Artificial pumping errors in the Kool-Parker scaling model of soil moisture hysteresis

Hysteresis models that eliminate the artificial pumping errors associated with the Kool-Parker (KP) soil moisture hysteresis model, such as the Parker-Lenhard (PL) method, can be computationally demanding in unsaturated transport models since they need to retain the wetting-drying history of the system. The pumping errors in these models need to be eliminated for correct simulation of cyclical systems (e.g. transport above a tidally forced watertable, infiltration and redistribution under periodic irrigation) if the soils exhibit significant hysteresis. A modification is made here to the PL method that allows it to be more readily applied to numerical models by eliminating the need to store a large number of soil moisture reversal points. The modified-PL method largely eliminates any artificial pumping error and so essentially retains the accuracy of the original PL approach. The modified-PL method is implemented in HYDRUS-1D (version 2.0), which is then used to simulate cyclic capillary fringe dynamics to show the influence of removing artificial pumping errors and to demonstrate the ease of implementation. Artificial pumping errors are shown to be significant for the soils and system characteristics used here in numerical experiments of transport above a fluctuating watertable. (c) 2005 Elsevier B.V. All rights reserved.

Effects of syllable structure in aphasic errors:implications for a new model of speech production

Current models of word production assume that words are stored as linear sequences of phonemes which are structured into syllables only at the moment of production. This is because syllable structure is always recoverable from the sequence of phonemes. In contrast, we present theoretical and empirical evidence that syllable structure is lexically represented. Storing syllable structure would have the advantage of making representations more stable and resistant to damage. On the other hand, re-syllabifications affect only a minimal part of phonological representations and occur only in some languages and depending on speech register. Evidence for these claims comes from analyses of aphasic errors which not only respect phonotactic constraints, but also avoid transformations which move the syllabic structure of the word further away from the original structure, even when equating for segmental complexity. This is true across tasks, types of errors, and, crucially, types of patients. The same syllabic effects are shown by apraxic patients and by phonological patients who have more central difficulties in retrieving phonological representations. If syllable structure was only computed after phoneme retrieval, it would have no way to influence the errors of phonological patients. Our results have implications for psycholinguistic and computational models of language as well as for clinical and educational practices.

Keratoconus prediction using a finite element model of the cornea with local biomechanical properties

PURPOSE: The ability to predict and understand which biomechanical properties of the cornea are responsible for the stability or progression of keratoconus may be an important clinical and surgical tool for the eye-care professional. We have developed a finite element model of the cornea, that tries to predicts keratoconus-like behavior and its evolution based on material properties of the corneal tissue. METHODS: Corneal material properties were modeled using bibliographic data and corneal topography was based on literature values from a schematic eye model. Commercial software was used to simulate mechanical and surface properties when the cornea was subject to different local parameters, such as elasticity. RESULTS: The simulation has shown that, depending on the corneal initial surface shape, changes in local material properties and also different intraocular pressures values induce a localized protuberance and increase in curvature when compared to the remaining portion of the cornea. CONCLUSIONS: This technique provides a quantitative and accurate approach to the problem of understanding the biomechanical nature of keratoconus. The implemented model has shown that changes in local material properties of the cornea and intraocular pressure are intrinsically related to keratoconus pathology and its shape/curvature.

A MODEL OF CREATINE DEFICIENCY SYNDROMES IN 3D BRAIN CELL CULTURES BY KNOCKDOWN OF GAMT AND SLC6A8 GENES

La créatine joue un rôle essentiel dans le métabolisme cellulaire par sa conversion, par la creatine kinase, en phosphocreatine permettant la régénération de l'ATP. La synthèse de créatine, chez les mammifères, s'effectue par une réaction en deux étapes impliquant Γ arginine: glycine amidinotransférase (AGAT) et la guanidinoacétate méthyltransférase (GAMT). L'entrée de créatine dans les cellules s'effectue par son transporteur, SLC6A8. Les déficiences en créatine, dues au déficit en GAMT, AGAT ou SLC6A8, sont fréquentes et caractérisées par une absence ou une forte baisse de créatine dans le système nerveux central. Alors qu'il est connu que AGAT, GAMT et SLC6A8 sont exprimés par le cerveau, les conséquences des déficiences en créatine sur les cellules nerveuses sont peu comprises. Le but de ce travail était de développer de nouveaux modèles expérimentaux des déficiences en Cr dans des cultures 3D de cellules nerveuses de rat en agrégats au moyen de l'interférence à l'ARN appliquée aux gènes GAMT et SLC6A8. Des séquences interférentes (shRNAs) pour les gènes GAMT et SLC6A8 ont été transduites par des vecteurs viraux AAV (virus adéno-associés), dans les cellules nerveuses en agrégats. Nous avons ainsi démontré une baisse de l'expression de GAMT au niveau protéique (mesuré par western blot), et ARN messager (mesuré par qPCR) ainsi qu'une variation caractérisitique de créatine et guanidinoacétate (mesuré par spectrométrie de masse). Après avoir validé nos modèles, nous avons montré que les knockdown de GAMT ou SLC6A8 affectent le développement des astrocytes et des neurones ou des oligodendrocytes et des astrocytes, respectivement, ainsi qu'une augmentation de la mort cellulaire et des modifications dans le pattern d'activation des voies de signalisation impliquant caspase 3 et p38 MAPK, ayant un rôle dans le processus d'apoptose. - Creatine plays essential roles in energy metabolism by the interconversion, by creatine kinase, to its phosphorylated analogue, phosphocreatine, allowing the regeneration of ATP. Creatine is synthesized in mammals by a two step mechanism involving arginine:glycine amidinotransferase (AGAT) and guanidinoacetate methyltransferase (GAMT). Creatine is taken up by cells by a specific transporter, SLC6A8. Creatine deficiency syndromes, due to defects in GAMT, AGAT and SLC6A8, are among the most frequent inborn errors of metabolism, and are characterized by an absence or a severe decrease of creatine in central nervous system, which is the main tissue affected. While it is known that AGAT, GAMT and SLC6A8 are expressed in CNS, many questions remain on the specific effects of AGAT, GAMT and SLC6A8 deficiencies on brain cells. Our aim was to develop new experimental models of creatine deficiencies by knockdown of GAMT and SLC6A8 genes by RNAi in 3D organotypic rat brain cell cultures in aggregates. Specific shRNAs for the GAMT and SLC6A8 genes were transduced in brain cell aggregates by adeno-associated viruses (AAV). The AAV-transduced shRNAs were able to efficiently knockdown the expression of our genes of interest, as shown by a strong decrease of protein by western blotting, a decrease of mRNA by qPCR or characteristic variations of creatine and guanidinoacetate by tandem mass spectrometry. After having validated our experimental models, we have also shown that GAMT and SLC6A8 knockdown affected the development of astrocytes and neurons or oligodendrocytes and astrocytes, respectively. We also observed an increase of cell death and variations in activation pattern of caspase 3 and p38 MAPK pathways, involved in apoptosis, in our experimental model.

The handaxe and the microscope: individual and social learning in a multidimensional model of adaptation

When individuals learn by trial-and-error, they perform randomly chosen actions and then reinforce those actions that led to a high payoff. However, individuals do not always have to physically perform an action in order to evaluate its consequences. Rather, they may be able to mentally simulate actions and their consequences without actually performing them. Such fictitious learners can select actions with high payoffs without making long chains of trial-and-error learning. Here, we analyze the evolution of an n-dimensional cultural trait (or artifact) by learning, in a payoff landscape with a single optimum. We derive the stochastic learning dynamics of the distance to the optimum in trait space when choice between alternative artifacts follows the standard logit choice rule. We show that for both trial-and-error and fictitious learners, the learning dynamics stabilize at an approximate distance of root n/(2 lambda(e)) away from the optimum, where lambda(e) is an effective learning performance parameter depending on the learning rule under scrutiny. Individual learners are thus unlikely to reach the optimum when traits are complex (n large), and so face a barrier to further improvement of the artifact. We show, however, that this barrier can be significantly reduced in a large population of learners performing payoff-biased social learning, in which case lambda(e) becomes proportional to population size. Overall, our results illustrate the effects of errors in learning, levels of cognition, and population size for the evolution of complex cultural traits. (C) 2013 Elsevier Inc. All rights reserved.

Method of numerical correction of errors occasioned by delay of records during the monitoring of environmental variables of interest for animal production

Thermal and air conditions inside animal facilities change during the day due to the influence of the external environment. For statistical and geostatistical analyses to be representative, a large number of points spatially distributed in the facility area must be monitored. This work suggests that the time variation of environmental variables of interest for animal production, monitored within animal facility, can be modeled accurately from discrete-time records. The aim of this study was to develop a numerical method to correct the temporal variations of these environmental variables, transforming the data so that such observations are independent of the time spent during the measurement. The proposed method approached values recorded with time delays to those expected at the exact moment of interest, if the data were measured simultaneously at the moment at all points distributed spatially. The correction model for numerical environmental variables was validated for environmental air temperature parameter, and the values corrected by the method did not differ by Tukey's test at 5% significance of real values recorded by data loggers.

Multibody Simulation Model of the Roller Test Rig

Multibody simulation model of the roller test rig is presented in this work. The roller test rig consists of a paper machine’s tube roll supported with a hard bearing type balancing machine. The simulation model includes non-idealities that are measured from the physical structure. These non-idealities are the shell thickness variation of the roll and roundness errors of the shafts of the roll. These kinds of non-idealities are harmful since they can cause subharmonic resonances of the rotor system. In this case, the natural vibration mode of the rotor is excited when the rotation speed is a fraction of the natural frequency of the system. With the simulation model, the half critical resonance is studied in detail and a sensitivity analysis is performed by simulating several analyses with slightly different input parameters. The model is verified by comparing the simulation results with those obtained by measuring the real structure. Comparison shows that good accuracy is achieved, since equivalent responses are achieved within the error limit of the input parameters.

Top-down and Bottom-up influences on ACC activation: Evaluation of a proposed model of the feedback-related negativity

The Feedback-Related Negativity (FRN) is thought to reflect the dopaminergic prediction error signal from the subcortical areas to the ACC (i.e., a bottom-up signal). Two studies were conducted in order to test a new model of FRN generation, which includes direct modulating influences of medial PFC (i.e., top-down signals) on the ACC at the time of the FRN. Study 1 examined the effects of one’s sense of control (top-down) and of informative cues (bottom-up) on the FRN measures. In Study 2, sense of control and instruction-based (top-down) and probability-based expectations (bottom-up) were manipulated to test the proposed model. The results suggest that any influences of medial PFC on the activity of the ACC that occur in the context of incentive tasks are not direct. The FRN was shown to be sensitive to salient stimulus characteristics. The results of this dissertation partially support the reinforcement learning theory, in that the FRN is a marker for prediction error signal from subcortical areas. However, the pattern of results outlined here suggests that prediction errors are based on salient stimulus characteristics and are not reward specific. A second goal of this dissertation was to examine whether ACC activity, measured through the FRN, is altered in individuals at-risk for problem-gambling behaviour (PG). Individuals in this group were more sensitive to the valence of the outcome in a gambling task compared to not at-risk individuals, suggesting that gambling contexts increase the sensitivity of the reward system to valence of the outcome in individuals at risk for PG. Furthermore, at-risk participants showed an increased sensitivity to reward characteristics and a decreased response to loss outcomes. This contrasts with those not at risk whose FRNs were sensitive to losses. As the results did not replicate previous research showing attenuated FRNs in pathological gamblers, it is likely that the size and time of the FRN does not change gradually with increasing risk of maladaptive behaviour. Instead, changes in ACC activity reflected by the FRN in general can be observed only after behaviour becomes clinically maladaptive or through comparison between different types of gain/loss outcomes.

Patient-specific anisotropic model of human trunk based on MR data

There are many ways to generate geometrical models for numerical simulation, and most of them start with a segmentation step to extract the boundaries of the regions of interest. This paper presents an algorithm to generate a patient-specific three-dimensional geometric model, based on a tetrahedral mesh, without an initial extraction of contours from the volumetric data. Using the information directly available in the data, such as gray levels, we built a metric to drive a mesh adaptation process. The metric is used to specify the size and orientation of the tetrahedral elements everywhere in the mesh. Our method, which produces anisotropic meshes, gives good results with synthetic and real MRI data. The resulting model quality has been evaluated qualitatively and quantitatively by comparing it with an analytical solution and with a segmentation made by an expert. Results show that our method gives, in 90% of the cases, as good or better meshes as a similar isotropic method, based on the accuracy of the volume reconstruction for a given mesh size. Moreover, a comparison of the Hausdorff distances between adapted meshes of both methods and ground-truth volumes shows that our method decreases reconstruction errors faster. Copyright © 2015 John Wiley & Sons, Ltd.

A high-order arbitrarily unstructured finite-volume model of the global atmosphere: tests solving the shallow-water equations

Simulations of the global atmosphere for weather and climate forecasting require fast and accurate solutions and so operational models use high-order finite differences on regular structured grids. This precludes the use of local refinement; techniques allowing local refinement are either expensive (eg. high-order finite element techniques) or have reduced accuracy at changes in resolution (eg. unstructured finite-volume with linear differencing). We present solutions of the shallow-water equations for westerly flow over a mid-latitude mountain from a finite-volume model written using OpenFOAM. A second/third-order accurate differencing scheme is applied on arbitrarily unstructured meshes made up of various shapes and refinement patterns. The results are as accurate as equivalent resolution spectral methods. Using lower order differencing reduces accuracy at a refinement pattern which allows errors from refinement of the mountain to accumulate and reduces the global accuracy over a 15 day simulation. We have therefore introduced a scheme which fits a 2D cubic polynomial approximately on a stencil around each cell. Using this scheme means that refinement of the mountain improves the accuracy after a 15 day simulation. This is a more severe test of local mesh refinement for global simulations than has been presented but a realistic test if these techniques are to be used operationally. These efficient, high-order schemes may make it possible for local mesh refinement to be used by weather and climate forecast models.

A model of net amino acid absorption and utilization by the portal-drained viscera of the lactating dairy cow

A more complete understanding of amino acid ( AA) metabolism by the various tissues of the body is required to improve upon current systems for predicting the use of absorbed AA. The objective of this work was to construct and parameterize a model of net removal of AA by the portal-drained viscera (PDV). Six cows were prepared with arterial, portal, and hepatic catheters and infused abomasally with 0, 200, 400, or 600 g of casein daily. Casein infusion increased milk yield quadratically and tended to increase milk protein yield quadratically. Arterial concentrations of a number of essential AA increased linearly with respect to infusion amount. When infused casein was assumed to have a true digestion coefficient of 0.95, the minimum likely true digestion coefficient for noninfused duodenal protein was found to be 0.80. Net PDV use of AA appeared to be linearly related to total supply (arterial plus absorption), and extraction percentages ranged from 0.5 to 7.25% for essential AA. Prediction errors for portal vein AA concentrations ranged from 4 to 9% of the observed mean concentrations. Removal of AA by PDV represented approximately 33% of total postabsorptive catabolic use, including use during absorption but excluding use for milk protein synthesis, and was apparently adequate to support endogenous N losses in feces of 18.4 g/d. As 69% of this use was from arterial blood, increased PDV catabolism of AA in part represents increased absorption of AA in excess of amounts required by other body tissues. Based on the present model, increased anabolic use of AA in the mammary and other tissues would reduce the catabolic use of AA by the PDV.

The effects of environmental perturbation and measurement error on estimates of the shape parameter in the theta-logistic model of population regulation

The theta-logistic is a widely used generalisation of the logistic model of regulated biological processes which is used in particular to model population regulation. Then the parameter theta gives the shape of the relationship between per-capita population growth rate and population size. Estimation of theta from population counts is however subject to bias, particularly when there are measurement errors. Here we identify factors disposing towards accurate estimation of theta by simulation of populations regulated according to the theta-logistic model. Factors investigated were measurement error, environmental perturbation and length of time series. Large measurement errors bias estimates of theta towards zero. Where estimated theta is close to zero, the estimated annual return rate may help resolve whether this is due to bias. Environmental perturbations help yield unbiased estimates of theta. Where environmental perturbations are large, estimates of theta are likely to be reliable even when measurement errors are also large. By contrast where the environment is relatively constant, unbiased estimates of theta can only be obtained if populations are counted precisely Our results have practical conclusions for the design of long-term population surveys. Estimation of the precision of population counts would be valuable, and could be achieved in practice by repeating counts in at least some years. Increasing the length of time series beyond ten or 20 years yields only small benefits. if populations are measured with appropriate accuracy, given the level of environmental perturbation, unbiased estimates can be obtained from relatively short censuses. These conclusions are optimistic for estimation of theta. (C) 2008 Elsevier B.V All rights reserved.

Does the PMSP connectionist model of single word reading learn to read in the same way as a child?

The Plaut, McClelland, Seidenberg and Patterson (1996) connectionist model of reading was evaluated at two points early in its training against reading data collected from British children on two occasions during their first year of literacy instruction. First, the network’s non-word reading was poor relative to word reading when compared with the children. Second, the network made more non-lexical than lexical errors, the opposite pattern to the children. Three adaptations were made to the training of the network to bring it closer to the learning environment of a child: an incremental training regime was adopted; the network was trained on grapheme– phoneme correspondences; and a training corpus based on words found in children’s early reading materials was used. The modifications caused a sharp improvement in non-word reading, relative to word reading, resulting in a near perfect match to the children’s data on this measure. The modified network, however, continued to make predominantly non-lexical errors, although evidence from a small-scale implementation of the full triangle framework suggests that this limitation stems from the lack of a semantic pathway. Taken together, these results suggest that, when properly trained, connectionist models of word reading can offer insights into key aspects of reading development in children.

Method of numerical correction of errors occasioned by delay of records during the monitoring of environmental variables of interest for animal production

As condições de ambiente térmico e aéreo, no interior de instalações para animais, alteram-se durante o dia, devido à influência do ambiente externo. Para que análises estatísticas e geoestatísticas sejam representativas, uma grande quantidade de pontos distribuídos espacialmente na área da instalação deve ser monitorada. Este trabalho propõe que a variação no tempo das variáveis ambientais de interesse para a produção animal, monitoradas no interior de instalações para animais, pode ser modelada com precisão a partir de registros discretos no tempo. O objetivo deste trabalho foi desenvolver um método numérico para corrigir as variações temporais dessas variáveis ambientais, transformando os dados para que tais observações independam do tempo gasto durante a aferição. O método proposto aproximou os valores registrados com retardos de tempo aos esperados no exato momento de interesse, caso os dados fossem medidos simultaneamente neste momento em todos os pontos distribuídos espacialmente. O modelo de correção numérica para variáveis ambientais foi validado para o parâmetro ambiental temperatura do ar, sendo que os valores corrigidos pelo método não diferiram pelo teste Tukey, a 5% de probabilidade dos valores reais registrados por meio de dataloggers.