that was used to perform pattern classification or `map typing` of 18- and 30-h sea level pressure forecasts from the National Meteorological Center`s Nested Grid Model (NGM). Lightning location data for the 1987-90 warm seasons were subsequently analyzed on a 12-km grid to determine the thunderstorm distribution for each of the predetermined map types. The analysis revealed organized coastal maxima in lightning activity related to land-sea-breeze convergence zones that form in direct response to the low-level wind flow. Surface effects were also indicated by the persistent minima in lightning activity over Lake Okeechobee and by the lightning maxima found in regions with shoreline curvature favoring localized convergence. Experimental thunderstorm probability equations for Florida were subsequently developed from climatological lightning frequencies and NGM forecast fields. The lightning frequencies were combined with the K stability index to form interactive predictors that take into account the temporal and spatial variations in lightning occurrence for each map type but modulate the climatology in response to the daily large-scale synoptic situation. The statistical forecast equations were developed for each map type in an attempt to simulate the effects of small-scale processes, such as land-sea-breeze convergence zones, on the subsequent development of peninsular-scale convection.

  5. Vertical fault mapping within the Gutingkeng Formation of southern Taiwan: implications for sub-aerial mud diapir tectonics

    NASA Astrophysics Data System (ADS)

    Gourley, J. R.; Lee, Y.; Ching, K.

    2012-12-01

    Vertical faults were mapped around the periphery of the mudstone-rich Plio-Pleistocene Gutingkeng Formation (Gtk) in southern Taiwan. The faults are manifested as black colored, penetrating shear bands that intersect bedding planes of the Gtk (shear band dips range from 60 - 90 degrees; shear band thicknesses range from several centimeters to several meters). Thin (1-2cm), friable calcite veins were found locally within the shear bands and often contain weakly developed slickensides. Where available, the sense of shear of these faults show consistent interior upward motion of the Gtk. The Chishan Fault is the southeastern bounding structure of the Gtk and where exposed, near-vertical shear bands were observed with a normal sense of shear (west-side-up). In addition, three exploratory cores drilled in 2010 along the western edge of the hanging wall of the Chishan Fault did not intersect the fault or the Gtk after nearly 200 meters of drilling. This suggests that the main Chishan Fault may not be a typical top-to-the-west reverse fault as previously mapped and does not fit the typical fold and thrust geometry that is prevalent in the western foothills of Taiwan. Instead, we interpret the collective field evidence to suggest that the Chishan Fault is a near vertical structure that is accommodating uplift of the Gtk, similar to mechanism by which sub-aqueous mud diapirs grow. A chain of mud diapirs is located off the southeastern coast of Taiwan and the Gtk may be the onshore extension of this chain. The sub-aerial mud diapir hypothesis is further supported by recent leveling data collected across the Gtk that shows the largest vertical uplift in the region to be centered within the Gtk. Finally, observations at the western end of the Highway 3 tunnel through the Chishan fault and overlying Wushan Formation indicate that there is recent west side (footwall) uplift along the Chishan Fault. The vertical faults mapped within the Gtk are significant for they may provide

  6. Improvements in Off Design Aeroengine Performance Prediction Using Analytic Compressor Map Interpolation

    NASA Astrophysics Data System (ADS)

    Mist'e, Gianluigi Alberto; Benini, Ernesto

    2012-06-01

    Compressor map interpolation is usually performed through the introduction of auxiliary coordinates (β). In this paper, a new analytical bivariate β function definition to be used in compressor map interpolation is studied. The function has user-defined parameters that must be adjusted to properly fit to a single map. The analytical nature of β allows for rapid calculations of the interpolation error estimation, which can be used as a quantitative measure of interpolation accuracy and also as a valid tool to compare traditional β function interpolation with new approaches (artificial neural networks, genetic algorithms, etc.). The quality of the method is analyzed by comparing the error output to the one of a well-known state-of-the-art methodology. This comparison is carried out for two different types of compressor and, in both cases, the error output using the method presented in this paper is found to be consistently lower. Moreover, an optimization routine able to locally minimize the interpolation error by shape variation of the β function is implemented. Further optimization introducing other important criteria is discussed.

  7. Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

    PubMed Central

    Edwards, Stefan M.; Sørensen, Izel F.; Sarup, Pernille; Mackay, Trudy F. C.; Sørensen, Peter

    2016-01-01

    Predicting individual quantitative trait phenotypes from high-resolution genomic polymorphism data is important for personalized medicine in humans, plant and animal breeding, and adaptive evolution. However, this is difficult for populations of unrelated individuals when the number of causal variants is low relative to the total number of polymorphisms and causal variants individually have small effects on the traits. We hypothesized that mapping molecular polymorphisms to genomic features such as genes and their gene ontology categories could increase the accuracy of genomic prediction models. We developed a genomic feature best linear unbiased prediction (GFBLUP) model that implements this strategy and applied it to three quantitative traits (startle response, starvation resistance, and chill coma recovery) in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. Our results indicate that subsetting markers based on genomic features increases the predictive ability relative to the standard genomic best linear unbiased prediction (GBLUP) model. Both models use all markers, but GFBLUP allows differential weighting of the individual genetic marker relationships, whereas GBLUP weighs the genetic marker relationships equally. Simulation studies show that it is possible to further increase the accuracy of genomic prediction for complex traits using this model, provided the genomic features are enriched for causal variants. Our GFBLUP model using prior information on genomic features enriched for causal variants can increase the accuracy of genomic predictions in populations of unrelated individuals and provides a formal statistical framework for leveraging and evaluating information across multiple experimental studies to provide novel insights into the genetic architecture of complex traits. PMID:27235308

  8. Formation, Mechanisms, and Predictability of the Aleutian-Icelandic Low Seesaw in Ensemble AGCM Simulations.

    NASA Astrophysics Data System (ADS)

    Honda, Meiji; Kushnir, Yochanan; Nakamura, Hisashi; Yamane, Shozo; Zebiak, Stephen E.

    2005-05-01

    The potential predictability associated with the remote influence of midlatitude tropospheric anomalies over the North Pacific or the North Atlantic, via a seesawlike interannual oscillation between the surface Aleutian and Icelandic lows (AL and IL, respectively) is investigated. Data from a 24-member ensemble of 50-yr atmospheric general circulation model simulation forced with observed sea surface temperature (SST) conditions are analyzed by separating the total simulated fluctuations into the external component forced by the prescribed SST and the internal component generated by atmospheric internal dynamics. The AL-IL seesaw can be identified in both the external and internal components of the variability. In the external variability, determined through the ensemble mean, the seesaw is gradually formed from December to March through the development of a Pacific-North American (PNA) pattern-like wave train, remotely forced by the El Niño-Southern Oscillation. The amplitudes of the externally forced North Atlantic anomalies are only about half as large as the North Pacific anomalies. The potential predictability of the Atlantic anomalies, defined as the ratio of the SST-forced variance to the total variance, does not exceed the 20% level. In the internal component of the variability, determined from the deviations of each ensemble member from the ensemble mean, the negative correlation between the AL and IL anomalies is modest but persistent through winter. It is confirmed that, regardless of the polarity of the AL-IL seesaw, the IL anomalies are formed through eastward wave activity propagation of the stationary Rossby wave train emanating from the AL region in the form of what may be called a “PNAA pattern,” the extension of the PNA-like wave train into the Atlantic. Thus, the midwinter development of North Pacific anomalies is found to be a necessary, though not sufficient, condition for the seesaw formation. The persistence of the North Pacific

  9. Differential effects of two types of formative assessment in predicting performance of first-year medical students.

    PubMed

    Krasne, Sally; Wimmers, Paul F; Relan, Anju; Drake, Thomas A

    2006-05-01

    Formative assessments are systematically designed instructional interventions to assess and provide feedback on students' strengths and weaknesses in the course of teaching and learning. Despite their known benefits to student attitudes and learning, medical school curricula have been slow to integrate such assessments into the curriculum. This study investigates how performance on two different modes of formative assessment relate to each other and to performance on summative assessments in an integrated, medical-school environment. Two types of formative assessment were administered to 146 first-year medical students each week over 8 weeks: a timed, closed-book component to assess factual recall and image recognition, and an un-timed, open-book component to assess higher order reasoning including the ability to identify and access appropriate resources and to integrate and apply knowledge. Analogous summative assessments were administered in the ninth week. Models relating formative and summative assessment performance were tested using Structural Equation Modeling. Two latent variables underlying achievement on formative and summative assessments could be identified; a "formative-assessment factor" and a "summative-assessment factor," with the former predicting the latter. A latent variable underlying achievement on open-book formative assessments was highly predictive of achievement on both open- and closed-book summative assessments, whereas a latent variable underlying closed-book assessments only predicted performance on the closed-book summative assessment. Formative assessments can be used as effective predictive tools of summative performance in medical school. Open-book, un-timed assessments of higher order processes appeared to be better predictors of overall summative performance than closed-book, timed assessments of factual recall and image recognition.

  10. Permeability evolution of fractured limestone due to reactive flow: Observation and prediction of wormhole formation

    NASA Astrophysics Data System (ADS)

    Deng, H.; Fitts, J. P.; Crandall, D.; McIntyre, D.; Peters, C. A.

    2014-12-01

    Fractures in porous media provide preferential pathways for flow and solute transport. Their hydraulic properties are critical parameters for determining fluid migration and leakage, and are subject to alterations when exposed to reactive flow, e.g. CO2-acidfied brine in the case of carbon storage. Our previous studies have shown how mineral heterogeneity could lead to increased roughness that mitigates the increase in fracture permeability. This study shows that, even in rocks with mineral homogeneity, fracture geometry is subject to complex alterations. In this presentation, we report an experimental study of CO2-acidified brine in fractured Indiana Limestone, with comprehensive characterization of effluent chemistry analyzed by ICP-OES, and 3D geometry evolution using micro-computed topography (xCT). Significant carbonate dissolution was observed but the reaction extent revealed by the effluent chemistry was less than what was predicted by simple reaction transport models. xCT imaging revealed the formation of wormhole channels in the fracture, and the channels grew larger downstream and more prominent over time. Using the fracture geometries derived from the xCT images, we simulated the flow field and inferred the evolution of fracture hydraulic properties. To interpret the process of wormholing and its impacts on fracture hydraulic properties, we used reactive transport modeling to simulate the interplay between fracture geometry, fluid flow and geochemical reactions. Our simulations predicted that wormholes were formed in fractures with initial roughness representative of natural subsurface systems. The presence of wormholes caused a disproportionately larger permeability increase than would be expected given the extent of volume change.

  11. The role of predictive models in the formation of auditory streams.

    PubMed

    Denham, S L; Winkler, I

    2006-01-01

    Sounds provide us with useful information about our environment which complements that provided by other senses, but also poses specific processing problems. How does the auditory system distentangle sounds from different sound sources? And what is it that allows intermittent sound events from the same source to be associated with each other? Here we review findings from a wide range of studies using the auditory streaming paradigm in order to formulate a unified account of the processes underlying auditory perceptual organization. We present new computational modelling results which replicate responses in primary auditory cortex [Fishman, Y.I., Arezzo, J.C., Steinschneider, M., 2004. Auditory stream segregation in monkey auditory cortex: effects of frequency separation, presentation rate, and tone duration. J. Acoust. Soc. Am. 116, 1656-1670; Fishman, Y. I., Reser, D. H., Arezzo, J.C., Steinschneider, M., 2001. Neural correlates of auditory stream segregation in primary auditory cortex of the awake monkey. Hear. Res. 151, 167-187] to tone sequences. We also present the results of a perceptual experiment which confirm the bi-stable nature of auditory streaming, and the proposal that the gradual build-up of streaming may be an artefact of averaging across many subjects [Pressnitzer, D., Hupé, J. M., 2006. Temporal dynamics of auditory and visual bi-stability reveal common principles of perceptual organization. Curr. Biol. 16(13), 1351-1357.]. Finally we argue that in order to account for all of the experimental findings, computational models of auditory stream segregation require four basic processing elements; segregation, predictive modelling, competition and adaptation, and that it is the formation of effective predictive models which allows the system to keep track of different sound sources in a complex auditory environment.

  12. Genesis of Pre-Hurricane Felix (2007). Part 2; Warm Core Formation, Precipitation Evolution, and Predictability

    NASA Technical Reports Server (NTRS)

    Wang, zhuo; Montgomery M. T.; Dunkerton, T. J.

    2010-01-01

    This is the second of a two-part study examining the simulated formation of Atlantic Hurricane Felix (2007) in a cloud-representing framework. Here several open issues are addressed concerning the formation of the storm's warm core, the evolution and respective contribution of stratiform versus convective precipitation within the parent wave's pouch, and the sensitivity of the development pathway reported in Part I to different model physics options and initial conditions. All but one of the experiments include ice microphysics as represented by one of several parameterizations, and the partition of convective versus stratiform precipitation is accomplished using a standard numerical technique based on the high-resolution control experiment. The transition to a warm-core tropical cyclone from an initially cold-core, lower tropospheric wave disturbance is analyzed first. As part of this transformation process, it is shown that deep moist convection is sustained near the pouch center. Both convective and stratiform precipitation rates increase with time. While stratiform precipitation occupies a larger area even at the tropical storm stage, deep moist convection makes a comparable contribution to the total rain rate at the pregenesis stage, and a larger contribution than stratiform processes at the storm stage. The convergence profile averaged near the pouch center is found to become dominantly convective with increasing deep moist convective activity there. Low-level convergence forced by interior diabatic heating plays a key role in forming and intensifying the near-surface closed circulation, while the midlevel convergence associated with stratiform precipitation helps to increase the midlevel circulation and thereby contributes to the formation and upward extension of a tropospheric-deep cyclonic vortex. Sensitivity tests with different model physics options and initial conditions demonstrate a similar pregenesis evolution. These tests suggest that the genesis

  13. Genesis of Pre-Hurricane Felix (2007). Part 2; Warm Core Formation, Precipitation Evolution, and Predictability

    NASA Technical Reports Server (NTRS)

    Wang, zhuo; Montgomery M. T.; Dunkerton, T. J.

    2010-01-01

    This is the second of a two-part study examining the simulated formation of Atlantic Hurricane Felix (2007) in a cloud-representing framework. Here several open issues are addressed concerning the formation of the storm's warm core, the evolution and respective contribution of stratiform versus convective precipitation within the parent wave's pouch, and the sensitivity of the development pathway reported in Part I to different model physics options and initial conditions. All but one of the experiments include ice microphysics as represented by one of several parameterizations, and the partition of convective versus stratiform precipitation is accomplished using a standard numerical technique based on the high-resolution control experiment. The transition to a warm-core tropical cyclone from an initially cold-core, lower tropospheric wave disturbance is analyzed first. As part of this transformation process, it is shown that deep moist convection is sustained near the pouch center. Both convective and stratiform precipitation rates increase with time. While stratiform precipitation occupies a larger area even at the tropical storm stage, deep moist convection makes a comparable contribution to the total rain rate at the pregenesis stage, and a larger contribution than stratiform processes at the storm stage. The convergence profile averaged near the pouch center is found to become dominantly convective with increasing deep moist convective activity there. Low-level convergence forced by interior diabatic heating plays a key role in forming and intensifying the near-surface closed circulation, while the midlevel convergence associated with stratiform precipitation helps to increase the midlevel circulation and thereby contributes to the formation and upward extension of a tropospheric-deep cyclonic vortex. Sensitivity tests with different model physics options and initial conditions demonstrate a similar pregenesis evolution. These tests suggest that the genesis

  14. The Use of Fluid Mechanics to Predict Regions of Microscopic Thrombus Formation in Pulsatile VADs

    PubMed Central

    Topper, Stephen R.; Navitsky, Michael A.; Medvitz, Richard B.; Paterson, Eric G.; Siedlecki, Christopher A.; Slattery, Margaret J.; Deutsch, Steven; Rosenberg, Gerson; Manning, Keefe B.

    2014-01-01

    We compare the velocity and shear obtained from particle image velocimetry (PIV) and computational fluid dynamics (CFD) in a pulsatile ventricular assist device (VAD) to further test our thrombus predictive methodology using microscopy data from an explanted VAD. To mimic physiological conditions in vitro, a mock circulatory loop is used with a blood analog that matched blood’s viscoelastic behavior at 40% hematocrit. Under normal physiologic pressures and for a heart rate of 75 bpm, PIV data is acquired and wall shear maps are produced. The resolution of the PIV shear rate calculations are tested using the CFD and found to be in the same range. A bovine study, using a model of the 50 cc Penn State V-2 VAD, for 30 days at a constant beat rate of 75 beats per minute (bpm) provides the microscopic data whereby after the 30 days, the device is explanted and the sac surface analyzed using scanning electron microscopy (SEM) and, after immunofluorescent labeling for platelets and fibrin, confocal microscopy. Areas are examined based on PIV measurements and CFD, with special attention to low shear regions where platelet and fibrin deposition are most likely to occur. Data collected within the outlet port in a direction normal to the front wall of the VAD shows that some regions experience wall shear rates less than 500 s−1, which increases the likelihood of platelet and fibrin deposition. Despite only one animal study, correlations between PIV, CFD, and in vivo data show promise. Deposition probability is quantified by the thrombus susceptibility potential, a calculation to correlate low shear and time of shear with deposition. PMID:24634700

  15. The Use of Fluid Mechanics to Predict Regions of Microscopic Thrombus Formation in Pulsatile VADs.

    PubMed

    Topper, Stephen R; Navitsky, Michael A; Medvitz, Richard B; Paterson, Eric G; Siedlecki, Christopher A; Slattery, Margaret J; Deutsch, Steven; Rosenberg, Gerson; Manning, Keefe B

    2014-03-01

    We compare the velocity and shear obtained from particle image velocimetry (PIV) and computational fluid dynamics (CFD) in a pulsatile ventricular assist device (VAD) to further test our thrombus predictive methodology using microscopy data from an explanted VAD. To mimic physiological conditions in vitro, a mock circulatory loop is used with a blood analog that matched blood's viscoelastic behavior at 40% hematocrit. Under normal physiologic pressures and for a heart rate of 75 bpm, PIV data is acquired and wall shear maps are produced. The resolution of the PIV shear rate calculations are tested using the CFD and found to be in the same range. A bovine study, using a model of the 50 cc Penn State V-2 VAD, for 30 days at a constant beat rate of 75 beats per minute (bpm) provides the microscopic data whereby after the 30 days, the device is explanted and the sac surface analyzed using scanning electron microscopy (SEM) and, after immunofluorescent labeling for platelets and fibrin, confocal microscopy. Areas are examined based on PIV measurements and CFD, with special attention to low shear regions where platelet and fibrin deposition are most likely to occur. Data collected within the outlet port in a direction normal to the front wall of the VAD shows that some regions experience wall shear rates less than 500 s(-1), which increases the likelihood of platelet and fibrin deposition. Despite only one animal study, correlations between PIV, CFD, and in vivo data show promise. Deposition probability is quantified by the thrombus susceptibility potential, a calculation to correlate low shear and time of shear with deposition.

  16. REGIONAL PARADOX FORMATION STRUCTURE AND ISOCHORE MAPS, BLANDING SUB-BASIN, UTAH

    SciTech Connect

    Kevin McClure; Craig D. Morgan; Thomas C. Chidsey Jr.; David E. Eby

    2003-12-01

    Over 400 million barrels (64 million m{sup 3}) of oil have been produced from the shallow-shelf carbonate reservoirs in the Pennsylvanian (Desmoinesian) Paradox Formation in the Paradox Basin, Utah and Colorado. With the exception of the giant Greater Aneth field, the other 100 plus oil fields in the basin typically contain 2 to 10 million barrels (0.3-1.6 million m{sup 3}) of original oil in place. Most of these fields are characterized by high initial production rates followed by a very short productive life (primary), and hence premature abandonment. Only 15 to 25 percent of the original oil in place is recoverable during primary production from conventional vertical wells. An extensive and successful horizontal drilling program has been conducted in the giant Greater Aneth field (figure 1). However, to date, only two horizontal wells have been drilled in small Ismay and Desert Creek fields. The results from these wells were disappointing due to poor understanding of the carbonate facies and diagenetic fabrics that create reservoir heterogeneity. These small fields, and similar fields in the basin, are at high risk of premature abandonment. At least 200 million barrels (31.8 million m{sup 3}) of oil will be left behind in these small fields because current development practices leave compartments of the heterogeneous reservoirs undrained. Through proper geological evaluation of the reservoirs, production may be increased by 20 to 50 percent through the drilling of low-cost single or multilateral horizontal legs from existing vertical development wells. In addition, horizontal drilling from existing wells minimizes surface disturbances and costs for field development, particularly in the environmentally sensitive areas of southeastern Utah and southwestern Colorado.

  17. Predicting impact of multi-paths on phase change in map-based vehicular ad hoc networks

    NASA Astrophysics Data System (ADS)

    Rahmes, Mark; Lemieux, George; Sonnenberg, Jerome; Chester, David B.

    2014-05-01

    Dynamic Spectrum Access, which through its ability to adapt the operating frequency of a radio, is widely believed to be a solution to the limited spectrum problem. Mobile Ad Hoc Networks (MANETs) can extend high capacity mobile communications over large areas where fixed and tethered-mobile systems are not available. In one use case with high potential impact cognitive radio employs spectrum sensing to facilitate identification of allocated frequencies not currently accessed by their primary users. Primary users own the rights to radiate at a specific frequency and geographic location, secondary users opportunistically attempt to radiate at a specific frequency when the primary user is not using it. We quantify optimal signal detection in map based cognitive radio networks with multiple rapidly varying phase changes and multiple orthogonal signals. Doppler shift occurs due to reflection, scattering, and rapid vehicle movement. Path propagation as well as vehicle movement produces either constructive or destructive interference with the incident wave. Our signal detection algorithms can assist the Doppler spread compensation algorithm by deciding how many phase changes in signals are present in a selected band of interest. Additionally we can populate a spatial radio environment map (REM) database with known information that can be leveraged in an ad hoc network to facilitate Dynamic Spectrum Access. We show how topography can help predict the impact of multi-paths on phase change, as well as about the prediction from dense traffic areas. Utilization of high resolution geospatial data layers in RF propagation analysis is directly applicable.

  18. Mapping ECoG channel contributions to trajectory and muscle activity prediction in human sensorimotor cortex

    PubMed Central

    Nakanishi, Yasuhiko; Yanagisawa, Takufumi; Shin, Duk; Kambara, Hiroyuki; Yoshimura, Natsue; Tanaka, Masataka; Fukuma, Ryohei; Kishima, Haruhiko; Hirata, Masayuki; Koike, Yasuharu

    2017-01-01

    Studies on brain-machine interface techniques have shown that electrocorticography (ECoG) is an effective modality for predicting limb trajectories and muscle activity in humans. Motor control studies have also identified distributions of “extrinsic-like” and “intrinsic-like” neurons in the premotor (PM) and primary motor (M1) cortices. Here, we investigated whether trajectories and muscle activity predicted from ECoG were obtained based on signals derived from extrinsic-like or intrinsic-like neurons. Three participants carried objects of three different masses along the same counterclockwise path on a table. Trajectories of the object and upper arm muscle activity were predicted using a sparse linear regression. Weight matrices for the predictors were then compared to determine if the ECoG channels contributed more information about trajectory or muscle activity. We found that channels over both PM and M1 contributed highly to trajectory prediction, while a channel over M1 was the highest contributor for muscle activity prediction. PMID:28361947

  19. Mapping ECoG channel contributions to trajectory and muscle activity prediction in human sensorimotor cortex.

    PubMed

    Nakanishi, Yasuhiko; Yanagisawa, Takufumi; Shin, Duk; Kambara, Hiroyuki; Yoshimura, Natsue; Tanaka, Masataka; Fukuma, Ryohei; Kishima, Haruhiko; Hirata, Masayuki; Koike, Yasuharu

    2017-03-31

    Studies on brain-machine interface techniques have shown that electrocorticography (ECoG) is an effective modality for predicting limb trajectories and muscle activity in humans. Motor control studies have also identified distributions of "extrinsic-like" and "intrinsic-like" neurons in the premotor (PM) and primary motor (M1) cortices. Here, we investigated whether trajectories and muscle activity predicted from ECoG were obtained based on signals derived from extrinsic-like or intrinsic-like neurons. Three participants carried objects of three different masses along the same counterclockwise path on a table. Trajectories of the object and upper arm muscle activity were predicted using a sparse linear regression. Weight matrices for the predictors were then compared to determine if the ECoG channels contributed more information about trajectory or muscle activity. We found that channels over both PM and M1 contributed highly to trajectory prediction, while a channel over M1 was the highest contributor for muscle activity prediction.

  20. Early Prediction of Cancer Progression by Depth-Resolved Nanoscale Mapping of Nuclear Architecture from Unstained Tissue Specimens.

    PubMed

    Uttam, Shikhar; Pham, Hoa V; LaFace, Justin; Leibowitz, Brian; Yu, Jian; Brand, Randall E; Hartman, Douglas J; Liu, Yang

    2015-11-15

    Early cancer detection currently relies on screening the entire at-risk population, as with colonoscopy and mammography. Therefore, frequent, invasive surveillance of patients at risk for developing cancer carries financial, physical, and emotional burdens because clinicians lack tools to accurately predict which patients will actually progress into malignancy. Here, we present a new method to predict cancer progression risk via nanoscale nuclear architecture mapping (nanoNAM) of unstained tissue sections based on the intrinsic density alteration of nuclear structure rather than the amount of stain uptake. We demonstrate that nanoNAM detects a gradual increase in the density alteration of nuclear architecture during malignant transformation in animal models of colon carcinogenesis and in human patients with ulcerative colitis, even in tissue that appears histologically normal according to pathologists. We evaluated the ability of nanoNAM to predict "future" cancer progression in patients with ulcerative colitis who did and did not develop colon cancer up to 13 years after their initial colonoscopy. NanoNAM of the initial biopsies correctly classified 12 of 15 patients who eventually developed colon cancer and 15 of 18 who did not, with an overall accuracy of 85%. Taken together, our findings demonstrate great potential for nanoNAM in predicting cancer progression risk and suggest that further validation in a multicenter study with larger cohorts may eventually advance this method to become a routine clinical test.

  1. Prediction of Hot Tear Formation in Vertical DC Casting of Aluminum Billets Using a Granular Approach

    NASA Astrophysics Data System (ADS)

    Sistaninia, M.; Drezet, J.-M.; Phillion, A. B.; Rappaz, M.

    2013-09-01

    A coupled hydromechanical granular model aimed at predicting hot tear formation and stress-strain behavior in metallic alloys during solidification is applied to the semicontinuous direct chill casting of aluminum alloy round billets. This granular model consists of four separate three-dimensional (3D) modules: (I) a solidification module that is used for generating the solid-liquid geometry at a given solid fraction, (II) a fluid flow module that is used to calculate the solidification shrinkage and deformation-induced pressure drop within the intergranular liquid, (III) a semisolid deformation module that is based on a combined finite element/discrete element method and simulates the rheological behavior of the granular structure, and (IV) a failure module that simulates crack initiation and propagation. To investigate hot tearing, the granular model has been applied to a representative volume within the direct chill cast billet that is located at the bottom of the liquid sump, and it reveals that semisolid deformations imposed on the mushy zone open the liquid channels due to localization of the deformation at grains boundaries. At a low casting speed, only individual pores are able to form in the widest channels because liquid feeding remains efficient. However, as the casting speed increases, the flow of liquid required to compensate for solidification shrinkage also increases and as a result the pores propagate and coalesce to form a centerline crack.

  2. Numerical modeling of the flow in intracranial aneurysms: prediction of regions prone to thrombus formation.

    PubMed

    Rayz, V L; Boussel, L; Lawton, M T; Acevedo-Bolton, G; Ge, L; Young, W L; Higashida, R T; Saloner, D

    2008-11-01

    The deposition of intralumenal thrombus in intracranial aneurysms adds a risk of thrombo-embolism over and above that posed by mass effect and rupture. In addition to biochemical factors, hemodynamic factors that are governed by lumenal geometry and blood flow rates likely play an important role in the thrombus formation and deposition process. In this study, patient-specific computational fluid dynamics (CFD) models of blood flow were constructed from MRA data for three patients who had fusiform basilar aneurysms that were thrombus free and then proceeded to develop intralumenal thrombus. In order to determine whether features of the flow fields could suggest which regions had an elevated potential for thrombus deposition, the flow was modeled in the baseline, thrombus-free geometries. Pulsatile flow simulations were carried out using patient-specific inlet flow conditions measured with MR velocimetry. Newtonian and non-Newtonian blood behavior was considered. A strong similarity was found between the intra-aneurysmal regions with CFD-predicted slow, recirculating flows and the regions of thrombus deposition observed in vivo in the follow-up MR studies. In two cases with larger aneurysms, the agreement between the low velocity zones and clotted-off regions improved when non-Newtonian blood behavior was taken into account. A similarity was also found between the calculated low shear stress regions and the regions that were later observed to clot.

  3. Using Planet Formation Simulations to Predict the Free-floating Planet Yield Expected from WFIRST

    NASA Astrophysics Data System (ADS)

    Barclay, Thomas; Quintana, Elisa V.

    2016-06-01

    Planets are thought to form in circumstellar disks as a product of star formation. Material in the disk ends up in one of three places, (a) it remains in the disk as part of a planet, minor body or as interplanetary material, (b) it falls into the star, or (c) it is ejected from the system. We explore the properties of this ejected material using N-body simulations. We find that in planetary systems like ours (with Jupiter and Saturn) about half the ejected material is in bodies smaller than 1 Lunar-mass and about half is in bodies larger than 1 Mars-mass. The ejections happen early and no planets more massive than half an earth-mass are ejected. When no giant planets are present in the system, very little material is ejected. We predict that future space-borne microlensing searches for free-floating terrestrial-mass planets, such as WFIRST, will discover large numbers of Mars-mass planets but will not make significant detections of Earth-mass planets.

  4. Prediction of Infarct Lesion Volumes by Processing Magnetic Resonance Apparent Diffusion Coefficient Maps in Patients with Acute Ischemic Stroke.

    PubMed

    Qian, Qi; Huang, Hai-Tao; Xu, Li; Jin, Ping; Lin, Min

    2016-12-01

    We aimed to investigate the diagnostic value of apparent diffusion coefficient (ADC) maps in magnetic resonance imaging (MRI) in the volume of acute cerebral infarction (ACI). A total of 207 ACI patients were selected in our study. The cerebral infarction (CI) volume in the initial diffusion-weighted imaging examination, minimum ADC value, relative apparent diffusion coefficient (rADC) value, and mean ADC value were measured. The correlations between age, smoking, drinking, hypertension, diabetes, coronary heart disease, clinical stage, the lowest ADC value, the mean ADC value, and the mean rADC value with CI volume were analyzed by logistic regression analysis. A receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of the ADC value in the ACI volume. There was a significant difference in the distribution of the CI volume in ACI patients (P <.05). A significant difference was found in the signal intensity and percentage distribution of ADC map in patients of different CI groups with different CI volumes (P <.05). The signal of the ADC map was positively correlated with the CI volume. The mean ADC and rADC values had significant differences between different CI volumes (all P <.05). Logistic regression analysis revealed that the mean ADC value was significantly correlated with the CI volume (P <.05). Analysis of the ROC curve showed that the quantitative value of ADC has a diagnostic value for the ACI volume. This study has shown that the signal intensity change on the ADC map in MRI and quantitative analysis of the ADC value can be used as a reference for predicting the ACI volume. Copyright © 2016 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  5. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts.

    PubMed

    Piontkivska, Helen; Yang, Mary Q; Larkin, Denis M; Lewin, Harris A; Reecy, James; Elnitski, Laura

    2009-04-24

    Bidirectional promoters are shared regulatory regions that influence the expression of two oppositely oriented genes. This type of regulatory architecture is found more frequently than expected by chance in the human genome, yet many specifics underlying the regulatory design are unknown. Given that the function of most orthologous genes is similar across species, we hypothesized that the architecture and regulation of bidirectional promoters might also be similar across species, representing a core regulatory structure and enabling annotation of these regions in additional mammalian genomes. By mapping the intergenic distances of genes in human, chimpanzee, bovine, murine, and rat, we show an enrichment for pairs of genes equal to or less than 1,000 bp between their adjacent 5' ends ("head-to-head") compared to pairs of genes that fall in the same orientation ("head-to-tail") or whose 3' ends are side-by-side ("tail-to-tail"). A representative set of 1,369 human bidirectional promoters was mapped to orthologous sequences in other mammals. We confirmed predictions for 5' UTRs in nine of ten manual picks in bovine based on comparison to the orthologous human promoter set and in six of seven predictions in human based on comparison to the bovine dataset. The two predictions that did not have orthology as bidirectional promoters in the other species resulted from unique events that initiated transcription in the opposite direction in only those species. We found evidence supporting the independent emergence of bidirectional promoters from the family of five RecQ helicase genes, which gained their bidirectional promoters and partner genes independently rather than through a duplication process. Furthermore, by expanding our comparisons from pairwise to multispecies analyses we developed a map representing a core set of bidirectional promoters in mammals. We show that the orthologous positions of bidirectional promoters provide a reliable guide to directly annotate over

  6. Prediction of terrestrial gamma dose rate based on geological formations and soil types in the Johor State, Malaysia.

    PubMed

    Saleh, Muneer Aziz; Ramli, Ahmad Termizi; bin Hamzah, Khaidzir; Alajerami, Yasser; Moharib, Mohammed; Saeed, Ismael

    2015-10-01

    This study aims to predict and estimate unmeasured terrestrial gamma dose rate (TGDR) using statistical analysis methods to derive a model from the actual measurement based on geological formation and soil type. The measurements of TGDR were conducted in the state of Johor with a total of 3873 measured points which covered all geological formations, soil types and districts. The measurements were taken 1 m above the soil surface using NaI [Ti] detector. The measured gamma dose rates ranged from 9 nGy h(-1) to 1237 nGy h(-1) with a mean value of 151 nGy h(-1). The data have been normalized to fit a normal distribution. Tests of significance were conducted among all geological formations and soil types, using the unbalanced one way ANOVA. The results indicated strong significant differences due to the different geological formations and soil types present in Johor State. Pearson Correlation was used to measure the relations between gamma dose rate based on geological formation and soil type (D(G,S)) with the gamma dose rate based on geological formation (D(G)) or soil type (D(s)). A very good correlation was found between D(G,S) and D(G) or D(G,S) and D(s). A total of 118 pairs of geological formations and soil types were used to derive the statistical contribution of geological formations and soil types to gamma dose rates. The contribution of the gamma dose rate from geological formation and soil type were found to be 0.594 and 0.399, respectively. The null hypotheses were accepted for 83% of examined data, therefore, the model could be used to predict gamma dose rates based on geological formation and soil type information. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Predicting a small molecule-kinase interaction map: A machine learning approach

    PubMed Central

    2011-01-01

    Background We present a machine learning approach to the problem of protein ligand interaction prediction. We focus on a set of binding data obtained from 113 different protein kinases and 20 inhibitors. It was attained through ATP site-dependent binding competition assays and constitutes the first available dataset of this kind. We extract information about the investigated molecules from various data sources to obtain an informative set of features. Results A Support Vector Machine (SVM) as well as a decision tree algorithm (C5/See5) is used to learn models based on the available features which in turn can be used for the classification of new kinase-inhibitor pair test instances. We evaluate our approach using different feature sets and parameter settings for the employed classifiers. Moreover, the paper introduces a new way of evaluating predictions in such a setting, where different amounts of information about the binding partners can be assumed to be available for training. Results on an external test set are also provided. Conclusions In most of the cases, the presented approach clearly outperforms the baseline methods used for comparison. Experimental results indicate that the applied machine learning methods are able to detect a signal in the data and predict binding affinity to some extent. For SVMs, the binding prediction can be improved significantly by using features that describe the active site of a kinase. For C5, besides diversity in the feature set, alignment scores of conserved regions turned out to be very useful. PMID:21708012

  8. Online or Face-to-Face Learning? Exploring the Personal Factors that Predict Students' Choice of Instructional Format

    ERIC Educational Resources Information Center

    Artino, Anthony R., Jr.

    2010-01-01

    Notwithstanding the growth of online learning, little is known about the personal factors that predict student decisions to enroll in online courses. This study examined the relations between several personal factors and students' choice of instructional format. After completing an online course, service academy undergraduates (N = 564) completed…

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

    NASA Astrophysics Data System (ADS)

    Cassanelli, J. P.; Head, J. W.

    2017-10-01

    Climate models suggest early Mars was cold and icy. To test this prediction we assess the influence of cold conditions and the presence of an ice-cemented substrate on the formation of the valley networks and compare results to morphometric data.

  10. Online or Face-to-Face Learning? Exploring the Personal Factors that Predict Students' Choice of Instructional Format

    ERIC Educational Resources Information Center

    Artino, Anthony R., Jr.

    2010-01-01

    Notwithstanding the growth of online learning, little is known about the personal factors that predict student decisions to enroll in online courses. This study examined the relations between several personal factors and students' choice of instructional format. After completing an online course, service academy undergraduates (N = 564) completed…

  11. Predictive mapping of seabirds, pinnipeds and cetaceans off the Pacific Coast of Washington

    USGS Publications Warehouse

    Menza, Charles; Leirness, Jeffery B.; White, Tim; Winship, Arliss; Kinlan, Brian P.; Kracker, Laura; Zamon, Jeannette E.; Ballance, Lisa; Becker, Elizabeth; Forney, Karin A.; Barlow, Jay; Adams, Josh; Pereksta, David; Pearson, Scott; Pierce, John; Jeffries, Steven J.; Calambokidis, John; Douglas, Annie; Hanson, Bradford C.; Benson, Scott R.; Antrim, Liam

    2016-01-01

    This research supports the National Oceanic and Atmospheric Administration (NOAA) Coastal Zone Management Program, a voluntary partnership between the federal government and U.S. coastal and Great Lakes states and territories authorized by the Coastal Zone Management Act (CZMA) of 1972 to address national coastal issues. The act provides the basis for protecting, restoring, and responsibly developing our nation’s diverse coastal communities and resources. To meet the goals of the CZMA, the national program takes a comprehensive approach to coastal resource management – balancing the often competing and occasionally conflicting demands of coastal resource use, economic development, and conservation. A wide range of issues are addressed through the program, including coastal development, water quality, public access, habitat protection, energy facility siting, ocean governance and planning, coastal hazards, and climate change. Accurate maps of seabird and marine mammal distributions are an important tool for making informed management decisions that affect all of these issues. 

  12. Geologic mapping as a method for the construction of a detailed and testable lithostratigraphic model for the Upper Triassic Chinle Formation of Petrified Forest National Park, Arizona

    NASA Astrophysics Data System (ADS)

    Skinner, L. A.; Martz, J. W.; Parker, W.; Raucci, J.; Umhoefer, P. J.

    2010-12-01

    The Upper Triassic Chinle Formation in Petrified Forest National Park represents some of the most intensively studied Upper Triassic strata in western North America. Five stratigraphic members are exposed within the park, from oldest to youngest: the Mesa Redondo, Blue Mesa, Sonsela, Petrified Forest, and Owl Rock Members. Despite numerous stratigraphic studies of the Chinle Formation and two attempts at mapping the park over the past sixty years, sandstone marker beds in the Sonsela Member at the north and south ends of the park were still poorly mapped and correlated. Studies in the years 2002 and 2006 claimed that two sandstones which previous workers had considered to lie at different stratigraphic levels (the Jasper Forest Bed and the Flattops One sandstones in the Martha’s Butte beds) were actually correlative. This correlation resulted in a three-part division of the Sonsela Member and had a major impact on vertebrate biostratigraphy. In a recent attempt to resolve confusions regarding Chinle Formation lithostratigraphy and biostratigraphy, we have completely walked out lithologic contacts through most of the park. The resulting new geologic map, revised lithostratigraphic model, and associated data resolves the 2002 and 2006 miscorrelations by demonstrating that the Jasper Forest Bed capping Blue Mesa and Agate Mesa and Flattops One sandstones (Martha’s Butte beds) are stratigraphically distinct, resulting in a thicker and more complex five-part model for the Sonsela Member, and considerably modifying the vertebrate biostratigraphy. New geologic mapping also resulted in a detailed lithostratigraphic framework for the northern park which has previously been poorly understood, and several important new marker beds, including a purple-gray bed that represents the base of the Owl Rock Member. The revised geologic map is an ArcGIS product that includes an updated lithostratigraphic model for the Chinle Formation, fossil localities, and hyperlinks to labeled

  13. Mapping the Gas Turbulence in the Coma Cluster: Predictions for Astro-H

    NASA Technical Reports Server (NTRS)

    ZuHone, J. A.; Markevitch, M.; Zhuravleva, I.

    2016-01-01

    Astro-H will be able for the first time to map gas velocities and detect turbulence in galaxy clusters. One of the best targets for turbulence studies is the Coma cluster, due to its proximity, absence of a cool core, and lack of a central active galactic nucleus. To determine what constraints Astro-H will be able to place on the Coma velocity field, we construct simulated maps of the projected gas velocity and compute the second-order structure function, an analog of the velocity power spectrum. We vary the injection scale, dissipation scale, slope, and normalization of the turbulent power spectrum, and apply measurement errors and finite sampling to the velocity field. We find that even with sparse coverage of the cluster, Astro-H will be able to measure the Mach number and the injection scale of the turbulent power spectrum-the quantities determining the energy flux down the turbulent cascade and the diffusion rate for everything that is advected by the gas (metals, cosmic rays, etc.). Astro-H will not be sensitive to the dissipation scale or the slope of the power spectrum in its inertial range, unless they are outside physically motivated intervals. We give the expected confidence intervals for the injection scale and the normalization of the power spectrum for a number of possible pointing configurations, combining the structure function and velocity dispersion data. Importantly, we also determine that measurement errors on the line shift will bias the velocity structure function upward, and show how to correct this bias.

  14. Mapping the Gas Turbulence in the Coma Cluster: Predictions for Astro-H

    NASA Technical Reports Server (NTRS)

    ZuHone, J. A.; Markevitch, M.; Zhuravleva, I.

    2016-01-01

    Astro-H will be able for the first time to map gas velocities and detect turbulence in galaxy clusters. One of the best targets for turbulence studies is the Coma cluster, due to its proximity, absence of a cool core, and lack of a central active galactic nucleus. To determine what constraints Astro-H will be able to place on the Coma velocity field, we construct simulated maps of the projected gas velocity and compute the second-order structure function, an analog of the velocity power spectrum. We vary the injection scale, dissipation scale, slope, and normalization of the turbulent power spectrum, and apply measurement errors and finite sampling to the velocity field. We find that even with sparse coverage of the cluster, Astro-H will be able to measure the Mach number and the injection scale of the turbulent power spectrum-the quantities determining the energy flux down the turbulent cascade and the diffusion rate for everything that is advected by the gas (metals, cosmic rays, etc.). Astro-H will not be sensitive to the dissipation scale or the slope of the power spectrum in its inertial range, unless they are outside physically motivated intervals. We give the expected confidence intervals for the injection scale and the normalization of the power spectrum for a number of possible pointing configurations, combining the structure function and velocity dispersion data. Importantly, we also determine that measurement errors on the line shift will bias the velocity structure function upward, and show how to correct this bias.

  15. MAPPING THE GAS TURBULENCE IN THE COMA CLUSTER: PREDICTIONS FOR ASTRO-H

    SciTech Connect

    ZuHone, J. A.; Markevitch, M.

    2016-02-01

    Astro-H will be able for the first time to map gas velocities and detect turbulence in galaxy clusters. One of the best targets for turbulence studies is the Coma cluster, due to its proximity, absence of a cool core, and lack of a central active galactic nucleus. To determine what constraints Astro-H will be able to place on the Coma velocity field, we construct simulated maps of the projected gas velocity and compute the second-order structure function, an analog of the velocity power spectrum. We vary the injection scale, dissipation scale, slope, and normalization of the turbulent power spectrum, and apply measurement errors and finite sampling to the velocity field. We find that even with sparse coverage of the cluster, Astro-H will be able to measure the Mach number and the injection scale of the turbulent power spectrum—the quantities determining the energy flux down the turbulent cascade and the diffusion rate for everything that is advected by the gas (metals, cosmic rays, etc.). Astro-H will not be sensitive to the dissipation scale or the slope of the power spectrum in its inertial range, unless they are outside physically motivated intervals. We give the expected confidence intervals for the injection scale and the normalization of the power spectrum for a number of possible pointing configurations, combining the structure function and velocity dispersion data. Importantly, we also determine that measurement errors on the line shift will bias the velocity structure function upward, and show how to correct this bias.

  16. MAPPING SPATIAL/TEMPORAL DISTRIBUTIONS OF GREEN MACROALGAE IN A PACIFIC NORTHWEST COASTAL ESTUARY VIA SMALL FORMAT COLOR INFRARED AERIAL PHOTOGRAPHY

    EPA Science Inventory

    A small format 35 mm hand-held camera with color infrared slide film was used to map blooms of benthic green macroalgae upon mudflats of Yaquina Bay estuary on the central Oregon coast, U.S.A. Oblique photographs were taken during a series of low tide events, when the intertidal...

  17. MAPPING SPATIAL/TEMPORAL DISTRIBUTIONS OF GREEN MACROALGAE IN A PACIFIC NORTHWEST COASTAL ESTUARY VIA SMALL FORMAT COLOR INFRARED AERIAL PHOTOGRAPHY

    EPA Science Inventory

    A small format 35 mm hand-held camera with color infrared slide film was used to map blooms of benthic green macroalgae upon mudflats of Yaquina Bay estuary on the central Oregon coast, U.S.A. Oblique photographs were taken during a series of low tide events, when the intertidal...

  18. Radar monitoring of hydrology in Maryland's forested coastal plain wetlands: Implications for predicted climate change and improved mapping

    NASA Astrophysics Data System (ADS)

    Weiner Lang, Megan

    Wetlands provide important services to society but Mid-Atlantic wetlands are at high risk for loss, with forested wetlands being especially vulnerable. Hydrology (flooding and soil moisture) controls wetland function and extent but it may be altered due to changes in climate and anthropogenic influence. Wetland hydrology must better understood in order to predict and mitigate the impact of these changes. Broad-scale forested wetland hydrology is difficult to monitor using ground-based and traditional remote sensing methods. C-band synthetic aperture radar (SAR) data could improve the capability to monitor forested wetland hydrology but the abilities and limitations of these data need further investigation. This study examined: (1) the link between climate and wetland hydrology; (2) the ability of ENVISAT SAR (C-HH and C-VV) data to monitor inundation and soil moisture in forested wetlands; (3) limitations inherent to C-band data (incidence angle, polarization, and phenology) when monitoring forested wetland hydrology; and (4) the accuracy of forested wetland maps produced using SAR data. The study was primarily conducted near the Patuxent River in Maryland but the influence of incidence angle was considered along the Roanoke River in North Carolina. This study showed: (1) climate was highly correlated with wetland inundation; (2) significant differences in C-VV and C-HH backscatter existed between forested areas of varying hydrology (uplands and wetlands) throughout the year; (3) C-HH backscatter was better correlated to hydrology than C-VV backscatter; (4) correlations were stronger during the leaf-off season; (5) the difference in backscatter between flooded and non-flooded areas did not sharply decline with incidence angle, as predicted; and (6) maps produced using SAR data had relatively high accuracy levels. Based on these findings, I concluded that hydrology is influenced by climate at the study site, and C-HH data should be able to monitor changes in

  19. Incremental and Predictive Utility of Formative Assessment Methods of Reading Comprehension

    ERIC Educational Resources Information Center

    Marcotte, Amanda M.; Hintze, John M.

    2009-01-01

    Formative assessment measures are commonly used in schools to assess reading and to design instruction accordingly. The purpose of this research was to investigate the incremental and concurrent validity of formative assessment measures of reading comprehension. It was hypothesized that formative measures of reading comprehension would contribute…

  20. MAPS OF MASSIVE CLUMPS IN THE EARLY STAGE OF CLUSTER FORMATION: TWO MODES OF CLUSTER FORMATION, COEVAL OR NON-COEVAL?

    SciTech Connect

    Higuchi, Aya E.; Saito, Masao; Mauersberger, Rainer; Kawabe, Ryohei; Kurono, Yasutaka; Naoi, Takahiro

    2013-03-10

    We present maps of seven young massive molecular clumps within five target regions in C{sup 18}O (J = 1-0) line emission, using the Nobeyama 45 m telescope. These clumps, which are not associated with clusters, lie at distances between 0.7 and 2.1 kpc. We find C{sup 18}O clumps with radii of 0.5-1.7 pc, masses of 470-4200 M{sub Sun }, and velocity widths of 1.4-3.3 km s{sup -1}. All of the clumps are massive and approximately in virial equilibrium, suggesting they will potentially form clusters. Three of our target regions are associated with H II regions (CWHRs), while the other two are unassociated with H II regions (CWOHRs). The C{sup 18}O clumps can be classified into two morphological types: CWHRs with a filamentary or shell-like structure and spherical CWOHRs. The two CWOHRs have systematic velocity gradients. Using the publicly released WISE database, Class I and Class II protostellar candidates are identified within the C{sup 18}O clumps. The fraction of Class I candidates among all YSO candidates (Class I+Class II) is {>=}50% in CWHRs and {<=}50% in CWOHRs. We conclude that effects from the H II regions can be seen in (1) the spatial distributions of the clumps: filamentary or shell-like structure running along the H II regions; (2) the velocity structures of the clumps: large velocity dispersion along shells; and (3) the small age spreads of YSOs. The small spreads in age of the YSOs show that the presence of H II regions tends to trigger coeval cluster formation.

  1. Growth, inactivation and histamine formation of Morganella psychrotolerans and Morganella morganii - development and evaluation of predictive models.

    PubMed

    Emborg, Jette; Dalgaard, Paw

    2008-12-10

    Mathematical models for growth, heat inactivation and histamine formation by Morganella psychrotolerans and Morganella morganii were studied to evaluate the importance of these bacteria in seafood. Curves for growth and histamine formation by M. psychrotolerans in broth and seafood were generated at constant and changing storage temperatures (n=12). Observed and predicted times to formation of 100, 500 and 2000 ppm histamine were used for evaluation of an existing M. psychrotolerans histamine formation model [Emborg, J., Dalgaard, P., 2008-this issue-this issue. Modelling and predicting the growth and histamine formation by Morganella psychrotolerans. International Journal of Food Microbiology. doi:10.1016/j.ijfoodmicro.2008.08.016] Growth rates for M. psychrotolerans and M. morganii were determined at different constant temperatures from 0 degrees C to 42.5 degrees C whereas heat inactivation was studied between 37.5 degrees C and 60 degrees C. A M. morganii growth and histamine formation model was developed by combining these new data (growth rate model) and data from the existing literature (maximum population density and yield factor for histamine formation). The developed M. morganii model was evaluated by comparison of predicted growth and histamine formation with data from the existing literature. Observed and predicted growth rates for M. psychrotolerans, at constant temperatures, were similar with bias- and accuracy factor values of 1.15 and 1.45, respectively (n=11). On average times to formation of critical concentrations of histamine by M. psychrotolerans were acceptably predicted but the model was not highly accurate. Nevertheless, predictions seemed useful to support decisions concerning safe shelf-life in relation to formulation, storage and distribution of chilled seafood. Parameters for the effect of temperature on growth and inactivation of M. psychrotolerans and M. morganii differed markedly with Tmin of -8.3 to -5.9 degrees C vs. 0.3 to 2

  2. Taxi-Aware Map: Identifying and Predicting Vacant Taxis in the City

    NASA Astrophysics Data System (ADS)

    Phithakkitnukoon, Santi; Veloso, Marco; Bento, Carlos; Biderman, Assaf; Ratti, Carlo

    Knowing where vacant taxis are and will be at a given time and location helps the users in daily planning and scheduling, as well as the taxi service providers in dispatching. In this paper, we present a predictive model for the number of vacant taxis in a given area based on time of the day, day of the week, and weather condition. The history is used to build the prior probability distributions for our inference engine, which is based on the naïve Bayesian classifier with developed error-based learning algorithm and method for detecting adequacy of historical data using mutual information. Based on 150 taxis in Lisbon, Portugal, we are able to predict for each hour with the overall error rate of 0.8 taxis per 1x1 km2 area.

  3. Inter-residue spatial distance map prediction by using integrating GA with RBFNN.

    PubMed

    Zhang, Guang-Zheng; Huang, De-Shuang

    2004-12-01

    The spatial ordering information of amino acid residue in protein primary sequence is an important determinant of protein three-dimensional structure. In this paper, we describe a radial basis function neural network (RBFNN), whose hidden centers and basis function widths are optimized by a genetic algorithm (GA), for the purpose of predicting three dimensional spatial distance location from primary sequence information. Experimental evidence on soybean protein sequences indicates the utility of this approach.

  4. Mapping developmental precursors of cyber-aggression: trajectories of risk predict perpetration and victimization.

    PubMed

    Modecki, Kathryn L; Barber, Bonnie L; Vernon, Lynette; Vernon, Lynnette

    2013-05-01

    Technologically mediated contexts are social arenas in which adolescents can be both perpetrators and victims of aggression. Yet, there remains little understanding of the developmental etiology of cyber aggression, itself, as experienced by either perpetrators or victims. The current study examines 3-year latent within-person trajectories of known correlates of cyber-aggression: problem behavior, (low) self-esteem, and depressed mood, in a large and diverse sample of youth (N = 1,364; 54.6% female; 12-14 years old at T1). Findings demonstrate that developmental increases in problem behavior across grades 8-10 predict both cyber-perpetration and victimization in grade 11. Developmental decreases in self-esteem also predicted both grade 11 perpetration and victimization. Finally, early depressed mood predicted both perpetration and victimization later on, regardless of developmental change in depressed mood in the interim. Our results reveal a clear link between risky developmental trajectories across the early high school years and later cyber-aggression and imply that mitigating trajectories of risk early on may lead to decreases in cyber-aggression at a later date.

  5. Historical maintenance relevant information road-map for a self-learning maintenance prediction procedural approach

    NASA Astrophysics Data System (ADS)

    Morales, Francisco J.; Reyes, Antonio; Cáceres, Noelia; Romero, Luis M.; Benitez, Francisco G.; Morgado, Joao; Duarte, Emanuel; Martins, Teresa

    2017-09-01

    A large percentage of transport infrastructures are composed of linear assets, such as roads and rail tracks. The large social and economic relevance of these constructions force the stakeholders to ensure a prolonged health/durability. Even though, inevitable malfunctioning, breaking down, and out-of-service periods arise randomly during the life cycle of the infrastructure. Predictive maintenance techniques tend to diminish the appearance of unpredicted failures and the execution of needed corrective interventions, envisaging the adequate interventions to be conducted before failures show up. This communication presents: i) A procedural approach, to be conducted, in order to collect the relevant information regarding the evolving state condition of the assets involved in all maintenance interventions; this reported and stored information constitutes a rich historical data base to train Machine Learning algorithms in order to generate reliable predictions of the interventions to be carried out in further time scenarios. ii) A schematic flow chart of the automatic learning procedure. iii) Self-learning rules from automatic learning from false positive/negatives. The description, testing, automatic learning approach and the outcomes of a pilot case are presented; finally some conclusions are outlined regarding the methodology proposed for improving the self-learning predictive capability.

  6. Arterial spin labeling-based Z-maps have high specificity and positive predictive value for neurodegenerative dementia compared to FDG-PET.

    PubMed

    Fällmar, David; Haller, Sven; Lilja, Johan; Danfors, Torsten; Kilander, Lena; Tolboom, Nelleke; Egger, Karl; Kellner, Elias; Croon, Philip M; Verfaillie, Sander C J; van Berckel, Bart N M; Ossenkoppele, Rik; Barkhof, Frederik; Larsson, Elna-Marie

    2017-04-03

    Cerebral perfusion analysis based on arterial spin labeling (ASL) MRI has been proposed as an alternative to FDG-PET in patients with neurodegenerative disease. Z-maps show normal distribution values relating an image to a database of controls. They are routinely used for FDG-PET to demonstrate disease-specific patterns of hypometabolism at the individual level. This study aimed to compare the performance of Z-maps based on ASL to FDG-PET. Data were combined from two separate sites, each cohort consisting of patients with Alzheimer's disease (n = 18 + 7), frontotemporal dementia (n = 12 + 8) and controls (n = 9 + 29). Subjects underwent pseudocontinuous ASL and FDG-PET. Z-maps were created for each subject and modality. Four experienced physicians visually assessed the 166 Z-maps in random order, blinded to modality and diagnosis. Discrimination of patients versus controls using ASL-based Z-maps yielded high specificity (84%) and positive predictive value (80%), but significantly lower sensitivity compared to FDG-PET-based Z-maps (53% vs. 96%, p < 0.001). Among true-positive cases, correct diagnoses were made in 76% (ASL) and 84% (FDG-PET) (p = 0.168). ASL-based Z-maps can be used for visual assessment of neurodegenerative dementia with high specificity and positive predictive value, but with inferior sensitivity compared to FDG-PET. • ASL-based Z-maps yielded high specificity and positive predictive value in neurodegenerative dementia. • ASL-based Z-maps had significantly lower sensitivity compared to FDG-PET-based Z-maps. • FDG-PET might be reserved for ASL-negative cases where clinical suspicion persists. • Findings were similar at two study sites.

  7. Looking Back and Looking Forward: Reprising the Promise and Predicting the Future of Formation Flying and Spaceborne GPS Navigation Systems

    NASA Technical Reports Server (NTRS)

    Bauer, Frank H.; Dennehy, Neil

    2015-01-01

    A retrospective consideration of two 15-year old Guidance, Navigation and Control (GN&C) technology 'vision' predictions will be the focus of this paper. A look back analysis and critique of these late 1990s technology roadmaps out-lining the future vision, for two then nascent, but rapidly emerging, GN&C technologies will be performed. Specifically, these two GN&C technologies were: 1) multi-spacecraft formation flying and 2) the spaceborne use and exploitation of global positioning system (GPS) signals to enable formation flying. This paper reprises the promise of formation flying and spaceborne GPS as depicted in the cited 1999 and 1998 papers. It will discuss what happened to cause that promise to be mostly unfulfilled and the reasons why the envisioned formation flying dream has yet to become a reality. The recent technology trends over the past few years will then be identified and a renewed government interest in spacecraft formation flying/cluster flight will be highlighted. The authors will conclude with a reality-tempered perspective, 15 years after the initial technology roadmaps were published, predicting a promising future of spacecraft formation flying technology development over the next decade.

  8. Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping.

    PubMed

    Wang, Tingting; Chen, Yi-Ping Phoebe; MacLeod, Iona M; Pryce, Jennie E; Goddard, Michael E; Hayes, Ben J

    2017-08-15

    Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some traits, the most accurate genomic predictions are achieved with non-linear Bayesian methods. However, as the number of variants and the size of the reference population increase, the computational time required to implement these Bayesian methods (typically with Monte Carlo Markov Chain sampling) becomes unfeasibly long. Here, we applied a new method, HyB_BR (for Hybrid BayesR), which implements a mixture model of normal distributions and hybridizes an Expectation-Maximization (EM) algorithm followed by Markov Chain Monte Carlo (MCMC) sampling, to genomic prediction in a large dairy cattle population with imputed whole genome sequence data. The imputed whole genome sequence data included 994,019 variant genotypes of 16,214 Holstein and Jersey bulls and cows. Traits included fat yield, milk volume, protein kg, fat% and protein% in milk, as well as fertility and heat tolerance. HyB_BR achieved genomic prediction accuracies as high as the full MCMC implementation of BayesR, both for predicting a validation set of Holstein and Jersey bulls (multi-breed prediction) and a validation set of Australian Red bulls (across-breed prediction). HyB_BR had a ten fold reduction in compute time, compared with the MCMC implementation of BayesR (48 hours versus 594 hours). We also demonstrate that in many cases HyB_BR identified sequence variants with a high posterior probability of affecting the milk production or fertility traits that were similar to those identified in BayesR. For heat tolerance, both HyB_BR and BayesR found variants in or close to promising candidate genes associated with this trait and not detected by previous studies. The results demonstrate that HyB_BR is a feasible method for simultaneous genomic prediction and QTL mapping with whole genome sequence in

  9. FireMap: A Web Tool for Dynamic Data-Driven Predictive Wildfire Modeling Powered by the WIFIRE Cyberinfrastructure

    NASA Astrophysics Data System (ADS)

    Block, J.; Crawl, D.; Artes, T.; Cowart, C.; de Callafon, R.; DeFanti, T.; Graham, J.; Smarr, L.; Srivas, T.; Altintas, I.

    2016-12-01

    The NSF-funded WIFIRE project has designed a web-based wildfire modeling simulation and visualization tool called FireMap. The tool executes FARSITE to model fire propagation using dynamic weather and fire data, configuration settings provided by the user, and static topography and fuel datasets already built-in. Using GIS capabilities combined with scalable big data integration and processing, FireMap enables simple execution of the model with options for running ensembles by taking the information uncertainty into account. The results are easily viewable, sharable, repeatable, and can be animated as a time series. From these capabilities, users can model real-time fire behavior, analyze what-if scenarios, and keep a history of model runs over time for sharing with collaborators. Firemap runs FARSITE with national and local sensor networks for real-time weather data ingestion and High-Resolution Rapid Refresh (HRRR) weather for forecasted weather. The HRRR is a NOAA/NCEP operational weather prediction system comprised of a numerical forecast model and an analysis/assimilation system to initialize the model. It is run with a horizontal resolution of 3 km, has 50 vertical levels, and has a temporal resolution of 15 minutes. The HRRR requires an Environmental Data Exchange (EDEX) server to receive the feed and generate secondary products out of it for the modeling. UCSD's EDEX server, funded by NSF, makes high-resolution weather data available to researchers worldwide and enables visualization of weather systems and weather events lasting months or even years. The high-speed server aggregates weather data from the University Consortium for Atmospheric Research by way of a subscription service from the Consortium called the Internet Data Distribution system. These features are part of WIFIRE's long term goals to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. Although Firemap is a

  10. Efficient Inverse Isoparametric Mapping Algorithm for Whole-Body Computed Tomography Registration Using Deformations Predicted by Nonlinear Finite Element Modeling

    PubMed Central

    Li, Mao; Wittek, Adam; Miller, Karol

    2014-01-01

    Biomechanical modeling methods can be used to predict deformations for medical image registration and particularly, they are very effective for whole-body computed tomography (CT) image registration because differences between the source and target images caused by complex articulated motions and soft tissues deformations are very large. The biomechanics-based image registration method needs to deform the source images using the deformation field predicted by finite element models (FEMs). In practice, the global and local coordinate systems are used in finite element analysis. This involves the transformation of coordinates from the global coordinate system to the local coordinate system when calculating the global coordinates of image voxels for warping images. In this paper, we present an efficient numerical inverse isoparametric mapping algorithm to calculate the local coordinates of arbitrary points within the eight-noded hexahedral finite element. Verification of the algorithm for a nonparallelepiped hexahedral element confirms its accuracy, fast convergence, and efficiency. The algorithm's application in warping of the whole-body CT using the deformation field predicted by means of a biomechanical FEM confirms its reliability in the context of whole-body CT registration. PMID:24828796

  11. Prediction and diagnosis of renal cell carcinoma using nuclear magnetic resonance-based serum metabolomics and self-organizing maps

    PubMed Central

    Zheng, Hong; Ji, Jiansong; Zhao, Liangcai; Chen, Minjiang; Shi, An; Pan, Linlin; Huang, Yiran; Zhang, Huajie; Dong, Baijun; Gao, Hongchang

    2016-01-01

    Diagnosis of renal cell carcinoma (RCC) at an early stage is challenging, but it provides the best chance for cure. We aimed to develop a predictive diagnostic method for early-stage RCC based on a biomarker cluster using nuclear magnetic resonance (NMR)-based serum metabolomics and self-organizing maps (SOMs). We trained and validated the SOM model using serum metabolome data from 104 participants, including healthy individuals and early-stage RCC patients. To assess the predictive capability of the model, we analyzed an independent cohort of 22 subjects. We then used our method to evaluate changes in the metabolic patterns of 23 RCC patients before and after nephrectomy. A biomarker cluster of 7 metabolites (alanine, creatine, choline, isoleucine, lactate, leucine, and valine) was identified for the early diagnosis of RCC. The trained SOM model using a biomarker cluster was able to classify 22 test subjects into the appropriate categories. Following nephrectomy, all RCC patients were classified as healthy, which was indicative of metabolic recovery. But using a diagnostic criterion of 0.80, only 3 of the 23 subjects could not be confidently assessed as metabolically recovered after nephrectomy. We successfully followed-up 17 RCC patients for 8 years post-nephrectomy. Eleven of these patients who diagnosed as metabolic recovery remained healthy after 8 years. Our data suggest that a SOM model using a biomarker cluster from serum metabolome can accurately predict early RCC diagnosis and can be used to evaluate postoperative metabolic recovery. PMID:27463020

  12. Prediction and diagnosis of renal cell carcinoma using nuclear magnetic resonance-based serum metabolomics and self-organizing maps.

    PubMed

    Zheng, Hong; Ji, Jiansong; Zhao, Liangcai; Chen, Minjiang; Shi, An; Pan, Linlin; Huang, Yiran; Zhang, Huajie; Dong, Baijun; Gao, Hongchang

    2016-09-13

    Diagnosis of renal cell carcinoma (RCC) at an early stage is challenging, but it provides the best chance for cure. We aimed to develop a predictive diagnostic method for early-stage RCC based on a biomarker cluster using nuclear magnetic resonance (NMR)-based serum metabolomics and self-organizing maps (SOMs). We trained and validated the SOM model using serum metabolome data from 104 participants, including healthy individuals and early-stage RCC patients. To assess the predictive capability of the model, we analyzed an independent cohort of 22 subjects. We then used our method to evaluate changes in the metabolic patterns of 23 RCC patients before and after nephrectomy. A biomarker cluster of 7 metabolites (alanine, creatine, choline, isoleucine, lactate, leucine, and valine) was identified for the early diagnosis of RCC. The trained SOM model using a biomarker cluster was able to classify 22 test subjects into the appropriate categories. Following nephrectomy, all RCC patients were classified as healthy, which was indicative of metabolic recovery. But using a diagnostic criterion of 0.80, only 3 of the 23 subjects could not be confidently assessed as metabolically recovered after nephrectomy. We successfully followed-up 17 RCC patients for 8 years post-nephrectomy. Eleven of these patients who diagnosed as metabolic recovery remained healthy after 8 years. Our data suggest that a SOM model using a biomarker cluster from serum metabolome can accurately predict early RCC diagnosis and can be used to evaluate postoperative metabolic recovery.

  13. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.

    PubMed

    Vital-Lopez, Francisco G; Reifman, Jaques; Wallqvist, Anders

    2015-10-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  14. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

    PubMed Central

    Vital-Lopez, Francisco G.; Reifman, Jaques; Wallqvist, Anders

    2015-01-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  15. Predicting the formation and the dispersion of toxic combustion products from the fires of dangerous substances

    NASA Astrophysics Data System (ADS)

    Nevrlý, V.; Bitala, P.; Danihelka, P.; Dobeš, P.; Dlabka, J.; Hejzlar, T.; Baudišová, B.; Míček, D.; Zelinger, Z.

    2012-04-01

    Natural events, such as wildfires, lightning or earthquakes represent a frequent trigger of industrial fires involving dangerous substances. Dispersion of smoke plume from such fires and the effects of toxic combustion products are one of the reference scenarios expected in the framework of major accident prevention. Nowadays, tools for impact assessment of these events are rather missing. Detailed knowledge of burning material composition, atmospheric conditions, and other factors are required in order to describe quantitatively the source term of toxic fire products and to evaluate the parameters of smoke plume. Nevertheless, an assessment of toxic emissions from large scale fires involves a high degree of uncertainty, because of the complex character of physical and chemical processes in the harsh environment of uncontrolled flame. Among the others, soot particle formation can be mentioned as still being one of the unresolved problems in combustion chemistry, as well as decomposition pathways of chemical substances. Therefore, simplified approach for estimating the emission factors from outdoor fires of dangerous chemicals, utilizable for major accident prevention and preparedness, was developed and the case study illustrating the application of the proposed method was performed. ALOFT-FT software tool based on large eddy simulation of buoyant fire plumes was employed for predicting the local toxic contamination in the down-wind vicinity of the fire. The database of model input parameters can be effectively modified enabling the simulation of the smoke plume from pool fires or jet fires of arbitrary flammable (or combustible) gas, liquid or solid. This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic via the project LD11012 (in the frame of the COST CM0901 Action) and the Ministry of Environment of the Czech Republic (project no. SPII 1a10 45/70).

  16. The sediment composition and predictive mapping of facies on the Propeller Mound—A cold-water coral mound (Porcupine Seabight, NE Atlantic)

    NASA Astrophysics Data System (ADS)

    Heindel, Katrin; Titschack, Jürgen; Dorschel, Boris; Huvenne, Veerle A. I.; Freiwald, André

    2010-10-01

    , and video-data. This method is tested for the first time for CWC ecosystems and provides areal estimates of the predicted facies, as well as suggests further occurrences of living coral frameworks, coral rubble, and dropstones, which are not discovered in the area yet. Thus, sediment composition analysis combined with facies prediction mapping might provide a potential new tool to estimate living CWC occurrences and sediment/facies distributions on CWC mounds, which is an important prerequisite for budget calculations and definition of marine protected areas, and which will improve our understanding of CWC mound formation.

  17. Incorporation of satellite remote sensing pan-sharpened imagery into digital soil prediction and mapping models to characterize soil property variability in small agricultural fields

    NASA Astrophysics Data System (ADS)

    Xu, Yiming; Smith, Scot E.; Grunwald, Sabine; Abd-Elrahman, Amr; Wani, Suhas P.

    2017-01-01

    Soil prediction models based on spectral indices from some multispectral images are too coarse to characterize spatial pattern of soil properties in small and heterogeneous agricultural lands. Image pan-sharpening has seldom been utilized in Digital Soil Mapping research before. This research aimed to analyze the effects of pan-sharpened (PAN) remote sensing spectral indices on soil prediction models in smallholder farm settings. This research fused the panchromatic band and multispectral (MS) bands of WorldView-2, GeoEye-1, and Landsat 8 images in a village in Southern India by Brovey, Gram-Schmidt and Intensity-Hue-Saturation methods. Random Forest was utilized to develop soil total nitrogen (TN) and soil exchangeable potassium (Kex) prediction models by incorporating multiple spectral indices from the PAN and MS images. Overall, our results showed that PAN remote sensing spectral indices have similar spectral characteristics with soil TN and Kex as MS remote sensing spectral indices. There is no soil prediction model incorporating the specific type of pan-sharpened spectral indices always had the strongest prediction capability of soil TN and Kex. The incorporation of pan-sharpened remote sensing spectral data not only increased the spatial resolution of the soil prediction maps, but also enhanced the prediction accuracy of soil prediction models. Small farms with limited footprint, fragmented ownership and diverse crop cycle should benefit greatly from the pan-sharpened high spatial resolution imagery for soil property mapping. Our results show that multiple high and medium resolution images can be used to map soil properties suggesting the possibility of an improvement in the maps' update frequency. Additionally, the results should benefit the large agricultural community through the reduction of routine soil sampling cost and improved prediction accuracy.

  18. Preliminary geologic mapping of Cretaceous and Tertiary formations in the eastern part of the Little Snake River coal field, Carbon County, Wyoming

    USGS Publications Warehouse

    Haacke, Jon E.; Barclay, C. S. Venable; Hettinger, Robert D.

    2016-09-30

    In the 1970s and 1980s, C.S. Venable Barclay conducted geologic mapping of areas primarily underlain by Cretaceous coals in the eastern part of the Little Snake River coal field (LSR) in Carbon County, southwest Wyoming. With some exceptions, most of the mapping data were never published. Subsequently, after his retirement from the U.S. Geological Survey (USGS), his field maps and field notebooks were archived in the USGS Field Records. Due to a pending USGS coal assessment of the Little Snake River coal field area and planned geological mapping to be conducted by the Wyoming State Geological Survey, Barclay’s mapping data needed to be published to support these efforts. Subsequently, geologic maps were scanned and georeferenced into a geographic information system, and project and field notes were scanned into Portable Document Format (PDF) files. Data for seventeen 7½-minute quadrangles are presented in this report. This publication is solely intended to compile the mapping data as it was last worked on by Barclay and provides no interpretation or modification of his work.

  19. An anterior temporal face patch in human cortex, predicted by macaque maps

    PubMed Central

    Rajimehr, Reza; Young, Jeremy C.; Tootell, Roger B. H.

    2009-01-01

    Increasing evidence suggests that primate visual cortex has a specialized architecture for processing discrete object categories such as faces. Human fMRI studies have described a localized region in the fusiform gyrus [the fusiform face area (FFA)] that responds selectively to faces. In contrast, in nonhuman primates, electrophysiological and fMRI studies have instead revealed 2 apparently analogous regions of face representation: the posterior temporal face patch (PTFP) and the anterior temporal face patch (ATFP). An earlier study suggested that human FFA is homologous to the PTFP in macaque. However, in humans, no obvious homologue of the macaque ATFP has been demonstrated. Here, we used fMRI to map face-selective sites in both humans and macaques, based on equivalent stimuli in a quantitative topographic comparison. This fMRI evidence suggests that such a face-selective area exists in human anterior inferotemporal cortex, comprising the apparent homologue of the fMRI-defined ATFP in macaques. PMID:19179278

  20. Cognitive Correlates of Map-Reading Ability.

    ERIC Educational Resources Information Center

    Sholl, M. Jeanne; Egeth, Howard E.

    1982-01-01

    When the mathematics and extended range vocabulary subtests on the Relief Format Assessment Test were factor analyzed, altitude estimation (predicted by mathematics aptitude) and terrain analysis (predicted by vocabulary skills) were found to underly map-reading performance. Solutions were found to be dependent on verbal-analytic ability more than…

  1. Direct mapping rather than motor prediction subserves modulation of corticospinal excitability during observation of actions in real time.

    PubMed

    Gueugneau, Nicolas; Mc Cabe, Sofia I; Villalta, Jorge I; Grafton, Scott T; Della-Maggiore, Valeria

    2015-06-01

    Motor facilitation refers to the specific increment in corticospinal excitability (CSE) elicited by the observation of actions performed by others. To date, the precise nature of the mechanism at the basis of this phenomenon is unknown. One possibility is that motor facilitation is driven by a predictive process reminiscent of the role of forward models in motor control. Alternatively, motor facilitation may result from a model-free mechanism by which the basic elements of the observed action are directly mapped onto their cortical representations. Our study was designed to discern these alternatives. To this aim, we recorded the time course of CSE for the first dorsal interosseous (FDI) and the abductor digiti minimi (ADM) during observation of three grasping actions in real time, two of which strongly diverged in kinematics from their natural (invariant) form. Although artificially slow movements used in most action observation studies might enhance the observer's discrimination performance, the use of videos in real time is crucial to maintain the time course of CSE within the physiological range of daily actions. CSE was measured at 4 time points within a 240-ms window that best captured the kinematic divergence from the invariant form. Our results show that CSE of the FDI, not the ADM, closely follows the functional role of the muscle despite the mismatch between the natural and the divergent kinematics. We propose that motor facilitation during observation of actions performed in real time reflects the model-free coding of perceived movement following a direct mapping mechanism.

  2. Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora.

    PubMed

    Osborne, Amy J; Brauning, Rudiger; Schultz, Jennifer K; Kennedy, Martin A; Slate, Jon; Gemmell, Neil J

    2011-05-01

    Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species. These correlations are sometimes driven by a subset of markers, and it is unclear whether this is because those markers best reflect genome-wide heterozygosity, or whether they are linked to fitness-related genes. Differentiating between these scenarios is hindered when the genomic location of markers is unknown. Here, we develop a predicted genomic map of pinniped microsatellite loci based on conservation of primary sequence and genomic location between dog, cat and giant panda. We mapped 210 of 260 (81%) microsatellites from pinnipeds to locations in dog, cat and giant panda genomes. Based on the demonstrable synteny between the genomes of closely related taxa within the Carnivora, we use these data to identify those microsatellites with the greatest chance of cross-species amplification success and demonstrate successful amplification of 21 of 26 loci for cat, dog and two seal species. We also demonstrate the potential to identify candidate genes that may underpin the functional relationship with individual fitness. Overall, we show that this approach provides a rapid and robust method to elucidate genome organisation for nonmodel organisms and have established a resource that facilitates further genetic research on pinnipeds that also has wider applicability to other carnivores.

  3. Predicting Hip Fracture Type With Cortical Bone Mapping (CBM) in the Osteoporotic Fractures in Men (MrOS) Study

    PubMed Central

    Gee, Andrew H; Tonkin, Carol; Ewing, Susan K; Cawthon, Peggy M; Black, Dennis M; Poole, Kenneth ES

    2015-01-01

    ABSTRACT Hip fracture risk is known to be related to material properties of the proximal femur, but fracture prediction studies adding richer quantitative computed tomography (QCT) measures to dual‐energy X‐ray (DXA)‐based methods have shown limited improvement. Fracture types have distinct relationships to predictors, but few studies have subdivided fracture into types, because this necessitates regional measurements and more fracture cases. This work makes use of cortical bone mapping (CBM) to accurately assess, with no prior anatomical presumptions, the distribution of properties related to fracture type. CBM uses QCT data to measure the cortical and trabecular properties, accurate even for thin cortices below the imaging resolution. The Osteoporotic Fractures in Men (MrOS) study is a predictive case‐cohort study of men over 65 years old: we analyze 99 fracture cases (44 trochanteric and 55 femoral neck) compared to a cohort of 308, randomly selected from 5994. To our knowledge, this is the largest QCT‐based predictive hip fracture study to date, and the first to incorporate CBM analysis into fracture prediction. We show that both cortical mass surface density and endocortical trabecular BMD are significantly different in fracture cases versus cohort, in regions appropriate to fracture type. We incorporate these regions into predictive models using Cox proportional hazards regression to estimate hazard ratios, and logistic regression to estimate area under the receiver operating characteristic curve (AUC). Adding CBM to DXA‐based BMD leads to a small but significant (p < 0.005) improvement in model prediction for any fracture, with AUC increasing from 0.78 to 0.79, assessed using leave‐one‐out cross‐validation. For specific fracture types, the improvement is more significant (p < 0.0001), with AUC increasing from 0.71 to 0.77 for trochanteric fractures and 0.76 to 0.82 for femoral neck fractures. In contrast, adding DXA‐based BMD to a

  4. Predicting Hip Fracture Type With Cortical Bone Mapping (CBM) in the Osteoporotic Fractures in Men (MrOS) Study.

    PubMed

    Treece, Graham M; Gee, Andrew H; Tonkin, Carol; Ewing, Susan K; Cawthon, Peggy M; Black, Dennis M; Poole, Kenneth E S

    2015-11-01

    Hip fracture risk is known to be related to material properties of the proximal femur, but fracture prediction studies adding richer quantitative computed tomography (QCT) measures to dual-energy X-ray (DXA)-based methods have shown limited improvement. Fracture types have distinct relationships to predictors, but few studies have subdivided fracture into types, because this necessitates regional measurements and more fracture cases. This work makes use of cortical bone mapping (CBM) to accurately assess, with no prior anatomical presumptions, the distribution of properties related to fracture type. CBM uses QCT data to measure the cortical and trabecular properties, accurate even for thin cortices below the imaging resolution. The Osteoporotic Fractures in Men (MrOS) study is a predictive case-cohort study of men over 65 years old: we analyze 99 fracture cases (44 trochanteric and 55 femoral neck) compared to a cohort of 308, randomly selected from 5994. To our knowledge, this is the largest QCT-based predictive hip fracture study to date, and the first to incorporate CBM analysis into fracture prediction. We show that both cortical mass surface density and endocortical trabecular BMD are significantly different in fracture cases versus cohort, in regions appropriate to fracture type. We incorporate these regions into predictive models using Cox proportional hazards regression to estimate hazard ratios, and logistic regression to estimate area under the receiver operating characteristic curve (AUC). Adding CBM to DXA-based BMD leads to a small but significant (p < 0.005) improvement in model prediction for any fracture, with AUC increasing from 0.78 to 0.79, assessed using leave-one-out cross-validation. For specific fracture types, the improvement is more significant (p < 0.0001), with AUC increasing from 0.71 to 0.77 for trochanteric fractures and 0.76 to 0.82 for femoral neck fractures. In contrast, adding DXA-based BMD to a CBM-based predictive model

  5. 5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

    NASA Astrophysics Data System (ADS)

    Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

    2015-08-01

    Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCity

  6. Connectivity mapping (ssCMap) to predict A20-inducing drugs and their antiinflammatory action in cystic fibrosis

    PubMed Central

    Malcomson, Beth; Wilson, Hollie; Veglia, Eleonora; Thillaiyampalam, Gayathri; Barsden, Ruth; Donegan, Shauna; El Banna, Amal; Elborn, Joseph S.; Ennis, Madeleine; Kelly, Catriona; Zhang, Shu-Dong; Schock, Bettina C.

    2016-01-01

    Cystic fibrosis (CF) lung disease is characterized by chronic and exaggerated inflammation in the airways. Despite recent developments to therapeutically overcome the underlying functional defect in the cystic fibrosis transmembrane conductance regulator, there is still an unmet need to also normalize the inflammatory response. The prolonged and heightened inflammatory response in CF is, in part, mediated by a lack of intrinsic down-regulation of the proinflammatory NF-κB pathway. We have previously identified reduced expression of the NF-κB down-regulator A20 in CF as a key target to normalize the inflammatory response. Here, we have used publicly available gene array expression data together with a statistically significant connections’ map (sscMap) to successfully predict drugs already licensed for the use in humans to induce A20 mRNA and protein expression and thereby reduce inflammation. The effect of the predicted drugs on A20 and NF-κB(p65) expression (mRNA) as well as proinflammatory cytokine release (IL-8) in the presence and absence of bacterial LPS was shown in bronchial epithelial cells lines (16HBE14o−, CFBE41o−) and in primary nasal epithelial cells from patients with CF (Phe508del homozygous) and non-CF controls. Additionally, the specificity of the drug action on A20 was confirmed using cell lines with tnfαip3 (A20) knockdown (siRNA). We also show that the A20-inducing effect of ikarugamycin and quercetin is lower in CF-derived airway epithelial cells than in non-CF cells. PMID:27286825

  7. Prebiotic Atmospheric Chemistry on Titan: Formation Kinetics via Ab Initio Calculations for Potential Energy Surface (PES) Mapping

    NASA Astrophysics Data System (ADS)

    Gonzalez, Dayana; Mebel, Alexander

    2016-03-01

    It has been recently shown that Titan provides a unique perspective in our solar system: its atmosphere is comparable to a model of prebiotic Earth's. Provided the organic cationic and anionic molecular species identified by the Cassini spacecraft, this research characterizes reaction pathways for the reactions of methyl derivatives of the cyclopropenyl cation, the methyl cation with methyl- and dimethyl-acetylene, and reactions of resonance structures of protonated acrylonitrile with CH2NH. Isomerization and dissociation reactions involving methyl-cyclopropenyl cations, the perinaphthenyl cation and anion, and cations of pyrimidine and purine precursors of nucleobases will be examined to locate reaction pathways, intermediates, transition states, and products of the reactions. Gaussian '09 software is used for ab initio calculations to map out the PES. Geometry optimizations and vibrational frequency computations are preformed via the double-hybrid density functional B2PLYP-D3. Single-point energies are refined by use of the explicitly-correlated coupled-cluster CCSD(T)-F12 method. Rate constants are calculated using microcanonical RRKM theory, and pressure effects evaluated used the Master Equation approach; these allow for prediction of absolute rate constants and product branching ratios at different pressures and temperatures.

  8. Potentiometric-surface map of water in the Lakota Formation and equivalent units in the northern Great Plains area of Montana

    USGS Publications Warehouse

    Levings, Gary Wayne

    1982-01-01

    The potentiometric surface of water in the lower Cretaceous Lakota Formation and equivalent units (Cut Bank Sandstone Member , Sunburst Sandstone Member, and Moulton Member of Kootenai formation; Third Cat Creek sandstone of Kootenai Formation; Pryor Conglomerate Member of Kootenai Formation) is shown on a base at a scale of 1:1,000,000. The map is one of a series produced as part of a regional study of aquifers of Cenozoic and Mesozoic age in the northern Great Plains of Montana. The contour interval is 200 feet. Water in the Lakota Formation and equivalent units occurs under water-table and artesian conditions. The direction of regional groundwater movement is east and north from the recharge areas in the Little Belt and Big Snowy Mountains. The average discharge from 20 wells is about 29 gallons per minute and the specific capacity of 18 wells averages 0.75 gallon per minute per foot of drawdown.

  9. Early error detection predicted by reduced pre-response control process: an ERP topographic mapping study.

    PubMed

    Pourtois, Gilles

    2011-01-01

    Advanced ERP topographic mapping techniques were used to study error monitoring functions in human adult participants, and test whether proactive attentional effects during the pre-response time period could later influence early error detection mechanisms (as measured by the ERN component) or not. Participants performed a speeded go/nogo task, and made a substantial number of false alarms that did not differ from correct hits as a function of behavioral speed or actual motor response. While errors clearly elicited an ERN component generated within the dACC following the onset of these incorrect responses, I also found that correct hits were associated with a different sequence of topographic events during the pre-response baseline time-period, relative to errors. A main topographic transition from occipital to posterior parietal regions (including primarily the precuneus) was evidenced for correct hits ~170-150 ms before the response, whereas this topographic change was markedly reduced for errors. The same topographic transition was found for correct hits that were eventually performed slower than either errors or fast (correct) hits, confirming the involvement of this distinctive posterior parietal activity in top-down attentional control rather than motor preparation. Control analyses further ensured that this pre-response topographic effect was not related to differences in stimulus processing. Furthermore, I found a reliable association between the magnitude of the ERN following errors and the duration of this differential precuneus activity during the pre-response baseline, suggesting a functional link between an anticipatory attentional control component subserved by the precuneus and early error detection mechanisms within the dACC. These results suggest reciprocal links between proactive attention control and decision making processes during error monitoring.

  10. Predicting a Multi-Parametric Probability Map of Active Tumor Extent Using Random Forests*

    PubMed Central

    Prior, Fred W.; Fouke, Sarah J.; Benzinger, Tammie; Boyd, Alicia; Chicoine, Michael; Cholleti, Sharath; Kelsey, Matthew; Keogh, Bart; Kim, Lauren; Milchenko, Mikhail; Politte, David G.; Tyree, Stephen; Weinberger, Kilian; Marcus, Daniel

    2014-01-01

    Glioblastoma Mulitforme is highly infiltrative, making precise delineation of tumor margin difficult. Multimodality or multi-parametric MR imaging sequences promise an advantage over anatomic sequences such as post contrast enhancement as methods for determining the spatial extent of tumor involvement. In considering multi-parametric imaging sequences however, manual image segmentation and classification is time-consuming and prone to error. As a preliminary step toward integration of multi-parametric imaging into clinical assessments of primary brain tumors, we propose a machine-learning based multi-parametric approach that uses radiologist generated labels to train a classifier that is able to classify tissue on a voxel-wise basis and automatically generate a tumor segmentation. A random forests classifier was trained using a leave-one-out experimental paradigm. A simple linear classifier was also trained for comparison. The random forests classifier accurately predicted radiologist generated segmentations and tumor extent. PMID:24111225

  11. Rift Valley Fever Prediction and Risk Mapping: 2014-2015 Season

    NASA Technical Reports Server (NTRS)

    Anyamba, Assaf

    2015-01-01

    Extremes in either direction (+-) of precipitation temperature have significant implications for disease vectors and pathogen emergence and spread Magnitude of ENSO influence on precipitation temperature cannot be currently predicted rely on average history and patterns. Timing of event and emergence disease can be exploited (GAP) in to undertake vector control and preparedness measures. Currently - no risk for ecologically-coupled RVFV activity however we need to be vigilant during the coming fall season due the ongoing buildup of energy in the central Pacific Ocean. Potential for the dual-use of the RVF Monitor system for other VBDs Need to invest in early ground surveillance and the use of rapid field diagnostic capabilities for vector identification and virus isolation.

  12. Predicting a multi-parametric probability map of active tumor extent using random forests.

    PubMed

    Prior, Fred W; Fouke, Sarah J; Benzinger, Tammie; Boyd, Alicia; Chicoine, Michael; Cholleti, Sharath; Kelsey, Matthew; Keogh, Bart; Kim, Lauren; Milchenko, Mikhail; Politte, David G; Tyree, Stephen; Weinberger, Kilian; Marcus, Daniel

    2013-01-01

    Glioblastoma Mulitforme is highly infiltrative, making precise delineation of tumor margin difficult. Multimodality or multi-parametric MR imaging sequences promise an advantage over anatomic sequences such as post contrast enhancement as methods for determining the spatial extent of tumor involvement. In considering multi-parametric imaging sequences however, manual image segmentation and classification is time-consuming and prone to error. As a preliminary step toward integration of multi-parametric imaging into clinical assessments of primary brain tumors, we propose a machine-learning based multi-parametric approach that uses radiologist generated labels to train a classifier that is able to classify tissue on a voxel-wise basis and automatically generate a tumor segmentation. A random forests classifier was trained using a leave-one-out experimental paradigm. A simple linear classifier was also trained for comparison. The random forests classifier accurately predicted radiologist generated segmentations and tumor extent.

  13. Sphingoid Base Metabolism in Yeast: Mapping Gene Expression Patterns Into Qualitative Metabolite Time Course Predictions

    PubMed Central

    2001-01-01

    Can qualitative metabolite time course predictions be inferred from measured mRNA expression patterns? Speaking against this possibility is the large number of ‘decoupling’ control points that lie between these variables, i.e. translation, protein degradation, enzyme inhibition and enzyme activation. Speaking for it is the notion that these control points might be coordinately regulated such that action exerted on the mRNA level is informative of action exerted on the protein and metabolite levels. A simple kinetic model of sphingoid base metabolism in yeast is postulated. When the enzyme activities in this model are modulated proportional to mRNA expression levels measured in heat shocked yeast, the model yields a transient rise and fall in sphingoid bases followed by a permanent rise in ceramide. This finding is in qualitative agreement with experiments and is thus consistent with the aforementioned coordinated control system hypothesis. PMID:18629242

  14. Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model.

    PubMed

    Dhulekar, Nimit; Ray, Shayoni; Yuan, Daniel; Baskaran, Abhirami; Oztan, Basak; Larsen, Melinda; Yener, Bulent

    2016-01-01

    This study considers the problem of describing and predicting cleft formation during the early stages of branching morphogenesis in mouse submandibular salivary glands (SMG) under the influence of varied concentrations of epidermal growth factors (EGF). Given a time-lapse video of a growing SMG, first we build a descriptive model that captures the underlying biological process and quantifies the ground truth. Tissue-scale (global) and morphological features related to regions of interest (local features) are used to characterize the biological ground truth. Second, we devise a predictive growth model that simulates EGF-modulated branching morphogenesis using a dynamic graph algorithm, which is driven by biological parameters such as EGF concentration, mitosis rate, and cleft progression rate. Given the initial configuration of the SMG, the evolution of the dynamic graph predicts the cleft formation, while maintaining the local structural characteristics of the SMG. We determined that higher EGF concentrations cause the formation of higher number of buds and comparatively shallow cleft depths. Third, we compared the prediction accuracy of our model to the Glazier-Graner-Hogeweg (GGH) model, an on-lattice Monte-Carlo simulation model, under a specific energy function parameter set that allows new rounds of de novo cleft formation. The results demonstrate that the dynamic graph model yields comparable simulations of gland growth to that of the GGH model with a significantly lower computational complexity. Fourth, we enhanced this model to predict the SMG morphology for an EGF concentration without the assistance of a ground truth time-lapse biological video data; this is a substantial benefit of our model over other similar models that are guided and terminated by information regarding the final SMG morphology. Hence, our model is suitable for testing the impact of different biological parameters involved with the process of branching morphogenesis in silico, while

  15. Prediction of Growth Factor Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model

    PubMed Central

    Dhulekar, Nimit; Ray, Shayoni; Yuan, Daniel; Baskaran, Abhirami; Oztan, Basak; Larsen, Melinda; Yener, Bülent

    2016-01-01

    This study considers the problem of describing and predicting cleft formation during the early stages of branching morphogenesis in mouse submandibular salivary glands (SMG) under the influence of varied concentrations of epidermal growth factors (EGF). Given a time-lapse video of a growing SMG, first we build a descriptive model that captures the underlying biological process and quantifies the ground truth. Tissue-scale (global) and morphological features related to regions of interest (local features) are used to characterize the biological ground truth. Second, we devise a predictive growth model that simulates EGF-modulated branching morphogenesis using a dynamic graph algorithm, which is driven by biological parameters such as EGF concentration, mitosis rate, and cleft progression rate. Given the initial configuration of the SMG, the evolution of the dynamic graph predicts the cleft formation, while maintaining the local structural characteristics of the SMG. We determined that higher EGF concentrations cause the formation of higher number of buds and comparatively shallow cleft depths. Third, we compared the prediction accuracy of our model to the Glazier-Graner-Hogeweg (GGH) model, an on-lattice Monte-Carlo simulation model, under a specific energy function parameter set that allows new rounds of de novo cleft formation. The results demonstrate that the dynamic graph model yields comparable simulations of gland growth to that of the GGH model with a significantly lower computational complexity. Fourth, we enhanced this model to predict the SMG morphology for an EGF concentration without the assistance of a ground truth time-lapse biological video data; this is a substantial benefit of our model over other similar models that are guided and terminated by information regarding the final SMG morphology. Hence, our model is suitable for testing the impact of different biological parameters involved with the process of branching morphogenesis in silico, while

  16. Global prediction of abyssal hill roughness statistics for use in ocean models from digital maps of paleo-spreading rate, paleo-ridge orientation, and sediment thickness

    NASA Astrophysics Data System (ADS)

    Goff, John A.; Arbic, Brian K.

    Abyssal hills are the dominant small-scale roughness fabric over much of the ocean floor. Created at mid-ocean ridges by combined volcanic and tectonic processes, they are rafted away by plate spreading and modified through time by mass wasting and sedimentation. Abyssal hills are morphological indicators of spreading rate and direction: they are lineated parallel to the ridge at the time of formation, and their heights and widths are inversely correlated to spreading rate. Knowledge of abyssal hill roughness statistics is important for high-resolution models, including models of internal wave generation and mixing driven by tidal and low-frequency flows over the rough bottom. In this paper we present a prediction of abyssal hill roughness statistical parameters world-wide via relationships for the average statistical properties of abyssal hills as a function of spreading rate and direction, and for the modification to these roughness parameters as a function of sediment thickness. These relationships are constrained by new publicly-available digital maps of paleo-spreading rate and direction, and sediment thickness. We also develop a new method for generating synthetic topography with variable statistical properties over a grid, and present an example of synthetic abyssal hill roughness generated for the North Atlantic on a 1/2-min grid.

  17. Direct statistical modeling and its implications for predictive mapping in mining exploration

    NASA Astrophysics Data System (ADS)

    Sterligov, Boris; Gumiaux, Charles; Barbanson, Luc; Chen, Yan; Cassard, Daniel; Cherkasov, Sergey; Zolotaya, Ludmila

    2010-05-01

    Recent advances in geosciences make more and more multidisciplinary data available for mining exploration. This allowed developing methodologies for computing forecast ore maps from the statistical combination of such different input parameters, all based on an inverse problem theory. Numerous statistical methods (e.g. algebraic method, weight of evidence, Siris method, etc) with varying degrees of complexity in their development and implementation, have been proposed and/or adapted for ore geology purposes. In literature, such approaches are often presented through applications on natural examples and the results obtained can present specificities due to local characteristics. Moreover, though crucial for statistical computations, "minimum requirements" needed for input parameters (number of minimum data points, spatial distribution of objects, etc) are often only poorly expressed. From these, problems often arise when one has to choose between one and the