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As fish cell cultures continue to be explored as alternatives to whole fish for evaluating the toxicity of environment chemicals, technical issues have emerged that influence results and thus need to be understood and standardized. These include carrier solvents, dosing protocols, exposure vessel, exposure media, viability endpoints, and cell lines. Some of these factors have been explored in this thesis for eight reactive contaminants exhibiting varied physicochemical properties using the rainbow trout cell lines RTgill-W1 and RTL-W1. Sodium dodecyl sulphate (SDS) was used as a reference (control) chemical. Cell viability was evaluated with alamar Blue, carboxyfluoroscein diacetate acetoxymethyl ester and neutral red as measures respectively of metabolic activity, plasma membrane integrity, and lysosomal function. Experimental in vitro EC50 values were compared to 1) pre-existing in vivo LC50s from the fathead minnow database and 2) pre-existing in vitro EC50s from the Halle database. Results point to good in vitro/in vivo correlations for menadione, dichlorophene, hexachlorophene, and acrolein. Poor correlations were observed for allyl alcohol, 4-fluoroaniline, acetaldehyde, and 2,3-dimethyl-1,3-butadiene due to a combination of solubility and volatility problems. Overall, the results suggest that the impact of different technical approaches on the evaluation of acute toxicity in vitro depends very much on the chemical class being investigated and less on the characteristics of the cell line. The in vitro cytotoxicity of reactive chemicals is challenging due to the nature of the chemicals’ physicochemical properties. Further improving the in vitro toxicity of reactive chemicals is a prerequisite for the ultimate goal of using fish cell cultures as acceptable, standard alternatives to the use of fish acute lethality assays.

As fish cell cultures continue to be explored as alternatives to whole fish for evaluating the toxicity of environment chemicals, technical issues have emerged that influence results and thus need to be understood and standardized. These include carrier solvents, dosing protocols, exposure vessel, exposure media, viability endpoints, and cell lines. Some of these factors have been explored in this thesis for eight reactive contaminants exhibiting varied physicochemical properties using the rainbow trout cell lines RTgill-W1 and RTL-W1. Sodium dodecyl sulphate (SDS) was used as a reference (control) chemical. Cell viability was evaluated with alamar Blue, carboxyfluoroscein diacetate acetoxymethyl ester and neutral red as measures respectively of metabolic activity, plasma membrane integrity, and lysosomal function. Experimental in vitro EC50 values were compared to 1) pre-existing in vivo LC50s from the fathead minnow database and 2) pre-existing in vitro EC50s from the Halle database. Results point to good in vitro/in vivo correlations for menadione, dichlorophene, hexachlorophene, and acrolein. Poor correlations were observed for allyl alcohol, 4-fluoroaniline, acetaldehyde, and 2,3-dimethyl-1,3-butadiene due to a combination of solubility and volatility problems. Overall, the results suggest that the impact of different technical approaches on the evaluation of acute toxicity in vitro depends very much on the chemical class being investigated and less on the characteristics of the cell line. The in vitro cytotoxicity of reactive chemicals is challenging due to the nature of the chemicals’ physicochemical properties. Further improving the in vitro toxicity of reactive chemicals is a prerequisite for the ultimate goal of using fish cell cultures as acceptable, standard alternatives to the use of fish acute lethality assays.

Magíster en Ciencias, Mención Computación / La tecnología de los agentes se ha convertido en la base de una gran cantidad de aplicaciones ya que permite la incorporación de bases de conocimiento de acciones y tareas para resolver problemas complejos. Por otro lado, se sabe que los Servidores Web se sustentan en el protocolo HTTP, protocolo que solo permite las solicitudes y respuestas entre Cliente y Servidor y no delegar funciones a otros Servidores separados geográficamente. Esta investigación consiste en un estudio exploratorio del concepto de la delegación en el contexto de la Web, donde agentes que residen en diferentes Servidores Web puedan cooperan entre sí para resolver tareas complejas. Para ello, se propone un lenguaje de especificación para la delegación de tareas en Servidores Web mediante agentes, con propiedades necesarias para su autonomía y que puedan ser utilizados con flexibilidad en entornos distribuidos bajo la restricción del protocolo de comunicación HTTP. En primer lugar, se presenta el modelo abstracto de la delegación en el entorno de la Web y los componentes necesarios para la elaboración del lenguaje especificación propuesto, mediante la definición de acciones básicas y opcionales que son implementadas por los agentes participantes en el proceso de la delegación. En segundo lugar, como caso de estudio, se desarrolla la implementación de NautiLOD de manera distribuida mediante agentes. NautiLOD es un lenguaje de expresión declarativo que está diseñado para especificar patrones de navegación en la red Linked Open Data, donde sus primeras propuestas de implementación han sido con un enfoque centralizado. En un tercer lugar, se presenta Agent Server, una plataforma flexible y escalable para Sistema MultiAgentes basados en el ambiente de la Web, desarrollado bajo los principios de REST, que permite gestionar agentes distribuidos. La principal conclusión de la tesis es la validación del lenguaje de especificación en una plataforma homogénea como es Linked Data que gracias a su semántica permite a los agentes procesar su contenido, razonar sobre este y realizar deducciones lógicas. Esto se realizó con consultas propias en los Endpoints SPARQL expresados en NautiLOD.

A presente revisão teve por objetivo indicar em literatura o uso do comportamento de locomoção de invertebrados aquáticos com indicador de toxicidade. Desde a década de 1960 é sabido que contaminantes tem efeitos deletérios em níveis populacionais e ecossistêmicos. A ecotoxicologia comportamental é um dos ramos da ecotoxicologia clássica que tem como objetivo interpretar os efeitos comportamentais dos contaminantes nos organismos. Esta abordagem tem ganhado espaço em função da continua busca de pesquisadores por enpoints que expressem efeitos populacionais relevantes. Além da importância econômica, os crustáceos aquáticos têm importância em cadeias alimentares e na aquicultura. Microcrustáceos são tidos pela ecotoxicologia como espécies-modelo, também utilizados para observações comportamentais em razão da sua participação em processos ecossistêmicos como as alças microbianas, ocupando posições intermediárias na cadeia trófica e sustentando níveis tróficos mais elevados. A locomoção de microcrustáceos aquáticos é o comportamento fundamental que garante a sobrevivência destes organismos no ambiente. Diversos processos vitais estão estritamente ligados à locomoção (e.g.: reprodução e alimentação). Sabe-se que compostos tóxicos tem a capacidade de alterar funções fisiológicas dos organismos, entre elas a locomoção. Atualmente, a quantificação do comportamento (endpoints comportamentais) tem sido utilizada para indicar mudanças induzidas por compostos orgânicos ou inorgânicos, favorecendo um panorama mais amplo sobre os efeitos adversos da contaminação aquática. / The present review aimed to indicate in literature the use of aquatic invertebrate swimming behavior as model to access contaminants toxicity. Since the 1960s it has been known that toxicants have deleterious effects at population and ecosystem levels. Behavioral ecotoxicology is one of the approaches of classical ecotoxicology that aims to interpret the behavioral effects of toxicants on organisms. This approach has gained space due to the continuous researchers\' investigation about enpoints that allow to find the ecological relevance. Besides economic importance, aquatic crustaceans are important in food chains and aquaculture. Microcrustaceans are considered by ecotoxicology as model species, also used for behavioral observations because of their participation in ecosystem processes such as the microbial loops, occupying intermediate positions in the trophic chain and sustaining higher trophic levels. The locomotion of aquatic microcrustaceans is the fundamental behavior that guarantees the survival of these organisms in the environment. Several vital processes are strictly linked to locomotion (e.g.: reproduction and feeding). It is known that toxic compounds can alter the physiological functions of organisms, including locomotion. Currently, behavioral quantification (behavioral endpoints) has been used to indicate changes induced by organic or inorganic toxic compounds, favoring a broader picture of the adverse effects of aquatic contamination.

In most randomised controlled trials (RCTs), a large number of patients need to be followed over many years, for the clinical benefit of the drug to be accurately quantified (1). Using an early proxy, or a surrogate endpoint, in place of the direct endpoint of overall survival (OS) could theoretically shorten the duration of RCTs and minimise the exposure of patients to ineffective or toxic treatments (2, 3). This thesis examined the relationship between surrogate endpoints and OS in metastatic colorectal cancer (CRC), advanced non-small cell lung cancer (NSCLC) and metastatic breast cancer (MBC). A review of the literature identified 144 RCTs in metastatic CRC, 189 in advanced NSCLC and 133 in MBC. The publications were generally of poor quality with incomplete reporting on many key variables, making comparisons between studies difficult. The introduction of the CONSORT statement was associated with improvements in the quality of reporting. For CRC (337 arms), NSCLC (429 arms) and MBC (290 arms) there were strong relationships between OS and progression free survival (PFS), time to progression (TTP), disease control rate (DCR), response rate (RR) and partial response (PR). Correlation was also demonstrated between OS and complete response (CR) in CRC and duration of response (DOR) in MBC. However, while strong relationships were found, the proportion of variance explained by the models was small. Prediction bands constructed to determine the surrogate threshold effect size indicated that large improvements in the surrogate endpoints were needed to predict overall survival gains. PFS and TTP showed the most promise as surrogates. The gain in PFS and TTP required to predict a significant gain in overall survival was between 1.2 and 7.0 months and 1.8 and 7.7 months respectively, depending on trial size and tumour type. DCR was a better potential predictor of OS than RR. The results of this study could be used to design future clinical trials with particular reference to the selection of surrogate endpoint and trial size.

In most randomised controlled trials (RCTs), a large number of patients need to be followed over many years, for the clinical benefit of the drug to be accurately quantified (1). Using an early proxy, or a surrogate endpoint, in place of the direct endpoint of overall survival (OS) could theoretically shorten the duration of RCTs and minimise the exposure of patients to ineffective or toxic treatments (2, 3). This thesis examined the relationship between surrogate endpoints and OS in metastatic colorectal cancer (CRC), advanced non-small cell lung cancer (NSCLC) and metastatic breast cancer (MBC). A review of the literature identified 144 RCTs in metastatic CRC, 189 in advanced NSCLC and 133 in MBC. The publications were generally of poor quality with incomplete reporting on many key variables, making comparisons between studies difficult. The introduction of the CONSORT statement was associated with improvements in the quality of reporting. For CRC (337 arms), NSCLC (429 arms) and MBC (290 arms) there were strong relationships between OS and progression free survival (PFS), time to progression (TTP), disease control rate (DCR), response rate (RR) and partial response (PR). Correlation was also demonstrated between OS and complete response (CR) in CRC and duration of response (DOR) in MBC. However, while strong relationships were found, the proportion of variance explained by the models was small. Prediction bands constructed to determine the surrogate threshold effect size indicated that large improvements in the surrogate endpoints were needed to predict overall survival gains. PFS and TTP showed the most promise as surrogates. The gain in PFS and TTP required to predict a significant gain in overall survival was between 1.2 and 7.0 months and 1.8 and 7.7 months respectively, depending on trial size and tumour type. DCR was a better potential predictor of OS than RR. The results of this study could be used to design future clinical trials with particular reference to the selection of surrogate endpoint and trial size.

Dans les essais cliniques randomisés (ECR) en cancérologie, un critère de substitution est une mesure biologique utilisée à la place d’un critère cliniquement pertinent pour le patient, par exemple la survie globale (SG), qui doit permettre de prédire l’effet attendu du traitement. Des critères alternatifs à la SG, par exemple la survie sans progression, sont de plus en plus fréquemment utilisés en tant que critère de jugement principal dans les ECR. En pratique cependant, les capacités de substitution à la SG de ces critères ne sont pas systématiquement évaluées. Nous avons dressé un état des lieux des critères de substitution validés en cancérologie à partir d’une revue systématique de la littérature. Par la suite, nous avons évalué par une approche méta-analytique des critères de substitution dans le contexte des sarcomes des tissus mous en situation avancée et du cancer du sein en situation adjuvante. Les résultats n’ont pas permis de définitivement valider de critères de substitution à la SG dans ces indications. La SG doit donc rester le critère de jugement principal des ECR, même si certains critères alternatifs restent informatifs dans des évaluations plus précoces (phase II, analyse de futilité), sous réserve que les données de survie continuent à être recueillies. Ce travail fournit des informations clés pour le développement des ECR en cancérologie afin notamment de sélectionner au mieux les critères de jugement de l’efficacité thérapeutique. / In cancer randomized controlled trials (RCT), a surrogate endpoint is intended to substitute a clinically relevant endpoint, e.g. overall survival (OS), and it is supposed to predict treatment effect. Alternative endpoints, for example progression-free survival, are increasingly being used in place of OS as primary efficacy endpoints in RCTs. In practice however, the surrogate properties of these endpoints are not systematically assessed. We performed a systematic literature review to identify surrogate endpoints validated in oncology. We next conducted MAs to evaluate surrogate endpoints in two cancer settings: advanced soft-tissue sarcoma and adjuvant breast cancer. Results could not definitely validate surrogate endpoints in these indications. OS must remain the primary efficacy endpoint in these settings, even though alternative endpoints may provide valuable input in earlier phase studies (phase II trials, futility analyses). This work provides key information for the design of cancer RCTs, in particular for the choice of primary endpoints to assess treatment efficacy.

Généralement, dans les situations d’hypothèses multiples on cherche à rejeter toutes les hypothèses ou bien une seule d’entre d’elles. Depuis quelques temps on voit apparaître le besoin de répondre à la question : « Peut-on rejeter au moins r hypothèses ? ». Toutefois, les outils statisques pour répondre à cette question sont rares dans la littérature. Nous avons donc entrepris de développer les formules générales de puissance pour les procédures les plus utilisées, soit celles de Bonferroni, de Hochberg et de Holm. Nous avons développé un package R pour le calcul de la taille échantilonnalle pour les tests à hypothèses multiples (multiple endpoints), où l’on désire qu’au moins r des m hypothèses soient significatives. Nous nous limitons au cas où toutes les variables sont continues et nous présentons quatre situations différentes qui dépendent de la structure de la matrice de variance-covariance des données. / Generally, in multiple endpoints situations we want to reject all hypotheses or at least only one of them. For some time now, we see emerge the need to answer the question : "Can we reject at least r hypotheses ?" However, the statistical tools to answer this new problem are rare in the litterature. We decide to develop general power formulas for the principals procedures : Bonferroni’s, Hochberg’s and Holm’s procedures. We also develop an R package for the sample size calculation for multiple endpoints, when we want to reject at least r hypotheses. We limit ourselves in the case where all the variables are continuous and we present four different situations depending on the structure of the data’s variance-covariance matrix.