Replications of fundamental research models in ultra high dilutions 1994 and 2015 - update on a bibliometric study

INTRODUCTION This paper focuses exclusively on experimental models with ultra high dilutions (i.e. beyond 10(-23)) that have been submitted to replication scrutiny. It updates previous surveys, considers suggestions made by the research community and compares the state of replication in 1994 with that in 2015. METHODS Following literature research, biochemical, immunological, botanical, cell biological and zoological studies on ultra high dilutions (potencies) were included. Reports were grouped into initial studies, laboratory-internal, multicentre and external replications. Repetition could yield either comparable, or zero, or opposite results. The null-hypothesis was that test and control groups would not be distinguishable (zero effect). RESULTS A total of 126 studies were found. From these, 28 were initial studies. When all 98 replicative studies were considered, 70.4% (i.e. 69) reported a result comparable to that of the initial study, 20.4% (20) zero effect and 9.2% (9) an opposite result. Both for the studies until 1994 and the studies 1995-2015 the null-hypothesis (dominance of zero results) should be rejected. Furthermore, the odds of finding a comparable result are generally higher than of finding an opposite result. Although this is true for all three types of replication studies, the fraction of comparable studies diminishes from laboratory-internal (total 82.9%) to multicentre (total 75%) to external (total 48.3%), while the fraction of opposite results was 4.9%, 10.7% and 13.8%. Furthermore, it became obvious that the probability of an external replication producing comparable results is bigger for models that had already been further scrutinized by the initial researchers. CONCLUSIONS We found 28 experimental models which underwent replication. In total, 24 models were replicated with comparable results, 12 models with zero effect, and 6 models with opposite results. Five models were externally reproduced with comparable results. We encourage further replications of studies in order to learn more about the model systems used.

Global models of planet formation and evolution

Despite the strong increase in observational data on extrasolar planets, the processes that led to the formation of these planets are still not well understood. However, thanks to the high number of extrasolar planets that have been discovered, it is now possible to look at the planets as a population that puts statistical constraints on theoretical formation models. A method that uses these constraints is planetary population synthesis where synthetic planetary populations are generated and compared to the actual population. The key element of the population synthesis method is a global model of planet formation and evolution. These models directly predict observable planetary properties based on properties of the natal protoplanetary disc, linking two important classes of astrophysical objects. To do so, global models build on the simplified results of many specialized models that address one specific physical mechanism. We thoroughly review the physics of the sub-models included in global formation models. The sub-models can be classified as models describing the protoplanetary disc (of gas and solids), those that describe one (proto)planet (its solid core, gaseous envelope and atmosphere), and finally those that describe the interactions (orbital migration and N-body interaction). We compare the approaches taken in different global models, discuss the links between specialized and global models, and identify physical processes that require improved descriptions in future work. We then shortly address important results of planetary population synthesis like the planetary mass function or the mass-radius relationship. With these statistical results, the global effects of physical mechanisms occurring during planet formation and evolution become apparent, and specialized models describing them can be put to the observational test. Owing to their nature as meta models, global models depend on the results of specialized models, and therefore on the development of the field of planet formation theory as a whole. Because there are important uncertainties in this theory, it is likely that the global models will in future undergo significant modifications. Despite these limitations, global models can already now yield many testable predictions. With future global models addressing the geophysical characteristics of the synthetic planets, it should eventually become possible to make predictions about the habitability of planets based on their formation and evolution.

THE NATURAL AND ORTHOGONAL INTERACTION (NOIA) MODELS FOR QUANTITATIVE TRAITS (QTs) AND COMPLEX DISEASES

My dissertation focuses on developing methods for gene-gene/environment interactions and imprinting effect detections for human complex diseases and quantitative traits. It includes three sections: (1) generalizing the Natural and Orthogonal interaction (NOIA) model for the coding technique originally developed for gene-gene (GxG) interaction and also to reduced models; (2) developing a novel statistical approach that allows for modeling gene-environment (GxE) interactions influencing disease risk, and (3) developing a statistical approach for modeling genetic variants displaying parent-of-origin effects (POEs), such as imprinting. In the past decade, genetic researchers have identified a large number of causal variants for human genetic diseases and traits by single-locus analysis, and interaction has now become a hot topic in the effort to search for the complex network between multiple genes or environmental exposures contributing to the outcome. Epistasis, also known as gene-gene interaction is the departure from additive genetic effects from several genes to a trait, which means that the same alleles of one gene could display different genetic effects under different genetic backgrounds. In this study, we propose to implement the NOIA model for association studies along with interaction for human complex traits and diseases. We compare the performance of the new statistical models we developed and the usual functional model by both simulation study and real data analysis. Both simulation and real data analysis revealed higher power of the NOIA GxG interaction model for detecting both main genetic effects and interaction effects. Through application on a melanoma dataset, we confirmed the previously identified significant regions for melanoma risk at 15q13.1, 16q24.3 and 9p21.3. We also identified potential interactions with these significant regions that contribute to melanoma risk. Based on the NOIA model, we developed a novel statistical approach that allows us to model effects from a genetic factor and binary environmental exposure that are jointly influencing disease risk. Both simulation and real data analyses revealed higher power of the NOIA model for detecting both main genetic effects and interaction effects for both quantitative and binary traits. We also found that estimates of the parameters from logistic regression for binary traits are no longer statistically uncorrelated under the alternative model when there is an association. Applying our novel approach to a lung cancer dataset, we confirmed four SNPs in 5p15 and 15q25 region to be significantly associated with lung cancer risk in Caucasians population: rs2736100, rs402710, rs16969968 and rs8034191. We also validated that rs16969968 and rs8034191 in 15q25 region are significantly interacting with smoking in Caucasian population. Our approach identified the potential interactions of SNP rs2256543 in 6p21 with smoking on contributing to lung cancer risk. Genetic imprinting is the most well-known cause for parent-of-origin effect (POE) whereby a gene is differentially expressed depending on the parental origin of the same alleles. Genetic imprinting affects several human disorders, including diabetes, breast cancer, alcoholism, and obesity. This phenomenon has been shown to be important for normal embryonic development in mammals. Traditional association approaches ignore this important genetic phenomenon. In this study, we propose a NOIA framework for a single locus association study that estimates both main allelic effects and POEs. We develop statistical (Stat-POE) and functional (Func-POE) models, and demonstrate conditions for orthogonality of the Stat-POE model. We conducted simulations for both quantitative and qualitative traits to evaluate the performance of the statistical and functional models with different levels of POEs. Our results showed that the newly proposed Stat-POE model, which ensures orthogonality of variance components if Hardy-Weinberg Equilibrium (HWE) or equal minor and major allele frequencies is satisfied, had greater power for detecting the main allelic additive effect than a Func-POE model, which codes according to allelic substitutions, for both quantitative and qualitative traits. The power for detecting the POE was the same for the Stat-POE and Func-POE models under HWE for quantitative traits.

Lesson from the habitat suitability models to evaluate the environmental of Pinus nigra Arnold and Pinus sylvesris L. in the Iberian Peninsula

PREDICT POTENTIAL DISTRIBUTION. Spatial and temporal evolution of the species under different climate scenarios. Generation of habitat suitability models (HSM)  high degree of uncertainty and limitations. The importance of their validation has been stressed. In this work we discuss the present potential distribution of P. sylvestris and P. nigra in the Iberian Peninsula by using MaxEnt, and evaluate the influence of the different environmental variables. Our intention is to select a set of environmental variables that explains better their current distribution, to achieve the most accurate and reliable models. Then we project them to the past climatic conditions (21 to 0 kyrs BP), to evaluate the outputs with existing palaeo-ecological data.

Flow and fracture behaviour of high performance alloys

Based on our needs, that is to say, through precise simulation of the impact phenomena that may occur inside a jet engine turbine with an explicit non-linear finite element code, four new material models are postulated. Each one of is calibrated for four high-performance alloys that can be encountered in a modern jet engine. A new uncoupled material model for high strain and ballistic is proposed. Based on a Johnson-Cook type model, the proposed formulation introduces the effect of the third deviatoric invariant by means of three different Lode angle dependent functions. The Lode dependent functions are added to both plasticity and failure models. The postulated model is calibrated for a 6061-T651 aluminium alloy with data taken from the literature. The fracture pattern predictability of the JCX material model is shown performing numerical simulations of various quasi-static and dynamic tests. As an extension of the above-mentioned model, a modification in the thermal softening behaviour due to phase transformation temperatures is developed (JCXt). Additionally, a Lode angle dependent flow stress is defined. Analysing the phase diagram and high temperature tests performed, phase transformation temperatures of the FV535 stainless steel are determined. The postulated material model constants for the FV535 stainless steel are calibrated. A coupled elastoplastic-damage material model for high strain and ballistic applications is presented (JCXd). A Lode angle dependent function is added to the equivalent plastic strain to failure definition of the Johnson-Cook failure criterion. The weakening in the elastic law and in the Johnson-Cook type constitutive relation implicitly introduces the Lode angle dependency in the elastoplastic behaviour. The material model is calibrated for precipitation hardened Inconel 718 nickel-base superalloy. The combination of a Lode angle dependent failure criterion with weakened constitutive equations is proven to predict fracture patterns of the mechanical tests performed and provide reliable results. A transversely isotropic material model for directionally solidified alloys is presented. The proposed yield function is based a single linear transformation of the stress tensor. The linear operator weighs the degree of anisotropy of the yield function. The elastic behaviour, as well as the hardening, are considered isotropic. To model the hardening, a Johnson-Cook type relation is adopted. A material vector is included in the model implementation. The failure is modelled with the Cockroft-Latham failure criterion. The material vector allows orienting the reference orientation in any other that the user may need. The model is calibrated for the MAR-M 247 directionally solidified nickel-base superalloy.

Improving the management of water and nitrogen resources in cropping systems by using simulation models

Los modelos de simulación de cultivos permiten analizar varias combinaciones de laboreo-rotación y explorar escenarios de manejo. El modelo DSSAT fue evaluado bajo condiciones de secano en un experimento de campo de 16 años en la semiárida España central. Se evaluó el efecto del sistema de laboreo y las rotaciones basadas en cereales de invierno, en el rendimiento del cultivo y la calidad del suelo. Los modelos CERES y CROPGRO se utilizaron para simular el crecimiento y rendimiento del cultivo, mientras que el modelo DSSAT CENTURY se utilizó en las simulaciones de SOC y SN. Tanto las observaciones de campo como las simulaciones con CERES-Barley, mostraron que el rendimiento en grano de la cebada era mas bajo para el cereal continuo (BB) que para las rotaciones de veza (VB) y barbecho (FB) en ambos sistemas de laboreo. El modelo predijo más nitrógeno disponible en el laboreo convencional (CT) que en el no laboreo (NT) conduciendo a un mayor rendimiento en el CT. El SOC y el SN en la capa superficial del suelo, fueron mayores en NT que en CT, y disminuyeron con la profundidad en los valores tanto observados como simulados. Las mejores combinaciones para las condiciones de secano estudiadas fueron CT-VB y CT-FB, pero CT presentó menor contenido en SN y SOC que NT. El efecto beneficioso del NT en SOC y SN bajo condiciones Mediterráneas semiáridas puede ser identificado por observaciones de campo y por simulaciones de modelos de cultivos. La simulación del balance de agua en sistemas de cultivo es una herramienta útil para estudiar como el agua puede ser utilizado eficientemente. La comparación del balance de agua de DSSAT , con una simple aproximación “tipping bucket”, con el modelo WAVE más mecanicista, el cual integra la ecuación de Richard , es un potente método para valorar el funcionamiento del modelo. Los parámetros de suelo fueron calibrados usando el método de optimización global Simulated Annealing (SA). Un lisímetro continuo de pesada en suelo desnudo suministró los valores observados de drenaje y evapotranspiración (ET) mientras que el contenido de agua en el suelo (SW) fue suministrado por sensores de capacitancia. Ambos modelos funcionaron bien después de la optimización de los parámetros de suelo con SA, simulando el balance de agua en el suelo para el período de calibración. Para el período de validación, los modelos optimizados predijeron bien el contenido de agua en el suelo y la evaporación del suelo a lo largo del tiempo. Sin embargo, el drenaje fue predicho mejor con WAVE que con DSSAT, el cual presentó mayores errores en los valores acumulados. Esto podría ser debido a la naturaleza mecanicista de WAVE frente a la naturaleza más funcional de DSSAT. Los buenos resultados de WAVE indican que, después de la calibración, este puede ser utilizado como "benchmark" para otros modelos para periodos en los que no haya medidas de campo del drenaje. El funcionamiento de DSSAT-CENTURY en la simulación de SOC y N depende fuertemente del proceso de inicialización. Se propuso como método alternativo (Met.2) la inicialización de las fracciones de SOC a partir de medidas de mineralización aparente del suelo (Napmin). El Met.2 se comparó con el método de inicialización de Basso et al. (2011) (Met.1), aplicando ambos métodos a un experimento de campo de 4 años en un área en regadío de España central. Nmin y Napmin fueron sobreestimados con el Met.1, ya que la fracción estable obtenida (SOC3) en las capas superficiales del suelo fue más baja que con Met.2. El N lixiviado simulado fue similar en los dos métodos, con buenos resultados en los tratamientos de barbecho y cebada. El Met.1 subestimó el SOC en la capa superficial del suelo cuando se comparó con una serie observada de 12 años. El crecimiento y rendimiento del cultivo fueron adecuadamente simulados con ambos métodos, pero el N en la parte aérea de la planta y en el grano fueron sobreestimados con el Met.1. Los resultados variaron significativamente con las fracciones iniciales de SOC, resaltando la importancia del método de inicialización. El Met.2 ofrece una alternativa para la inicialización del modelo CENTURY, mejorando la simulación de procesos de N en el suelo. La continua emergencia de nuevas variedades de híbridos modernos de maíz limita la aplicación de modelos de simulación de cultivos, ya que estos nuevos híbridos necesitan ser calibrados en el campo para ser adecuados para su uso en los modelos. El desarrollo de relaciones basadas en la duración del ciclo, simplificaría los requerimientos de calibración facilitando la rápida incorporación de nuevos cultivares en DSSAT. Seis híbridos de maiz (FAO 300 hasta FAO 700) fueron cultivados en un experimento de campo de dos años en un área semiárida de regadío en España central. Los coeficientes genéticos fueron obtenidos secuencialmente, comenzando con los parámetros de desarrollo fenológico (P1, P2, P5 and PHINT), seguido de los parámetros de crecimiento del cultivo (G2 and G3). Se continuó el procedimiento hasta que la salida de las simulaciones estuvo en concordancia con las observaciones fenológicas de campo. Después de la calibración, los parámetros simulados se ajustaron bien a los parámetros observados, con bajos RMSE en todos los casos. Los P1 y P5 calibrados, incrementaron con la duración del ciclo. P1 fue una función lineal del tiempo térmico (TT) desde emergencia hasta floración y P5 estuvo linealmente relacionada con el TT desde floración a madurez. No hubo diferencias significativas en PHINT entre híbridos de FAO-500 a 700 , ya que tuvieron un número de hojas similar. Como los coeficientes fenológicos estuvieron directamente relacionados con la duración del ciclo, sería posible desarrollar rangos y correlaciones que permitan estimar dichos coeficientes a partir de la clasificación del ciclo. ABSTRACT Crop simulation models allow analyzing various tillage-rotation combinations and exploring management scenarios. DSSAT model was tested under rainfed conditions in a 16-year field experiment in semiarid central Spain. The effect of tillage system and winter cereal-based rotations on the crop yield and soil quality was evaluated. The CERES and CROPGRO models were used to simulate crop growth and yield, while the DSSAT CENTURY was used in the SOC and SN simulations. Both field observations and CERES-Barley simulations, showed that barley grain yield was lower for continuous cereal (BB) than for vetch (VB) and fallow (FB) rotations for both tillage systems. The model predicted higher nitrogen availability in the conventional tillage (CT) than in the no tillage (NT) leading to a higher yield in the CT. The SOC and SN in the top layer, were higher in NT than in CT, and decreased with depth in both simulated and observed values. The best combinations for the dry land conditions studied were CT-VB and CT-FB, but CT presented lower SN and SOC content than NT. The beneficial effect of NT on SOC and SN under semiarid Mediterranean conditions can be identified by field observations and by crop model simulations. The simulation of the water balance in cropping systems is a useful tool to study how water can be used efficiently. The comparison of DSSAT soil water balance, with a simpler “tipping bucket” approach, with the more mechanistic WAVE model, which integrates Richard’s equation, is a powerful method to assess model performance. The soil parameters were calibrated by using the Simulated Annealing (SA) global optimizing method. A continuous weighing lysimeter in a bare fallow provided the observed values of drainage and evapotranspiration (ET) while soil water content (SW) was supplied by capacitance sensors. Both models performed well after optimizing soil parameters with SA, simulating the soil water balance components for the calibrated period. For the validation period, the optimized models predicted well soil water content and soil evaporation over time. However, drainage was predicted better by WAVE than by DSSAT, which presented larger errors in the cumulative values. That could be due to the mechanistic nature of WAVE against the more functional nature of DSSAT. The good results from WAVE indicate that, after calibration, it could be used as benchmark for other models for periods when no drainage field measurements are available. The performance of DSSAT-CENTURY when simulating SOC and N strongly depends on the initialization process. Initialization of the SOC pools from apparent soil N mineralization (Napmin) measurements was proposed as alternative method (Met.2). Method 2 was compared to the Basso et al. (2011) initialization method (Met.1), by applying both methods to a 4-year field experiment in a irrigated area of central Spain. Nmin and Napmin were overestimated by Met.1, since the obtained stable pool (SOC3) in the upper layers was lower than from Met.2. Simulated N leaching was similar for both methods, with good results in fallow and barley treatments. Method 1 underestimated topsoil SOC when compared with a 12-year observed serial. Crop growth and yield were properly simulated by both methods, but N in shoots and grain were overestimated by Met.1. Results varied significantly with the initial SOC pools, highlighting the importance of the initialization procedure. Method 2 offers an alternative to initialize the CENTURY model, enhancing the simulation of soil N processes. The continuous emergence of new varieties of modern maize hybrids limits the application of crop simulation models, since these new hybrids should be calibrated in the field to be suitable for model use. The development of relationships based on the cycle duration, would simplify the calibration requirements facilitating the rapid incorporation of new cultivars into DSSAT. Six maize hybrids (FAO 300 through FAO 700) were grown in a 2-year field experiment in a semiarid irrigated area of central Spain. Genetic coefficients were obtained sequentially, starting with the phenological development parameters (P1, P2, P5 and PHINT), followed by the crop growth parameters (G2 and G3). The procedure was continued until the simulated outputs were in good agreement with the field phenological observations. After calibration, simulated parameters matched observed parameters well, with low RMSE in most cases. The calibrated P1 and P5 increased with the duration of the cycle. P1 was a linear function of the thermal time (TT) from emergence to silking and P5 was linearly related with the TT from silking to maturity . There were no significant differences in PHINT between hybrids from FAO-500 to 700 , as they had similar leaf number. Since phenological coefficients were directly related with the cycle duration, it would be possible to develop ranges and correlations which allow to estimate such coefficients from the cycle classification.

Métodos computacionales para visco-hiperelasticidad anisótropa en grandes deformaciones

El comportamiento mecánico de muchos materiales biológicos y poliméricos en grandes deformaciones se puede describir adecuadamente mediante formulaciones isocóricas hiperelásticas y viscoelásticas. Las ecuaciones de comportamiento elástico y viscoelástico y las formulaciones computacionales para materiales incompresibles isótropos en deformaciones finitas están ampliamente desarrolladas en la actualidad. Sin embargo, el desarrollo de modelos anisótropos no lineales y de sus correspondientes formulaciones computacionales sigue siendo un tema de investigación de gran interés. Cuando se consideran grandes deformaciones, existen muchas medidas de deformación disponibles con las que poder formular las ecuaciones de comportamiento. Los modelos en deformaciones cuadráticas facilitan la implementación en códigos de elementos finitos, ya que estas medidas surgen de forma natural en la formulación. No obstante, pueden dificultar la interpretación de los modelos y llevar a resultados pocos realistas. El uso de deformaciones logarítmicas permite el desarrollo de modelos más simples e intuitivos, aunque su formulación computacional debe ser adaptada a las exigencias del programa. Como punto de partida, en esta tesis se demuestra que las deformaciones logarítmicas representan la extensión natural de las deformaciones infinitesimales, tanto axiales como angulares, al campo de las grandes deformaciones. Este hecho permite explicar la simplicidad de las ecuaciones resultantes. Los modelos hiperelásticos predominantes en la actualidad están formulados en invariantes de deformaciones cuadráticas. Estos modelos, ya sean continuos o microestructurales, se caracterizan por tener una forma analítica predefinida. Su expresión definitiva se calcula mediante un ajuste de curvas a datos experimentales. Un modelo que no sigue esta metodología fue desarrollado por Sussman y Bathe. El modelo es sólo válido para isotropía y queda definido por una función de energía interpolada con splines, la cual reproduce los datos experimentales de forma exacta. En esta tesis se presenta su extensión a materiales transversalmente isótropos y ortótropos utilizando deformaciones logarítmicas. Asimismo, se define una nueva propiedad que las funciones de energía anisótropas deben satisfacer para que su convergencia al caso isótropo sea correcta. En visco-hiperelasticidad, aparte de las distintas funciones de energía disponibles, hay dos aproximaciones computational típicas basadas en variables internas. El modelo original de Simó está formulado en tensiones y es válido para materiales anisótropos, aunque sólo es adecuado para pequeñas desviaciones con respecto al equilibrio termodinámico. En cambio, el modelo basado en deformaciones de Reese y Govindjee permite grandes deformaciones no equilibradas pero es, en esencia, isótropo. Las formulaciones anisótropas en este último contexto son microestructurales y emplean el modelo isótropo para cada uno de los constituyentes. En esta tesis se presentan dos formulaciones fenomenológicas viscoelásticas definidas mediante funciones hiperelásticas anisótropas y válidas para grandes desviaciones con respecto al equilibrio termodinámico. El primero de los modelos está basado en la descomposición multiplicativa de Sidoroff y requiere un comportamiento viscoso isótropo. La formulación converge al modelo de Reese y Govindjee en el caso especial de isotropía elástica. El segundo modelo se define a partir de una descomposición multiplicativa inversa. Esta formulación está basada en una descripción co-rotacional del problema, es sustancialmente más compleja y puede dar lugar a tensores constitutivos ligeramente no simétricos. Sin embargo, su rango de aplicación es mucho mayor ya que permite un comportamiento anisótropo tanto elástico como viscoso. Varias simulaciones de elementos finitos muestran la gran versatilidad de estos modelos cuando se combinan con funciones hiperelásticas formadas por splines. ABSTRACT The mechanical behavior of many polymeric and biological materials may be properly modelled be means of isochoric hyperelastic and viscoelastic formulations. These materials may sustain large strains. The viscoelastic computational formulations for isotropic incompressible materials at large strains may be considered well established; for example Ogden’s hyperelastic function and the visco-hyperelastic model of Reese and Govindjee are well known models for isotropy. However, anisotropic models and computational procedures both for hyperelasticity and viscohyperelasticity are still under substantial research. Anisotropic hyperelastic models are typically based on structural invariants obtained from quadratic strain measures. These models may be microstructurallybased or phenomenological continuum formulations, and are characterized by a predefined analytical shape of the stored energy. The actual final expression of the stored energy depends on some material parameters which are obtained from an optimization algorithm, typically the Levenberg-Marquardt algorithm. We present in this work anisotropic spline-based hyperelastic stored energies in which the shape of the stored energy is obtained as part of the procedure and which (exactly in practice) replicates the experimental data. These stored energies are based on invariants obtained from logarithmic strain measures. These strain measures preserve the metric and the physical meaning of the trace and deviator operators and, hence, are interesting and meaningful for anisotropic formulations. Furthermore, the proposed stored energies may be formulated in order to have material-symmetries congruency both from a theoretical and from a numerical point of view, which are new properties that we define in this work. On the other hand, visco-hyperelastic formulations for anisotropic materials are typically based on internal stress-like variables following a procedure used by Sim´o. However, it can be shown that this procedure is not adequate for large deviations from thermodynamic equilibrium. In contrast, a formulation given by Reese and Govindjee is valid for arbitrarily large deviations from thermodynamic equilibrium but not for anisotropic stored energy functions. In this work we present two formulations for visco-hyperelasticity valid for anisotropic stored energies and large deviations from thermodynamic equilibrium. One of the formulations is based on the Sidoroff multiplicative decomposition and converges to the Reese and Govindjee formulation for the case of isotropy. However, the formulation is restricted to isotropy for the viscous component. The second formulation is based on a reversed multiplicative decomposition. This last formulation is substantially more complex and based on a corotational description of the problem. It can also result in a slightly nonsymmetric tangent. However, the formulation allows for anisotropy not only in the equilibrated and non-equilibrated stored energies, but also in the viscous behavior. Some examples show finite element implementation, versatility and interesting characteristics of the models.

Testing of crop Models for Accurate Predictions of Evapotranspiration and crop Water Use

All crop models, whether site-specific or global-gridded and regardless of crop, simulate daily crop transpiration and soil evaporation during the crop life cycle, resulting in seasonal crop water use. Modelers use several methods for predicting daily potential evapotranspiration (ET), including FAO-56, Penman-Monteith, Priestley-Taylor, Hargreaves, full energy balance, and transpiration water efficiency. They use extinction equations to partition energy to soil evaporation or transpiration, depending on leaf area index. Most models simulate soil water balance and soil-root water supply for transpiration, and limit transpiration if water uptake is insufficient, and thereafter reduce dry matter production. Comparisons among multiple crop and global gridded models in the Agricultural Model Intercomparison and Improvement Project (AgMIP) show surprisingly large differences in simulated ET and crop water use for the same climatic conditions. Model intercomparisons alone are not enough to know which approaches are correct. There is an urgent need to test these models against field-observed data on ET and crop water use. It is important to test various ET modules/equations in a model platform where other aspects such as soil water balance and rooting are held constant, to avoid compensation caused by other parts of models. The CSM-CROPGRO model in DSSAT already has ET equations for Priestley-Taylor, Penman-FAO-24, Penman-Monteith-FAO-56, and an hourly energy balance approach. In this work, we added transpiration-efficiency modules to DSSAT and AgMaize models and tested the various ET equations against available data on ET, soil water balance, and season-long crop water use of soybean, fababean, maize, and other crops where runoff and deep percolation were known or zero. The different ET modules created considerable differences in predicted ET, growth, and yield.

Depth Averaged Models for Fast Landslide Propagation: Mathematical, Rheological and Numerical Aspects

This paper presents an overview of depth averaged modelling of fast catastrophic landslides where coupling of solid skeleton and pore fluid (air and water) is important. The first goal is to show how Biot-Zienkiewicz models can be applied to develop depth integrated, coupled models. The second objective of the paper is to consider a link which can be established between rheological and constitutive models. Perzyna´s viscoplasticity can be considered a general framework within which rheological models such as Bingham and cohesive frictional fluids can be derived. Among the several alternative numerical models, we will focus here on SPH which has not been widely applied by engineers to model landslide propagation. We propose an improvement, based on combining Finite Difference meshes associated to SPH nodes to describe pore pressure evolution inside the landslide mass. We devote a Section to analyze the performance of the models, considering three sets of tests and examples which allows to assess the model performance and limitations: (i) Problems having an analytical solution, (ii) Small scale laboratory tests, and (iii) Real cases for which we have had access to reliable information

Schleiermacher's Doctrine of Biblical Authority: An Alternative to Content-Based/Supernaturalist and Function-Based Rationalist Models

Author: Kerry W. Holton Title: SCHLEIERMACHER’S DOCTRINE OF BIBLICAL AUTHORITY: AN ALTERNATIVE TO CONTENT-BASED/SUPERNATURALIST AND FUNCTION- BASED/RATIONALIST MODELS Advisor: Theodore M. Vial, Jr. Degree Date: August 2015 This dissertation examines Friedrich Schleiermacher’s understanding of biblical authority and argues that, as an alternative to strictly supernaturalistic and rationalistic models, his understanding allows the New Testament to speak authoritatively in Christian religion in an age of critical, historical awareness. After classifying Schleiermacher’s position in a typology of the doctrine of biblical authority, this dissertation explores his conception of divine revelation and inspiration vis-à-vis scripture. It demonstrates that although he did not believe there is warrant for the claim of a direct connection between divine revelation and scripture, or that scripture is the foundation of faith, he nonetheless asserted that the New Testament is authoritative. He asserted the normative authority of the New Testament on the basis that it is the first presentation of Christian faith. This dissertation examines Schleiermacher’s “canon within the canon,” as well as his denial that the Old Testament shares the same normative worth and inspiration of the New. Although this dissertation finds difficulty with some of Schleiermacher’s views regarding the Old Testament, it names two significant strengths of what is identified as his evangelical, content-based, and rationalist approach to biblical authority. First, it recognizes and values the co-presence and co-activity of the supernatural and the natural !ii in the production of the New Testament canon. This allows both scripture and the church to share religious authority. Second, it allows Christian faith and the historical-method to coexist, as it does not require people to contradict what they know to be the case about science, history, and philosophy. Thus, this dissertation asserts that Schleiermacher’s understanding of biblical authority is a robust one, since, for him, the authority of scripture does not lie in some property of the texts themselves that historians or unbelievers can take away.

Analysis of Melanoma Onset: Assessing Familial Aggregation by Using Estimating Equations and Fitting Variance Components via Bayesian Random Effects Models

We investigate whether relative contributions of genetic and shared environmental factors are associated with an increased risk in melanoma. Data from the Queensland Familial Melanoma Project comprising 15,907 subjects arising from 1912 families were analyzed to estimate the additive genetic, common and unique environmental contributions to variation in the age at onset of melanoma. Two complementary approaches for analyzing correlated time-to-onset family data were considered: the generalized estimating equations (GEE) method in which one can estimate relationship-specific dependence simultaneously with regression coefficients that describe the average population response to changing covariates; and a subject-specific Bayesian mixed model in which heterogeneity in regression parameters is explicitly modeled and the different components of variation may be estimated directly. The proportional hazards and Weibull models were utilized, as both produce natural frameworks for estimating relative risks while adjusting for simultaneous effects of other covariates. A simple Markov Chain Monte Carlo method for covariate imputation of missing data was used and the actual implementation of the Bayesian model was based on Gibbs sampling using the free ware package BUGS. In addition, we also used a Bayesian model to investigate the relative contribution of genetic and environmental effects on the expression of naevi and freckles, which are known risk factors for melanoma.

Effects of potential models on the adsorption of ethane and ethylene on graphitized thermal carbon black. Study of two-dimensional critical temperature and isosteric heat versus loading

Adsorption of ethylene and ethane on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers is studied in detail to investigate the packing efficiency, the two-dimensional critical temperature, and the variation of the isosteric heat of adsorption with loading and temperature. Here we used a Monte Carlo simulation method with a grand canonical Monte Carlo ensemble. A number of two-center Lennard-Jones (LJ) potential models are investigated to study the impact of the choice of potential models in the description of adsorption behavior. We chose two 2C-LJ potential models in our investigation of the (i) UA-TraPPE-LJ model of Martin and Siepmann (J. Phys. Chem. B 1998,102, 25692577) for ethane and Wick et al. (J. Phys. Chem. B 2000,104, 8008-8016) for ethylene and (ii) AUA4-LJ model of Ungerer et al. (J. Chem. Phys. 2000,112, 5499-5510) for ethane and Bourasseau et al. (J. Chem. Phys. 2003, 118, 3020-3034) for ethylene. These models are used to study the adsorption of ethane and ethylene on graphitized thermal carbon black. It is found that the solid-fluid binary interaction parameter is a function of adsorbate and temperature, and the adsorption isotherms and heat of adsorption are well described by both the UA-TraPPE and AUA models, although the UA-TraPPE model performs slightly better. However, the local distributions predicted by these two models are slightly different. These two models are used to explore the two-dimensional condensation for the graphitized thermal carbon black, and these values are 110 K for ethylene and 120 K for ethane.

Equivalence of the Peleg, Pilosof and Singh-Kulshrestha models for water absorption in food

The similarity between the Peleg, Pilosof –Boquet–Batholomai and Singh–Kulshrestha models was investigated using the hydration behaviours of whey protein concentrate, wheat starch and whey protein isolate at 30 °C in 100% relative humidity. The three models were shown to be mathematically the same within experimental variations, and they yielded parameters that are related. The models, in their linear and original forms, were suitable (r2 > 0.98) in describing the sorption behaviours of the samples, and are sensitive to the length of the sorption segment used in the computation. The whey proteins absorbed more moisture than the wheat starch, and the isolate exhibited a higher sorptive ability than the concentrate.

A comparison of linear forecasting models and neural networks:an application to Euro inflation and Euro Divisia

Linear models reach their limitations in applications with nonlinearities in the data. In this paper new empirical evidence is provided on the relative Euro inflation forecasting performance of linear and non-linear models. The well established and widely used univariate ARIMA and multivariate VAR models are used as linear forecasting models whereas neural networks (NN) are used as non-linear forecasting models. It is endeavoured to keep the level of subjectivity in the NN building process to a minimum in an attempt to exploit the full potentials of the NN. It is also investigated whether the historically poor performance of the theoretically superior measure of the monetary services flow, Divisia, relative to the traditional Simple Sum measure could be attributed to a certain extent to the evaluation of these indices within a linear framework. Results obtained suggest that non-linear models provide better within-sample and out-of-sample forecasts and linear models are simply a subset of them. The Divisia index also outperforms the Simple Sum index when evaluated in a non-linear framework. © 2005 Taylor & Francis Group Ltd.

Techniques to improve forecasting models: applications to energy demand and price

This thesis is a study of three techniques to improve performance of some standard fore-casting models, application to the energy demand and prices. We focus on forecasting demand and price one-day ahead. First, the wavelet transform was used as a pre-processing procedure with two approaches: multicomponent-forecasts and direct-forecasts. We have empirically compared these approaches and found that the former consistently outperformed the latter. Second, adaptive models were introduced to continuously update model parameters in the testing period by combining ?lters with standard forecasting methods. Among these adaptive models, the adaptive LR-GARCH model was proposed for the fi?rst time in the thesis. Third, with regard to noise distributions of the dependent variables in the forecasting models, we used either Gaussian or Student-t distributions. This thesis proposed a novel algorithm to infer parameters of Student-t noise models. The method is an extension of earlier work for models that are linear in parameters to the non-linear multilayer perceptron. Therefore, the proposed method broadens the range of models that can use a Student-t noise distribution. Because these techniques cannot stand alone, they must be combined with prediction models to improve their performance. We combined these techniques with some standard forecasting models: multilayer perceptron, radial basis functions, linear regression, and linear regression with GARCH. These techniques and forecasting models were applied to two datasets from the UK energy markets: daily electricity demand (which is stationary) and gas forward prices (non-stationary). The results showed that these techniques provided good improvement to prediction performance.