961 resultados para PREDICTIVE PERFORMANCE


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Thesis (Master's)--University of Washington, 2016-06

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Patient outcomes in transplantation would improve if dosing of immunosuppressive agents was individualized. The aim of this study is to develop a population pharmacokinetic model of tacrolimus in adult liver transplant recipients and test this model in individualizing therapy. Population analysis was performed on data from 68 patients. Estimates were sought for apparent clearance (CL/F) and apparent volume of distribution (V/F) using the nonlinear mixed effects model program (NONMEM). Factors screened for influence on these parameters were weight, age, sex, transplant type, biliary reconstructive procedure, postoperative day, days of therapy, liver function test results, creatinine clearance, hematocrit, corticosteroid dose, and interacting drugs. The predictive performance of the developed model was evaluated through Bayesian forecasting in an independent cohort of 36 patients. No linear correlation existed between tacrolimus dosage and trough concentration (r(2) = 0.005). Mean individual Bayesian estimates for CL/F and V/F were 26.5 8.2 (SD) L/hr and 399 +/- 185 L, respectively. CL/F was greater in patients with normal liver function. V/F increased with patient weight. CL/F decreased with increasing hematocrit. Based on the derived model, a 70-kg patient with an aspartate aminotransferase (AST) level less than 70 U/L would require a tacrolimus dose of 4.7 mg twice daily to achieve a steady-state trough concentration of 10 ng/mL. A 50-kg patient with an AST level greater than 70 U/L would require a dose of 2.6 mg. Marked interindividual variability (43% to 93%) and residual random error (3.3 ng/mL) were observed. Predictions made using the final model were reasonably nonbiased (0.56 ng/mL), but imprecise (4.8 ng/mL). Pharmacokinetic information obtained will assist in tacrolimus dosing; however, further investigation into reasons for the pharmacokinetic variability of tacrolimus is required.

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The aim of this study was to determine the most informative sampling time(s) providing a precise prediction of tacrolimus area under the concentration-time curve (AUC). Fifty-four concentration-time profiles of tacrolimus from 31 adult liver transplant recipients were analyzed. Each profile contained 5 tacrolimus whole-blood concentrations (predose and 1, 2, 4, and 6 or 8 hours postdose), measured using liquid chromatography-tandem mass spectrometry. The concentration at 6 hours was interpolated for each profile, and 54 values of AUC(0-6) were calculated using the trapezoidal rule. The best sampling times were then determined using limited sampling strategies and sensitivity analysis. Linear mixed-effects modeling was performed to estimate regression coefficients of equations incorporating each concentration-time point (C0, C1, C2, C4, interpolated C5, and interpolated C6) as a predictor of AUC(0-6). Predictive performance was evaluated by assessment of the mean error (ME) and root mean square error (RMSE). Limited sampling strategy (LSS) equations with C2, C4, and C5 provided similar results for prediction of AUC(0-6) (R-2 = 0.869, 0.844, and 0.832, respectively). These 3 time points were superior to C0 in the prediction of AUC. The ME was similar for all time points; the RMSE was smallest for C2, C4, and C5. The highest sensitivity index was determined to be 4.9 hours postdose at steady state, suggesting that this time point provides the most information about the AUC(0-12). The results from limited sampling strategies and sensitivity analysis supported the use of a single blood sample at 5 hours postdose as a predictor of both AUC(0-6) and AUC(0-12). A jackknife procedure was used to evaluate the predictive performance of the model, and this demonstrated that collecting a sample at 5 hours after dosing could be considered as the optimal sampling time for predicting AUC(0-6).

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Background: Lean bodyweight (LBW) has been recommended for scaling drug doses. However, the current methods for predicting LBW are inconsistent at extremes of size and could be misleading with respect to interpreting weight-based regimens. Objective: The objective of the present study was to develop a semi-mechanistic model to predict fat-free mass (FFM) from subject characteristics in a population that includes extremes of size. FFM is considered to closely approximate LBW. There are several reference methods for assessing FFM, whereas there are no reference standards for LBW. Patients and methods: A total of 373 patients (168 male, 205 female) were included in the study. These data arose from two populations. Population A (index dataset) contained anthropometric characteristics, FFM estimated by dual-energy x-ray absorptiometry (DXA - a reference method) and bioelectrical impedance analysis (BIA) data. Population B (test dataset) contained the same anthropometric measures and FFM data as population A, but excluded BIA data. The patients in population A had a wide range of age (18-82 years), bodyweight (40.7-216.5kg) and BMI values (17.1-69.9 kg/m(2)). Patients in population B had BMI values of 18.7-38.4 kg/m(2). A two-stage semi-mechanistic model to predict FFM was developed from the demographics from population A. For stage 1 a model was developed to predict impedance and for stage 2 a model that incorporated predicted impedance was used to predict FFM. These two models were combined to provide an overall model to predict FFM from patient characteristics. The developed model for FFM was externally evaluated by predicting into population B. Results: The semi-mechanistic model to predict impedance incorporated sex, height and bodyweight. The developed model provides a good predictor of impedance for both males and females (r(2) = 0.78, mean error [ME] = 2.30 x 10(-3), root mean square error [RMSE] = 51.56 [approximately 10% of mean]). The final model for FFM incorporated sex, height and bodyweight. The developed model for FFM provided good predictive performance for both males and females (r(2) = 0.93, ME = -0.77, RMSE = 3.33 [approximately 6% of mean]). In addition, the model accurately predicted the FFM of subjects in population B (r(2) = 0.85, ME -0.04, RMSE = 4.39 [approximately 7% of mean]). Conclusions: A semi-mechanistic model has been developed to predict FFM (and therefore LBW) from easily accessible patient characteristics. This model has been prospectively evaluated and shown to have good predictive performance.

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The aim of this study was to ascertain the most suitable dosing schedule for gentamicin in patients receiving hemodialysis. We developed a model to describe the concentrationtime course of gentamicin in patients receiving hemodialysis. Using the model, an optimal dosing schedule was evaluated. Various dosing regimens were compared in their ability to achieve maximum concentration (C-max, >= 8 mg/L) and area under the concentration time-curve (AUC >= 70 mg(.)h/L and <= 120 mg(.)h/L per 24 hours). The model was evaluated by comparing model predictions against real data collected retrospectively. Simulations from the model confirmed the benefits of predialysis dosing. The mean optimal dose was 230 mg administered immediately before dialysis. The model was found to have good predictive performance when simulated data were compared to data observed in real patients. In summary, a model was developed that describes gentamicin pharmacokinetics in patients receiving hemodialysis. Predialysis dosing provided a superior pharmacokinetic profile than did postdialysis dosing.

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When making predictions with complex simulators it can be important to quantify the various sources of uncertainty. Errors in the structural specification of the simulator, for example due to missing processes or incorrect mathematical specification, can be a major source of uncertainty, but are often ignored. We introduce a methodology for inferring the discrepancy between the simulator and the system in discrete-time dynamical simulators. We assume a structural form for the discrepancy function, and show how to infer the maximum-likelihood parameter estimates using a particle filter embedded within a Monte Carlo expectation maximization (MCEM) algorithm. We illustrate the method on a conceptual rainfall-runoff simulator (logSPM) used to model the Abercrombie catchment in Australia. We assess the simulator and discrepancy model on the basis of their predictive performance using proper scoring rules. This article has supplementary material online. © 2011 International Biometric Society.

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MOTIVATION: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. RESULTS: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases.

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It is well established that accent recognition can be as accurate as up to 95% when the signals are noise-free, using feature extraction techniques such as mel-frequency cepstral coefficients and binary classifiers such as discriminant analysis, support vector machine and k-nearest neighbors. In this paper, we demonstrate that the predictive performance can be reduced by as much as 15% when the signals are noisy. Specifically, in this paper we perturb the signals with different levels of white noise, and as the noise become stronger, the out-of-sample predictive performance deteriorates from 95% to 80%, although the in-sample prediction gives overly-optimistic results. ACM Computing Classification System (1998): C.3, C.5.1, H.1.2, H.2.4., G.3.

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An abstract of a thesis devoted to using helix-coil models to study unfolded states.\\

Research on polypeptide unfolded states has received much more attention in the last decade or so than it has in the past. Unfolded states are thought to be implicated in various

misfolding diseases and likely play crucial roles in protein folding equilibria and folding rates. Structural characterization of unfolded states has proven to be

much more difficult than the now well established practice of determining the structures of folded proteins. This is largely because many core assumptions underlying

folded structure determination methods are invalid for unfolded states. This has led to a dearth of knowledge concerning the nature of unfolded state conformational

distributions. While many aspects of unfolded state structure are not well known, there does exist a significant body of work stretching back half a century that

has been focused on structural characterization of marginally stable polypeptide systems. This body of work represents an extensive collection of experimental

data and biophysical models associated with describing helix-coil equilibria in polypeptide systems. Much of the work on unfolded states in the last decade has not been devoted

specifically to the improvement of our understanding of helix-coil equilibria, which arguably is the most well characterized of the various conformational equilibria

that likely contribute to unfolded state conformational distributions. This thesis seeks to provide a deeper investigation of helix-coil equilibria using modern

statistical data analysis and biophysical modeling techniques. The studies contained within seek to provide deeper insights and new perspectives on what we presumably

know very well about protein unfolded states. \\

Chapter 1 gives an overview of recent and historical work on studying protein unfolded states. The study of helix-coil equilibria is placed in the context

of the general field of unfolded state research and the basics of helix-coil models are introduced.\\

Chapter 2 introduces the newest incarnation of a sophisticated helix-coil model. State of the art modern statistical techniques are employed to estimate the energies

of various physical interactions that serve to influence helix-coil equilibria. A new Bayesian model selection approach is utilized to test many long-standing

hypotheses concerning the physical nature of the helix-coil transition. Some assumptions made in previous models are shown to be invalid and the new model

exhibits greatly improved predictive performance relative to its predecessor. \\

Chapter 3 introduces a new statistical model that can be used to interpret amide exchange measurements. As amide exchange can serve as a probe for residue-specific

properties of helix-coil ensembles, the new model provides a novel and robust method to use these types of measurements to characterize helix-coil ensembles experimentally

and test the position-specific predictions of helix-coil models. The statistical model is shown to perform exceedingly better than the most commonly used

method for interpreting amide exchange data. The estimates of the model obtained from amide exchange measurements on an example helical peptide

also show a remarkable consistency with the predictions of the helix-coil model. \\

Chapter 4 involves a study of helix-coil ensembles through the enumeration of helix-coil configurations. Aside from providing new insights into helix-coil ensembles,

this chapter also introduces a new method by which helix-coil models can be extended to calculate new types of observables. Future work on this approach could potentially

allow helix-coil models to move into use domains that were previously inaccessible and reserved for other types of unfolded state models that were introduced in chapter 1.

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The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

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Este trabalho incide na análise dos açúcares majoritários nos alimentos (glucose, frutose e sacarose) com uma língua eletrónica potenciométrica através de calibração multivariada com seleção de sensores. A análise destes compostos permite contribuir para a avaliação do impacto dos açúcares na saúde e seu efeito fisiológico, além de permitir relacionar atributos sensoriais e atuar no controlo de qualidade e autenticidade dos alimentos. Embora existam diversas metodologias analíticas usadas rotineiramente na identificação e quantificação dos açúcares nos alimentos, em geral, estes métodos apresentam diversas desvantagens, tais como lentidão das análises, consumo elevado de reagentes químicos e necessidade de pré-tratamentos destrutivos das amostras. Por isso se decidiu aplicar uma língua eletrónica potenciométrica, construída com sensores poliméricos selecionados considerando as sensibilidades aos açucares obtidas em trabalhos anteriores, na análise dos açúcares nos alimentos, visando estabelecer uma metodologia analítica e procedimentos matemáticos para quantificação destes compostos. Para este propósito foram realizadas análises em soluções padrão de misturas ternárias dos açúcares em diferentes níveis de concentração e em soluções de dissoluções de amostras de mel, que foram previamente analisadas em HPLC para se determinar as concentrações de referência dos açúcares. Foi então feita uma análise exploratória dos dados visando-se remover sensores ou observações discordantes através da realização de uma análise de componentes principais. Em seguida, foram construídos modelos de regressão linear múltipla com seleção de variáveis usando o algoritmo stepwise e foi verificado que embora fosse possível estabelecer uma boa relação entre as respostas dos sensores e as concentrações dos açúcares, os modelos não apresentavam desempenho de previsão satisfatório em dados de grupo de teste. Dessa forma, visando contornar este problema, novas abordagens foram testadas através da construção e otimização dos parâmetros de um algoritmo genético para seleção de variáveis que pudesse ser aplicado às diversas ferramentas de regressão, entre elas a regressão pelo método dos mínimos quadrados parciais. Foram obtidos bons resultados de previsão para os modelos obtidos com o método dos mínimos quadrados parciais aliado ao algoritmo genético, tanto para as soluções padrão quanto para as soluções de mel, com R²ajustado acima de 0,99 e RMSE inferior a 0,5 obtidos da relação linear entre os valores previstos e experimentais usando dados dos grupos de teste. O sistema de multi-sensores construído se mostrou uma ferramenta adequada para a análise dos iii açúcares, quando presentes em concentrações maioritárias, e alternativa a métodos instrumentais de referência, como o HPLC, por reduzir o tempo da análise e o valor monetário da análise, bem como, ter um preparo mínimo das amostras e eliminar produtos finais poluentes.

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As azeitonas de mesa são consumidas e apreciadas em todo o mundo e, embora a sua classificação comercial não seja legalmente exigida, o Conselho Oleícola Internacional sugere que seja regulamentada com base na avaliação sensorial por um painel de provadores. A implementação de tal requer o cumprimento de diretrizes estabelecidas pelo Conselho Oleícola Internacional, resultando numa tarefa complexa, demorada e cujas avaliações não estão isentas de subjetividade. Neste trabalho, pela primeira vez, uma língua eletrónica foi utilizada com o intuito de classificar azeitonas de mesa em categorias comerciais, estipuladas com base na presença e na mediana das intensidades do defeito organolético predominante percebido pelo painel de provadores. Modelos de discriminação lineares foram estabelecidos com base em subconjuntos de sinais potenciométricos de sensores da língua eletrónica, selecionados recorrendo ao algoritmo de arrefecimento simulado. Os desempenhos qualitativo de previsão dos modelos de classificação estabelecidos foram avaliados recorrendo à técnica de validação cruzada leave-one-out e à técnica de validação cruzada K-folds com repetição, que permite minimizar o risco de sobreajustamento, permitindo obter resultados mais realistas. O potencial desta abordagem qualitativa, baseada nos perfis eletroquímicos gerados pela língua eletrónica, foi satisfatoriamente demonstrado: (i) na classificação correta (sensibilidades ≥ 93%) de soluções padrão (ácido n-butírico, 2-mercaptoetanol e ácido ciclohexanocarboxílico) de acordo com o defeito sensorial que mimetizam (butírico, pútrido ou sapateira); (ii) na classificação correta (sensibilidades ≥ 93%) de amostras de referência de azeitonas e salmouras (presença de um defeito único intenso) de acordo com o tipo de defeito percebido (avinhado-avinagrado, butírico, mofo, pútrido ou sapateira), e selecionadas pelo painel de provadores; e, (iii) na classificação correta (sensibilidade ≥ 86%) de amostras de azeitonas de mesa com grande heterogeneidade, contendo um ou mais defeitos organoléticos percebidos pelo painel de provadores nas azeitona e/ou salmouras, de acordo com a sua categoria comercial (azeitona extra sem defeito, extra, 1ª escolha, 2ª escolha e azeitonas que não podem ser comercializadas como azeitonas de mesa). Por fim, a capacidade língua eletrónica em quantificar as medianas das intensidades dos atributos negativos detetados pelo painel nas azeitonas de mesa foi demonstrada recorrendo a modelos de regressão linear múltipla-algoritmo de arrefecimento simulado, com base em subconjuntos selecionados de sinais gerados pela língua eletrónica durante a análise potenciométrica das azeitonas e salmouras. O xii desempenho de previsão dos modelos quantitativos foi validado recorrendo às mesmas duas técnicas de validação cruzada. Os modelos estabelcidos para cada um dos 5 defeitos sensoriais presentes nas amostras de azeitona de mesa, permitiram quantificar satisfatoriamente as medianas das intensidades dos defeitos (R² ≥ 0,97). Assim, a qualidade satisfatória dos resultados qualitativos e quantitativos alcançados permite antever, pela primeira vez, uma possível aplicação prática das línguas eletrónicas como uma ferramenta de análise sensorial de defeitos em azeitonas de mesa, podendo ser usada como uma técnica rápida, económica e útil na avaliação organolética de atributos negativos, complementar à tradicional análise sensorial por um painel de provadores.

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In this work, the relationship between diameter at breast height (d) and total height (h) of individual-tree was modeled with the aim to establish provisory height-diameter (h-d) equations for maritime pine (Pinus pinaster Ait.) stands in the Lomba ZIF, Northeast Portugal. Using data collected locally, several local and generalized h-d equations from the literature were tested and adaptations were also considered. Model fitting was conducted by using usual nonlinear least squares (nls) methods. The best local and generalized models selected, were also tested as mixed models applying a first-order conditional expectation (FOCE) approximation procedure and maximum likelihood methods to estimate fixed and random effects. For the calibration of the mixed models and in order to be consistent with the fitting procedure, the FOCE method was also used to test different sampling designs. The results showed that the local h-d equations with two parameters performed better than the analogous models with three parameters. However a unique set of parameter values for the local model can not be used to all maritime pine stands in Lomba ZIF and thus, a generalized model including covariates from the stand, in addition to d, was necessary to obtain an adequate predictive performance. No evident superiority of the generalized mixed model in comparison to the generalized model with nonlinear least squares parameters estimates was observed. On the other hand, in the case of the local model, the predictive performance greatly improved when random effects were included. The results showed that the mixed model based in the local h-d equation selected is a viable alternative for estimating h if variables from the stand are not available. Moreover, it was observed that it is possible to obtain an adequate calibrated response using only 2 to 5 additional h-d measurements in quantile (or random) trees from the distribution of d in the plot (stand). Balancing sampling effort, accuracy and straightforwardness in practical applications, the generalized model from nls fit is recommended. Examples of applications of the selected generalized equation to the forest management are presented, namely how to use it to complete missing information from forest inventory and also showing how such an equation can be incorporated in a stand-level decision support system that aims to optimize the forest management for the maximization of wood volume production in Lomba ZIF maritime pine stands.

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Mechanistic models used for prediction should be parsimonious, as models which are over-parameterised may have poor predictive performance. Determining whether a model is parsimonious requires comparisons with alternative model formulations with differing levels of complexity. However, creating alternative formulations for large mechanistic models is often problematic, and usually time-consuming. Consequently, few are ever investigated. In this paper, we present an approach which rapidly generates reduced model formulations by replacing a model’s variables with constants. These reduced alternatives can be compared to the original model, using data based model selection criteria, to assist in the identification of potentially unnecessary model complexity, and thereby inform reformulation of the model. To illustrate the approach, we present its application to a published radiocaesium plant-uptake model, which predicts uptake on the basis of soil characteristics (e.g. pH, organic matter content, clay content). A total of 1024 reduced model formulations were generated, and ranked according to five model selection criteria: Residual Sum of Squares (RSS), AICc, BIC, MDL and ICOMP. The lowest scores for RSS and AICc occurred for the same reduced model in which pH dependent model components were replaced. The lowest scores for BIC, MDL and ICOMP occurred for a further reduced model in which model components related to the distinction between adsorption on clay and organic surfaces were replaced. Both these reduced models had a lower RSS for the parameterisation dataset than the original model. As a test of their predictive performance, the original model and the two reduced models outlined above were used to predict an independent dataset. The reduced models have lower prediction sums of squares than the original model, suggesting that the latter may be overfitted. The approach presented has the potential to inform model development by rapidly creating a class of alternative model formulations, which can be compared.

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A Lontra Euroasiática foi alvo de quatro prospeções na Península Ibérica (1990-2008). Em 2003, foi publicado um modelo de distribuição da lontra, com base nos dados de presença/ausência das prospeções publicadas em 1998. Dadas as suas características, este tipo de modelos pode tornar-se um elemento chave nas estratégias de recuperação da lontra como também, de outras espécies, se comprovada a sua fiabilidade e capacidade de antecipar tendências na distribuição das mesmas. Assim, esta dissertação confrontou as previsões do modelo com os dados de distribuição de 2008, a fim de identificar potências áreas de discordância. Os resultados revelam que, o modelo de distribuição de lontra proposto, apesar de ter por base dados de 1998 e de não considerar explicitamente processos biológicos, conseguiu captar o essencial da relação espécie-ambiente, resultando num bom desempenho preditivo para a distribuição da mesma em Espanha, uma década depois da sua construção; Evolution of otter (Lutra lutra L.) distribution in the Iberian Peninsula: Models at different scales and their projection through space and time Abstract: The Eurasian otter was already surveyed four times in the Iberian Peninsula (1990-2008). In 2003, a distribution model for the otter based on presence/absence data from the survey published in 1998, was published. This type of models has advantages that can make it in a key element for otter conservation strategies and also, for other species, but only, if their reliability and capability to predict species distribution tendencies are validated. The present thesis compares the model predictions with 2008 data, in order to find potential mismatch areas. Results suggest that, although the distribution model for the otter was based on data from 1998 and, doesn’t include explicitly biological mechanisms, it managed to correctly identify the essence of the species-environment relationship, what was translated in a good predictive performance for its actual distribution in Spain, after a decade of its construction.