Improvement of therapeutic drug monitoring of imatinib by Bayesian prediction of trough levels. Personalized drug dosage

Aims: Plasma concentrations of imatinib differ largely between patients despite same dosage, owing to large inter-individual variability in pharmacokinetic (PK) parameters. As the drug concentration at the end of the dosage interval (Cmin) correlates with treatment response and tolerability, monitoring of Cmin is suggested for therapeutic drug monitoring (TDM) of imatinib. Due to logistic difficulties, random sampling during the dosage interval is however often performed in clinical practice, thus rendering the respective results not informative regarding Cmin values.Objectives: (I) To extrapolate randomly measured imatinib concentrations to more informative Cmin using classical Bayesian forecasting. (II) To extend the classical Bayesian method to account for correlation between PK parameters. (III) To evaluate the predictive performance of both methods.Methods: 31 paired blood samples (random and trough levels) were obtained from 19 cancer patients under imatinib. Two Bayesian maximum a posteriori (MAP) methods were implemented: (A) a classical method ignoring correlation between PK parameters, and (B) an extended one accounting for correlation. Both methods were applied to estimate individual PK parameters, conditional on random observations and covariate-adjusted priors from a population PK model. The PK parameter estimates were used to calculate trough levels. Relative prediction errors (PE) were analyzed to evaluate accuracy (one-sample t-test) and to compare precision between the methods (F-test to compare variances).Results: Both Bayesian MAP methods allowed non-biased predictions of individual Cmin compared to observations: (A) - 7% mean PE (CI95% - 18 to 4 %, p = 0.15) and (B) - 4% mean PE (CI95% - 18 to 10 %, p = 0.69). Relative standard deviations of actual observations from predictions were 22% (A) and 30% (B), i.e. comparable to the intraindividual variability reported. Precision was not improved by taking into account correlation between PK parameters (p = 0.22).Conclusion: Clinical interpretation of randomly measured imatinib concentrations can be assisted by Bayesian extrapolation to maximum likelihood Cmin. Classical Bayesian estimation can be applied for TDM without the need to include correlation between PK parameters. Both methods could be adapted in the future to evaluate other individual pharmacokinetic measures correlated to clinical outcomes, such as area under the curve(AUC).

Prediction of free imatinib concentrations based on total plasma concentrations in patients with gastrointestinal stromal tumours.

AIM: Total imatinib concentrations are currently measured for the therapeutic drug monitoring of imatinib, whereas only free drug equilibrates with cells for pharmacological action. Due to technical and cost limitations, routine measurement of free concentrations is generally not performed. In this study, free and total imatinib concentrations were measured to establish a model allowing the confident prediction of imatinib free concentrations based on total concentrations and plasma proteins measurements. METHODS: One hundred and fifty total and free plasma concentrations of imatinib were measured in 49 patients with gastrointestinal stromal tumours. A population pharmacokinetic model was built up to characterize mean total and free concentrations with inter-patient and intrapatient variability, while taking into account α1 -acid glycoprotein (AGP) and human serum albumin (HSA) concentrations, in addition to other demographic and environmental covariates. RESULTS: A one compartment model with first order absorption was used to characterize total and free imatinib concentrations. Only AGP influenced imatinib total clearance. Imatinib free concentrations were best predicted using a non-linear binding model to AGP, with a dissociation constant Kd of 319 ng ml(-1) , assuming a 1:1 molar binding ratio. The addition of HSA in the equation did not improve the prediction of imatinib unbound concentrations. CONCLUSION: Although free concentration monitoring is probably more appropriate than total concentrations, it requires an additional ultrafiltration step and sensitive analytical technology, not always available in clinical laboratories. The model proposed might represent a convenient approach to estimate imatinib free concentrations. However, therapeutic ranges for free imatinib concentrations remain to be established before it enters into routine practice.

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

High-throughput prioritization of cancer-causing mutations (drivers) is a key challenge of cancer genome projects, due to the number of somatic variants detected in tumors. One important step in this task is to assess the functional impact of tumor somatic mutations. A number of computational methods have been employed for that purpose, although most were originally developed to distinguish disease-related nonsynonymous single nucleotide variants (nsSNVs) from polymorphisms. Our new method, transformed Functional Impact score for Cancer (transFIC), improves the assessment of the functional impact of tumor nsSNVs by taking into account the baseline tolerance of genes to functional variants.

A nuclear defect in the 4p16 region predisposes to multiple mitochondrial DNA deletions in families with Wolfram syndrome.

Wolfram syndrome is a progressive neurodegenerative disorder transmitted in an autosomal recessive mode. We report two Wolfram syndrome families harboring multiple deletions of mitochondrial DNA. The deletions reached percentages as high as 85-90% in affected tissues such as the central nervous system of one patient, while in other tissues from the same patient and from other members of the family, the percentages of deleted mitochondrial DNA genomes were only 1-10%. Recently, a Wolfram syndrome gene has been linked to markers on 4p16. In both families linkage between the disease locus and 4p16 markers gave a maximum multipoint lod score of 3.79 at theta = 0 (Pi<0.03) with respect to D4S431. In these families, the syndrome was caused by mutations in this nucleus-encoded gene which deleteriously interacts with the mitochondrial genome. This is the first evidence of the implication of both genomes in a recessive disease.

A nuclear defect in the 4p16 region predisposes to multiple mitochondrial DNA deletions in families with Wolfram syndrome.

Wolfram syndrome is a progressive neurodegenerative disorder transmitted in an autosomal recessive mode. We report two Wolfram syndrome families harboring multiple deletions of mitochondrial DNA. The deletions reached percentages as high as 85-90% in affected tissues such as the central nervous system of one patient, while in other tissues from the same patient and from other members of the family, the percentages of deleted mitochondrial DNA genomes were only 1-10%. Recently, a Wolfram syndrome gene has been linked to markers on 4p16. In both families linkage between the disease locus and 4p16 markers gave a maximum multipoint lod score of 3.79 at theta = 0 (Pi<0.03) with respect to D4S431. In these families, the syndrome was caused by mutations in this nucleus-encoded gene which deleteriously interacts with the mitochondrial genome. This is the first evidence of the implication of both genomes in a recessive disease.

Pulmonary hypertension complicating isolated atrial septal defect.

Atrial septal defect (ASD) typically is asymptomatic in infancy and early childhood and elective defect closure usually is performed at an age between 4 - 6 years. Severe pulmonary hypertension (PHT) complicating an ASD is seen in adulthood and has only occasionally been reported in small children. A retrospective study was undertaken to evaluate the incidence of severe PHT complicating an isolated ASD and requiring early surgical correction in the fi rst year of life. 355 pediatric patients underwent treatment for an isolated ASD either surgically or by catheter intervention during a 10 year period (1996 - 2006) at two tertiary referral centers. 297 patients had secundum ASD and 58 primum ASD with mild to moderate mitral regurgitation. 8 infants were found with isolated ASD (six with secundum and two with primum ASD) associated with signifi cant PHT, accounting for 2.2% of all ASD patients in our centers. These 8 infants had invasively measured pulmonary artery pressures between 50 and 100% of systemic pressure. Median size of the ASD at the time of surgery was 14mm (7 - 20). They were operated in the fi rst year of life and had complicated postoperative courses requiring specifi c treatment for PHT for up to 16 weeks (median 12) postoperatively. Compared to ASD patients without PHT these infants had prolonged postoperative ICU stay of 5 - 9 days (median 8) and prolonged perioperative overall hospital stay of 8 - 32 days (median 15). Ultimate outcome in all 8 infants was good with persistent normalization of pulmonary pressures during mid-term follow-up of between 8 to 60 months (median 28). All other ASD patients had normal pulmonary pressures and mean age at defect closure was higher being 6.2 years for secundum ASD and 3.2 years for primum ASD. In conclusion, ASD is rarely associated with signifi cant PHT in infancy but then requires early surgery to normalize the prognosis of the patients.

Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the cross-recognition.

Frequency of severe pulmonary hypertension complicating "isolated" atrial septal defect in infancy.

Atrial septal defects (ASDs) are typically asymptomatic in infancy and early childhood, and elective defect closure is usually performed at ages of 4 to 6 years. Severe pulmonary hypertension (PH) complicating an ASD is seen in adulthood and has only occasionally been reported in small children. A retrospective study was undertaken to evaluate the incidence of severe PH complicating an isolated ASD and requiring early surgical correction. During a 10-year period (1996 to 2006), 355 pediatric patients underwent treatment for isolated ASDs either surgically or by catheter intervention at 2 tertiary referral centers. Two hundred ninety-seven patients had secundum ASDs, and 58 had primum ASDs with mild to moderate mitral regurgitation. Eight infants were found with isolated ASDs (6 with secundum ASDs and 2 with primum ASDs) associated with significant PH, accounting for 2.2% of all patients with ASDs at the centers. These 8 infants had invasively measured pulmonary artery pressures of 50% to 100% of systemic pressure. They were operated in the first year of life and had complicated postoperative courses requiring specific treatment for PH for up to 16 weeks postoperatively. The ultimate outcomes in all 8 infants were good, with persistent normalization of pulmonary pressures during midterm follow-up of up to 60 months (median 28). All other patients with ASDs had normal pulmonary pressures, and the mean age at defect closure was significantly older, at 6.2 years for secundum ASDs and 3.2 years for primum ASDs. In conclusion, ASDs were rarely associated with significant PH in infancy but then required early surgery and were associated with excellent midterm outcomes in these patients.

Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Abstract Background: Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful. Results: In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. Conclusions: To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the Mycoplasma species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.

Machine learning for spatial environmental data. Theory, applications and software

The book presents the state of the art in machine learning algorithms (artificial neural networks of different architectures, support vector machines, etc.) as applied to the classification and mapping of spatially distributed environmental data. Basic geostatistical algorithms are presented as well. New trends in machine learning and their application to spatial data are given, and real case studies based on environmental and pollution data are carried out. The book provides a CD-ROM with the Machine Learning Office software, including sample sets of data, that will allow both students and researchers to put the concepts rapidly to practice.

Open source software in translator training

La formació de traductors implica l´ús de procediments i eines que permetin els estudiants familiaritzar-se amb contextos professionals. El software lliure especialitzat inclou eines de qualitat professional i procediments accessibles per a les institucions acadèmiques i els estudiants a distància que treballen a casa seva. Els projectes reals que utilitzen software lliure i traducció col·laborativa (crowdsourcing) constitueixen recursos indispensables en la formació de traductors.

Evaluación y optimización de los servicios de un taller de mantenimiento mediante el software de simulación ARENA

Debido a la necesidad de diferenciarse y hacer frente a la competencia, las empresas han apostado por desarrollar operaciones que den valor al cliente, por eso muchas de ellas han visto en las herramientas lean la oportunidad para mejorar sus operaciones. Esta mejora implica la reducción de dinero, personas, equipos grandes, inventario y espacio, con dos objetivos: eliminar despilfarro y reducir la variabilidad. Para conseguir los objetivos estratégicos de la empresa es imprescindible qué éstos estén alineados con los planes de la gerencia a nivel medio y a su vez con el trabajo realizado por los empleados para asegurar que cada persona está alineada en la misma dirección y al mismo tiempo. Ésta es la filosofía de la planificación estratégica. Por ello uno de los objetivos de este proyecto será el desarrollar una herramienta que facilite la exposición de los objetivos de la empresa y la comunicación de los mismos a todos los niveles de la organización para a partir de ellos y tomando como referencia la necesidad de reducir inventarios en la cadena de suministro se realizará un estudio de la producción de un componente de control del aerogenerador para conseguir nivelarla y reducir su inventario de producto terminado. Los objetivos particulares en este apartado serán reducir el inventario en un 28%, nivelar la producción reduciendo la variabilidad del 31% al 24%, mantener un stock máximo de 24 unidades garantizando el suministro ante una demanda variable, incrementar la rotación del inventario en un 10% y establecer un plan de acción para reducir el lead time entre un 40-50%. Todo ello será posible gracias a la realización del mapa de valor presente y futuro para eliminar desperdicios y crear un flujo continuo y el cálculo de un supermercado que mantenga el stock en un nivel óptimo.

Las TIC como instrumento para la colaboración en red, en el ámbito de la Formación Profesional: Una aplicación de Software Libre para colaboración entre centro-empresa en el I.E.S El Palau.

En la era digital actual, Internet forma parte de nuestras vidas, y ha aportado cambios a lasociedad globalizada. Algunos de estos cambios nos permiten nuevas formas de relacionarnos y degestionar el conocimiento, dando sentido al término que hoy entendemos como sociedad-red.Por eso, en el entorno que nos envuelve existen continuamente acciones colaborativas globales quefomentan la comunicación y se comparte información de diversos tipos, con la finalidad deaprender y mantenerse constantemente informado. Específicamente, los centros educativos no sequedan al margen ya que requiere preparar estudiantes para esta sociedad.Estos cambios en la sociedad presentan grandes desafíos para el centro educativo, que nopermiten ser afrontados solamente desde el aula. Los centros requieren adaptarse a un modelocompatible con la sociedad-red, y por ello, se sugieren un modelo centro-red, que presente unaestructura de una organización compatible con la era en el que estamos inmersos.Las redes de colaboración en los centros permite intercambiar información y aportar valor a laeducación con el objetivo de la mejora educativa. En este sentido, los centros educativos debendisponer de características que permitan ser flexibles, adaptarse a los agentes y organizaciones quele envuelven. Pero la estructura actual de un centro educativo es rígida y por tanto esta evoluciónrepresenta uno de los mayores desafíos para el sistema educativo.En esta linea, en los centros de Formación Profesional existe una tendencia hacia modeloscolaborativos con el tejido empresarial, entre otros agentes, y es en este punto donde este proyectopretende centrar el foco de la investigación. Con más exactitud, en la creación de una red decolaboración con el agente que el centro educativo seleccione.Específicamente las TIC forman un papel esencial, y se deben poner al servicio del problemaque apuntábamos para ayudar a solventarlo. En este sentido, es adecuado un diseño del artefactocon Software Libre que tiene múltiples beneficios para este objetivo, pero que destacamos el que ami parecer es el más importante; la vinculación con la filosofía de compartir el conocimiento, quegarantiza la simbiosis con la red colaborativa y es por esta razón que el tema de la investigación esrelevante para el centro educativo.Tal y como se mencionaba previamente, las TIC pueden ayudar a fomentar la red colaborativa,pero no sólo el artefacto TIC generado en este proyecto debe cumplir características como laflexibilidad, también es crítico que el centro educativo y los agentes de la red interioricen la culturacolaborativa en sus acciones con la implicación y compromiso que se requiere. Pero como podemosPágina 6Universitat Oberta de Catalunya Trabajo Final de Máster - Software Libreimaginar, ese cambio de cultura, no es una tarea sencilla y presenta problemas. Para mitigarlos yfomentar la cultura en red, se requieren procesos específicos que permitan incorporarla en la medidade lo posible. Para ello, la combinación de la innovación sistémica y el diseño de la investigación eneducación resultan metodologías apropiadas.Por eso, investigaremos durante este proceso cómo las redes de colaboración y el SoftwareLibre permiten adaptar el centro al entorno, cómo pueden ayudar al centro a potenciar la FormaciónProfesional y garantizar la durabilidad de las acciones, con el objetivo que perdure el conocimientoy la propia red de colaboración para una mejora educativa.

Symptomatic intracranial hemorrhage after stroke thrombolysis: comparison of prediction scores.

BACKGROUND AND PURPOSE: Several prognostic scores have been developed to predict the risk of symptomatic intracranial hemorrhage (sICH) after ischemic stroke thrombolysis. We compared the performance of these scores in a multicenter cohort. METHODS: We merged prospectively collected data of patients with consecutive ischemic stroke who received intravenous thrombolysis in 7 stroke centers. We identified and evaluated 6 scores that can provide an estimate of the risk of sICH in hyperacute settings: MSS (Multicenter Stroke Survey); HAT (Hemorrhage After Thrombolysis); SEDAN (blood sugar, early infarct signs, [hyper]dense cerebral artery sign, age, NIH Stroke Scale); GRASPS (glucose at presentation, race [Asian], age, sex [male], systolic blood pressure at presentation, and severity of stroke at presentation [NIH Stroke Scale]); SITS (Safe Implementation of Thrombolysis in Stroke); and SPAN (stroke prognostication using age and NIH Stroke Scale)-100 positive index. We included only patients with available variables for all scores. We calculated the area under the receiver operating characteristic curve (AUC-ROC) and also performed logistic regression and the Hosmer-Lemeshow test. RESULTS: The final cohort comprised 3012 eligible patients, of whom 221 (7.3%) had sICH per National Institute of Neurological Disorders and Stroke, 141 (4.7%) per European Cooperative Acute Stroke Study II, and 86 (2.9%) per Safe Implementation of Thrombolysis in Stroke criteria. The performance of the scores assessed with AUC-ROC for predicting European Cooperative Acute Stroke Study II sICH was: MSS, 0.63 (95% confidence interval, 0.58-0.68); HAT, 0.65 (0.60-0.70); SEDAN, 0.70 (0.66-0.73); GRASPS, 0.67 (0.62-0.72); SITS, 0.64 (0.59-0.69); and SPAN-100 positive index, 0.56 (0.50-0.61). SEDAN had significantly higher AUC-ROC values compared with all other scores, except for GRASPS where the difference was nonsignificant. SPAN-100 performed significantly worse compared with other scores. The discriminative ranking of the scores was the same for the National Institute of Neurological Disorders and Stroke, and Safe Implementation of Thrombolysis in Stroke definitions, with SEDAN performing best, GRASPS second, and SPAN-100 worst. CONCLUSIONS: SPAN-100 had the worst predictive power, and SEDAN constantly the highest predictive power. However, none of the scores had better than moderate performance.