User-centric need-driven affect modeling for spoken conversational agents: design and evaluation

It is easy to get frustrated at spoken conversational agents (SCAs), perhaps because they seem to be callous. By and large, the quality of human-computer interaction is affected due to the inability of the SCAs to recognise and adapt to user emotional state. Now with the mass appeal of artificially-mediated communication, there has been an increasing need for SCAs to be socially and emotionally intelligent, that is, to infer and adapt to their human interlocutors’ emotions on the fly, in order to ascertain an affective, empathetic and naturalistic interaction. An enhanced quality of interaction would reduce users’ frustrations and consequently increase their satisfactions. These reasons have motivated the development of SCAs towards including socio-emotional elements, turning them into affective and socially-sensitive interfaces. One barrier to the creation of such interfaces has been the lack of methods for modelling emotions in a task-independent environment. Most emotion models for spoken dialog systems are task-dependent and thus cannot be used “as-is” in different applications. This Thesis focuses on improving this, in which it concerns computational modeling of emotion, personality and their interrelationship for task-independent autonomous SCAs. The generation of emotion is driven by needs, inspired by human’s motivational systems. The work in this Thesis is organised in three stages, each one with its own contribution. The first stage involved defining, integrating and quantifying the psychological-based motivational and emotional models sourced from. Later these were transformed into a computational model by implementing them into software entities. The computational model was then incorporated and put to test with an existing SCA host, a HiFi-control agent. The second stage concerned automatic prediction of affect, which has been the main challenge towards the greater aim of infusing social intelligence into the HiFi agent. In recent years, studies on affect detection from voice have moved on to using realistic, non-acted data, which is subtler. However, it is more challenging to perceive subtler emotions and this is demonstrated in tasks such as labelling and machine prediction. In this stage, we attempted to address part of this challenge by considering the roles of user satisfaction ratings and conversational/dialog features as the respective target and predictors in discriminating contentment and frustration, two types of emotions that are known to be prevalent within spoken human-computer interaction. The final stage concerned the evaluation of the emotional model through the HiFi agent. A series of user studies with 70 subjects were conducted in a real-time environment, each in a different phase and with its own conditions. All the studies involved the comparisons between the baseline non-modified and the modified agent. The findings have gone some way towards enhancing our understanding of the utility of emotion in spoken dialog systems in several ways; first, an SCA should not express its emotions blindly, albeit positive. Rather, it should adapt its emotions to user states. Second, low performance in an SCA may be compensated by the exploitation of emotion. Third, the expression of emotion through the exploitation of prosody could better improve users’ perceptions of an SCA compared to exploiting emotions through just lexical contents. Taken together, these findings not only support the success of the emotional model, but also provide substantial evidences with respect to the benefits of adding emotion in an SCA, especially in mitigating users’ frustrations and ultimately improving their satisfactions. Resumen Es relativamente fácil experimentar cierta frustración al interaccionar con agentes conversacionales (Spoken Conversational Agents, SCA), a menudo porque parecen ser un poco insensibles. En general, la calidad de la interacción persona-agente se ve en cierto modo afectada por la incapacidad de los SCAs para identificar y adaptarse al estado emocional de sus usuarios. Actualmente, y debido al creciente atractivo e interés de dichos agentes, surge la necesidad de hacer de los SCAs unos seres cada vez más sociales y emocionalmente inteligentes, es decir, con capacidad para inferir y adaptarse a las emociones de sus interlocutores humanos sobre la marcha, de modo que la interacción resulte más afectiva, empática y, en definitiva, natural. Una interacción mejorada en este sentido permitiría reducir la posible frustración de los usuarios y, en consecuencia, mejorar el nivel de satisfacción alcanzado por los mismos. Estos argumentos justifican y motivan el desarrollo de nuevos SCAs con capacidades socio-emocionales, dotados de interfaces afectivas y socialmente sensibles. Una de las barreras para la creación de tales interfaces ha sido la falta de métodos de modelado de emociones en entornos independientes de tarea. La mayoría de los modelos emocionales empleados por los sistemas de diálogo hablado actuales son dependientes de tarea y, por tanto, no pueden utilizarse "tal cual" en diferentes dominios o aplicaciones. Esta tesis se centra precisamente en la mejora de este aspecto, la definición de modelos computacionales de las emociones, la personalidad y su interrelación para SCAs autónomos e independientes de tarea. Inspirada en los sistemas motivacionales humanos en el ámbito de la psicología, la tesis propone un modelo de generación/producción de la emoción basado en necesidades. El trabajo realizado en la presente tesis está organizado en tres etapas diferenciadas, cada una con su propia contribución. La primera etapa incluyó la definición, integración y cuantificación de los modelos motivacionales de partida y de los modelos emocionales derivados a partir de éstos. Posteriormente, dichos modelos emocionales fueron plasmados en un modelo computacional mediante su implementación software. Este modelo computacional fue incorporado y probado en un SCA anfitrión ya existente, un agente con capacidad para controlar un equipo HiFi, de alta fidelidad. La segunda etapa se orientó hacia el reconocimiento automático de la emoción, aspecto que ha constituido el principal desafío en relación al objetivo mayor de infundir inteligencia social en el agente HiFi. En los últimos años, los estudios sobre reconocimiento de emociones a partir de la voz han pasado de emplear datos actuados a usar datos reales en los que la presencia u observación de emociones se produce de una manera mucho más sutil. El reconocimiento de emociones bajo estas condiciones resulta mucho más complicado y esta dificultad se pone de manifiesto en tareas tales como el etiquetado y el aprendizaje automático. En esta etapa, se abordó el problema del reconocimiento de las emociones del usuario a partir de características o métricas derivadas del propio diálogo usuario-agente. Gracias a dichas métricas, empleadas como predictores o indicadores del grado o nivel de satisfacción alcanzado por el usuario, fue posible discriminar entre satisfacción y frustración, las dos emociones prevalentes durante la interacción usuario-agente. La etapa final corresponde fundamentalmente a la evaluación del modelo emocional por medio del agente Hifi. Con ese propósito se llevó a cabo una serie de estudios con usuarios reales, 70 sujetos, interaccionando con diferentes versiones del agente Hifi en tiempo real, cada uno en una fase diferente y con sus propias características o capacidades emocionales. En particular, todos los estudios realizados han profundizado en la comparación entre una versión de referencia del agente no dotada de ningún comportamiento o característica emocional, y una versión del agente modificada convenientemente con el modelo emocional propuesto. Los resultados obtenidos nos han permitido comprender y valorar mejor la utilidad de las emociones en los sistemas de diálogo hablado. Dicha utilidad depende de varios aspectos. En primer lugar, un SCA no debe expresar sus emociones a ciegas o arbitrariamente, incluso aunque éstas sean positivas. Más bien, debe adaptar sus emociones a los diferentes estados de los usuarios. En segundo lugar, un funcionamiento relativamente pobre por parte de un SCA podría compensarse, en cierto modo, dotando al SCA de comportamiento y capacidades emocionales. En tercer lugar, aprovechar la prosodia como vehículo para expresar las emociones, de manera complementaria al empleo de mensajes con un contenido emocional específico tanto desde el punto de vista léxico como semántico, ayuda a mejorar la percepción por parte de los usuarios de un SCA. Tomados en conjunto, los resultados alcanzados no sólo confirman el éxito del modelo emocional, sino xv que constituyen además una evidencia decisiva con respecto a los beneficios de incorporar emociones en un SCA, especialmente en cuanto a reducir el nivel de frustración de los usuarios y, en última instancia, mejorar su satisfacción.

Modeling the evolution of item rating networks using time-domain preferential attachment

The understanding of the structure and dynamics of the intricate network of connections among people that consumes products through Internet appears as an extremely useful asset in order to study emergent properties related to social behavior. This knowledge could be useful, for example, to improve the performance of personal recommendation algorithms. In this contribution, we analyzed five-year records of movie-rating transactions provided by Netflix, a movie rental platform where users rate movies from an online catalog. This dataset can be studied as a bipartite user-item network whose structure evolves in time. Even though several topological properties from subsets of this bipartite network have been reported with a model that combines random and preferential attachment mechanisms [Beguerisse Díaz et al., 2010], there are still many aspects worth to be explored, as they are connected to relevant phenomena underlying the evolution of the network. In this work, we test the hypothesis that bursty human behavior is essential in order to describe how a bipartite user-item network evolves in time. To that end, we propose a novel model that combines, for user nodes, a network growth prescription based on a preferential attachment mechanism acting not only in the topological domain (i.e. based on node degrees) but also in time domain. In the case of items, the model mixes degree preferential attachment and random selection. With these ingredients, the model is not only able to reproduce the asymptotic degree distribution, but also shows an excellent agreement with the Netflix data in several time-dependent topological properties.

The Role of Knowledge Modeling Techniques in Software Development: A General Approach Based on a Knowledge Management Tool

The aim of the paper is to discuss the use of knowledge models to formulate general applications. First, the paper presents the recent evolution of the software field where increasing attention is paid to conceptual modeling. Then, the current state of knowledge modeling techniques is described where increased reliability is available through the modern knowledge acquisition techniques and supporting tools. The KSM (Knowledge Structure Manager) tool is described next. First, the concept of knowledge area is introduced as a building block where methods to perform a collection of tasks are included together with the bodies of knowledge providing the basic methods to perform the basic tasks. Then, the CONCEL language to define vocabularies of domains and the LINK language for methods formulation are introduced. Finally, the object oriented implementation of a knowledge area is described and a general methodology for application design and maintenance supported by KSM is proposed. To illustrate the concepts and methods, an example of system for intelligent traffic management in a road network is described. This example is followed by a proposal of generalization for reuse of the resulting architecture. Finally, some concluding comments are proposed about the feasibility of using the knowledge modeling tools and methods for general application design.

Modelización de servicios ecosistémicos en una cuenca hidrológica del área mediterránea = Modeling ecosystem services in a mediterranean area river basin

La modelización es un proceso por el que se obtienen modelos de los procesos del ´mundo real´ mediante la utilización de simplificaciones. Sin embargo, las estimaciones obtenidas con el modelo llevan implícitas incertidumbre que se debe evaluar. Mediante un análisis de sensibilidad se puede mejorar la confianza en los resultados, sin embargo, este paso a veces no se realiza debido básicamente al trabajo que lleva consigo este tipo de análisis. Además, al crear un modelo, hay que mantener un equilibrio entre la obtención de resultados lo más exactos posible mediante un modelo lo más sencillo posible. Por ello, una vez creado un modelo, es imprescindible comprobar si es necesario o no incluir más procesos que en un principio no se habían incluido. Los servicios ecosistémicos son los procesos mediante los cuales los ecosistemas mantienen y satisfacen el bienestar humano. La importancia que los servicios ecosistémicos y sus beneficios asociados tienen, junto con la necesidad de realizar una buena gestión de los mismos, han estimulado la aparición de modelos y herramientas para cuantificarlos. InVEST (Integrated Valuation of Ecosystem Services and Tradoffs) es una de estas herramientas específicas para calcular servicios eco-sistémicos, desarrollada por Natural Capital Project (Universidad de Stanford, EEUU). Como resultado del creciente interés en calcular los servicios eco-sistémicos, se prevé un incremento en la aplicación del InVEST. La investigación desarrollada en esta Tesis pretende ayudar en esas otras importantes fases necesarias después de la creación de un modelo, abarcando los dos siguientes trabajos. El primero es la aplicación de un análisis de sensibilidad al modelo en una cuenca concreta mediante la metodología más adecuada. El segundo es relativo a los procesos dentro de la corriente fluvial que actualmente no se incluyen en el modelo mediante la creación y aplicación de una metodología que estudiara el papel que juegan estos procesos en el modelo InVEST de retención de nutrientes en el área de estudio. Los resultados de esta Tesis contribuirán a comprender la incertidumbre involucrada en el proceso de modelado. También pondrá de manifiesto la necesidad de comprobar el comportamiento de un modelo antes de utilizarlo y en el momento de interpretar los resultados obtenidos. El trabajo en esta Tesis contribuirá a mejorar la plataforma InVEST, que es una herramienta importante en el ámbito de los servicios de los ecosistemas. Dicho trabajo beneficiará a los futuros usuarios de la herramienta, ya sean investigadores (en investigaciones futuras), o técnicos (en futuros trabajos de toma de decisiones o gestión ecosistemas). ABSTRACT Modeling is the process to idealize real-world situations through simplifications in order to obtain a model. However, model estimations lead to uncertainties that have to be evaluated formally. The role of the sensitivity analysis (SA) is to assign model output uncertainty based on the inputs and can increase confidence in model, however, it is often omitted in modelling, usually as a result of the growing effort it involves. In addition, the balance between accuracy and simplicity is not easy to assess. For this reason, when a model is developed, it is necessary to test it in order to understand its behavior and to include, if necessary, more complexity to get a better response. Ecosystem services are the conditions and processes through which natural ecosystems, and their constituent species, sustain and fulfill human life. The relevance of ecosystem services and the need to better manage them and their associated benefits have stimulated the emergence of models and tools to measure them. InVEST, Integrated Valuation of Ecosystem Services and Tradoffs, is one of these ecosystem services-specific tools developed by the Natural Capital Project (Stanford University, USA). As a result of the growing interest in measuring ecosystem services, the use of InVEST is anticipated to grow exponentially in the coming years. However, apart from model development, making a model involves other crucial stages such as its evaluation and application in order to validate estimations. The work developed in this thesis tries to help in this relevant and imperative phase of the modeling process, and does so in two different ways. The first one is to conduct a sensitivity analysis of the model, which consists in choosing and applying a methodology in an area and analyzing the results obtained. The second is related to the in-stream processes that are not modeled in the current model, and consists in creating and applying a methodology for testing the streams role in the InVEST nutrient retention model in a case study, analyzing the results obtained. The results of this Thesis will contribute to the understanding of the uncertainties involved in the modeling process. It will also illustrate the need to check the behavior of every model developed before putting them in production and illustrate the importance of understanding their behavior in terms of correctly interpreting the results obtained in light of uncertainty. The work in this thesis will contribute to improve the InVEST platform, which is an important tool in the field of ecosystem services. Such work will benefit future users, whether they are researchers (in their future research), or technicians (in their future work in ecosystem conservation or management decisions).

Generation of human computational models with machine learning

Services in smart environments pursue to increase the quality of people?s lives. The most important issues when developing this kind of environments is testing and validating such services. These tasks usually imply high costs and annoying or unfeasible real-world testing. In such cases, artificial societies may be used to simulate the smart environment (i.e. physical environment, equipment and humans). With this aim, the CHROMUBE methodology guides test engineers when modeling human beings. Such models reproduce behaviors which are highly similar to the real ones. Originally, these models are based on automata whose transitions are governed by random variables. Automaton?s structure and the probability distribution functions of each random variable are determined by a manual test and error process. In this paper, it is presented an alternative extension of this methodology which avoids the said manual process. It is based on learning human behavior patterns automatically from sensor data by using machine learning techniques. The presented approach has been tested on a real scenario, where this extension has given highly accurate human behavior models,

Perceptual distortion modeling for side-by-side 3D video delivery

A frame-level distortion model based on perceptual features of the human visual system is proposed to improve the performance of unequal error protection strategies and provide better quality of experience to users in Side-by-Side 3D video delivery systems.

Modelización de servicios ecosistémicos en una cuenca hidrológica del área mediterránea = Modeling ecosystem services in a mediterranean area river basin

La modelización es un proceso por el que se obtienen modelos de los procesos del ´mundo real´ mediante la utilización de simplificaciones. Sin embargo, las estimaciones obtenidas con el modelo llevan implícitas incertidumbre que se debe evaluar. Mediante un análisis de sensibilidad se puede mejorar la confianza en los resultados, sin embargo, este paso a veces no se realiza debido básicamente al trabajo que lleva consigo este tipo de análisis. Además, al crear un modelo, hay que mantener un equilibrio entre la obtención de resultados lo más exactos posible mediante un modelo lo más sencillo posible. Por ello, una vez creado un modelo, es imprescindible comprobar si es necesario o no incluir más procesos que en un principio no se habían incluido. Los servicios ecosistémicos son los procesos mediante los cuales los ecosistemas mantienen y satisfacen el bienestar humano. La importancia que los servicios ecosistémicos y sus beneficios asociados tienen, junto con la necesidad de realizar una buena gestión de los mismos, han estimulado la aparición de modelos y herramientas para cuantificarlos. InVEST (Integrated Valuation of Ecosystem Services and Tradoffs) es una de estas herramientas específicas para calcular servicios eco-sistémicos, desarrollada por Natural Capital Project (Universidad de Stanford, EEUU). Como resultado del creciente interés en calcular los servicios eco-sistémicos, se prevé un incremento en la aplicación del InVEST. La investigación desarrollada en esta Tesis pretende ayudar en esas otras importantes fases necesarias después de la creación de un modelo, abarcando los dos siguientes trabajos. El primero es la aplicación de un análisis de sensibilidad al modelo en una cuenca concreta mediante la metodología más adecuada. El segundo es relativo a los procesos dentro de la corriente fluvial que actualmente no se incluyen en el modelo mediante la creación y aplicación de una metodología que estudiara el papel que juegan estos procesos en el modelo InVEST de retención de nutrientes en el área de estudio. Los resultados de esta Tesis contribuirán a comprender la incertidumbre involucrada en el proceso de modelado. También pondrá de manifiesto la necesidad de comprobar el comportamiento de un modelo antes de utilizarlo y en el momento de interpretar los resultados obtenidos. El trabajo en esta Tesis contribuirá a mejorar la plataforma InVEST, que es una herramienta importante en el ámbito de los servicios de los ecosistemas. Dicho trabajo beneficiará a los futuros usuarios de la herramienta, ya sean investigadores (en investigaciones futuras), o técnicos (en futuros trabajos de toma de decisiones o gestión ecosistemas). ABSTRACT Modeling is the process to idealize real-world situations through simplifications in order to obtain a model. However, model estimations lead to uncertainties that have to be evaluated formally. The role of the sensitivity analysis (SA) is to assign model output uncertainty based on the inputs and can increase confidence in model, however, it is often omitted in modelling, usually as a result of the growing effort it involves. In addition, the balance between accuracy and simplicity is not easy to assess. For this reason, when a model is developed, it is necessary to test it in order to understand its behavior and to include, if necessary, more complexity to get a better response. Ecosystem services are the conditions and processes through which natural ecosystems, and their constituent species, sustain and fulfill human life. The relevance of ecosystem services and the need to better manage them and their associated benefits have stimulated the emergence of models and tools to measure them. InVEST, Integrated Valuation of Ecosystem Services and Tradoffs, is one of these ecosystem services-specific tools developed by the Natural Capital Project (Stanford University, USA). As a result of the growing interest in measuring ecosystem services, the use of InVEST is anticipated to grow exponentially in the coming years. However, apart from model development, making a model involves other crucial stages such as its evaluation and application in order to validate estimations. The work developed in this thesis tries to help in this relevant and imperative phase of the modeling process, and does so in two different ways. The first one is to conduct a sensitivity analysis of the model, which consists in choosing and applying a methodology in an area and analyzing the results obtained. The second is related to the in-stream processes that are not modeled in the current model, and consists in creating and applying a methodology for testing the streams role in the InVEST nutrient retention model in a case study, analyzing the results obtained. The results of this Thesis will contribute to the understanding of the uncertainties involved in the modeling process. It will also illustrate the need to check the behavior of every model developed before putting them in production and illustrate the importance of understanding their behavior in terms of correctly interpreting the results obtained in light of uncertainty. The work in this thesis will contribute to improve the InVEST platform, which is an important tool in the field of ecosystem services. Such work will benefit future users, whether they are researchers (in their future research), or technicians (in their future work in ecosystem conservation or management decisions).

Modeling and Simulation of Upper Brachial Plexus Injury

This article presents the first musculoskeletal model and simulation of upper plexus brachial injury. From this model is possible to analyse forces and movement ranges in order to develop a robotic exoskeleton to improve rehabilitation. The software that currently exists for musculoskeletal modeling is varied and most have advanced features for proper analysis and study of motion simulations. Whilst more powerful computer packages are usually expensive, there are other free and open source packages available which offer different tools to perform animations and simulations and which obtain forces and moments of inertia. Among them, Musculoskeletal Modeling Software was selected to construct a model of the upper limb, which has 7 degrees of freedom and 10 muscles. These muscles are important for two of the movements simulated in this article that are part of the post-surgery rehabilitation protocol. We performed different movement animations which are made using the inertial measurement unit to capture real data from movements made by a human being. We also performed the simulation of forces produced in elbow flexion-extension and arm abduction-adduction of a healthy subject and one with upper brachial plexus injury in a postoperative state to compare the force that is capable of being produced in both cases.

The design, computer modeling, solution structure, and biological evaluation of synthetic analogs of bryostatin 1

The bryostatins are a unique family of emerging cancer chemotherapeutic candidates isolated from marine bryozoa. Although the biochemical basis for their therapeutic activity is not known, these macrolactones exhibit high affinities for protein kinase C (PKC) isozymes, compete for the phorbol ester binding site on PKC, and stimulate kinase activity in vitro and in vivo. Unlike the phorbol esters, they are not first-stage tumor promoters. The design, computer modeling, NMR solution structure, PKC binding, and functional assays of a unique class of synthetic bryostatin analogs are described. These analogs (7b, 7c, and 8) retain the putative recognition domain of the bryostatins but are simplified through deletions and modifications in the C4-C14 spacer domain. Computer modeling of an analog prototype (7a) indicates that it exists preferentially in two distinct conformational classes, one in close agreement with the crystal structure of bryostatin 1. The solution structure of synthetic analog 7c was determined by NMR spectroscopy and found to be very similar to the previously reported structures of bryostatins 1 and 10. Analogs 7b, 7c, and 8 bound strongly to PKC isozymes with Ki = 297, 3.4, and 8.3 nM, respectively. Control 7d, like the corresponding bryostatin derivative, exhibited weak PKC affinity, as did the derivative, 9, lacking the spacer domain. Like bryostatin, acetal 7c exhibited significant levels of in vitro growth inhibitory activity (1.8–170 ng/ml) against several human cancer cell lines, providing an important step toward the development of simplified, synthetically accessible analogs of the bryostatins.

Analysis of human cytochrome P450 3A4 cooperativity: Construction and characterization of a site-directed mutant that displays hyperbolic steroid hydroxylation kinetics

Cytochrome P450 3A4 is generally considered to be the most important human drug-metabolizing enzyme and is known to catalyze the oxidation of a number of substrates in a cooperative manner. An allosteric mechanism is usually invoked to explain the cooperativity. Based on a structure–activity study from another laboratory using various effector–substrate combinations and on our own studies using site-directed mutagenesis and computer modeling of P450 3A4, the most likely location of effector binding is in the active site along with the substrate. Our study was designed to test this hypothesis by replacing residues Leu-211 and Asp-214 with the larger Phe and Glu, respectively. These residues were predicted to constitute a portion of the effector binding site, and the substitutions were designed to mimic the action of the effector by reducing the size of the active site. The L211F/D214E double mutant displayed an increased rate of testosterone and progesterone 6β-hydroxylation at low substrate concentrations and a decreased level of heterotropic stimulation elicited by α-naphthoflavone. Kinetic analyses of the double mutant revealed the absence of homotropic cooperativity with either steroid substrate. At low substrate concentrations the steroid 6β-hydroxylase activity of the wild-type enzyme was stimulated by a second steroid, whereas L211F/D214E displayed simple substrate inhibition. To analyze L211F/D214E at a more mechanistic level, spectral binding studies were carried out. Testosterone binding by the wild-type enzyme displayed homotropic cooperativity, whereas substrate binding by L211F/D214E displayed hyperbolic behavior.

The chitinase PfCHT1 from the human malaria parasite Plasmodium falciparum lacks proenzyme and chitin-binding domains and displays unique substrate preferences

Within hours after the ingestion of a blood meal, the mosquito midgut epithelium synthesizes a chitinous sac, the peritrophic matrix. Plasmodium ookinetes traverse the peritrophic matrix while escaping the mosquito midgut. Chitinases (EC 3.2.1.14) are critical for parasite invasion of the midgut: the presence of the chitinase inhibitor, allosamidin, in an infectious blood meal prevents oocyst development. A chitinase gene, PgCHT1, recently has been identified in the avian malaria parasite P. gallinaceum. We used the sequence of PgCHT1 to identify a P. falciparum chitinase gene, PfCHT1, in the P. falciparum genome database. PfCHT1 differs from PgCHT1 in that the P. falciparum gene lacks proenzyme and chitin-binding domains. PfCHT1 was expressed as an active recombinant enzyme in Escherichia coli. PfCHT1 shares with PgCHT1 a substrate preference unique to Plasmodium chitinases: the enzymes cleave tri- and tetramers of GlcNAc from penta- and hexameric oligomers and are unable to cleave smaller native chitin oligosaccharides. The pH activity profile of PfCHT1 and its IC50 (40 nM) to allosamidin are distinct from endochitinase activities secreted by P. gallinaceum ookinetes. Homology modeling predicts that PgCHT1 has a novel pocket in the catalytic active site that PfCHT1 lacks, which may explain the differential sensitivity of PfCHT1 and PgCHT1 to allosamidin. PfCHT1 may be the ortholog of a second, as yet unidentified, chitinase gene of P. gallinaceum. These results may allow us to develop novel strategies of blocking human malaria transmission based on interfering with P. falciparum chitinase.

Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain

The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.

From cell death to embryo arrest: Mathematical models of human preimplantation embryo development

Human preimplantation embryos exhibit high levels of apoptotic cells and high rates of developmental arrest during the first week in vitro. The relation between the two is unclear and difficult to determine by conventional experimental approaches, partly because of limited numbers of embryos. We apply a mixture of experiment and mathematical modeling to show that observed levels of cell death can be reconciled with the high levels of embryo arrest seen in the human only if the developmental competence of embryos is already established at the zygote stage, and environmental factors merely modulate this. This suggests that research on improving in vitro fertilization success rates should move from its current concentration on optimizing culture media to focus more on the generation of a healthy zygote and on understanding the mechanisms that cause chromosomal and other abnormalities during early cleavage stages.

Site-specific mutations in the mature form of human IL-18 with enhanced biological activity and decreased neutralization by IL-18 binding protein

IL-18 can be considered a proinflammatory cytokine mediating disease as well as an immunostimulatory cytokine that is important for host defense against infection and cancer. The high-affinity, constitutively expressed, and circulating IL-18 binding protein (IL-18BP), which competes with cell surface receptors for IL-18 and neutralizes IL-18 activity, may act as a natural antiinflammatory as well as immunosuppressive molecule. In the present studies, the IL-18 precursor caspase-1 cleavage site was changed to a factor Xa site, and, after expression in Escherichia coli, mature IL-18 was generated by factor Xa cleavage. Mature IL-18 generated by factor Xa cleavage was fully active. Single point mutations in the mature IL-18 peptide were made, and the biological activities of the wild-type (WT) IL-18 were compared with those of the mutants. Mutants E42A and K89A exhibited 2-fold increased activity compared with WT IL-18. A double mutant, E42A plus K89A, exhibited 4-fold greater activity. Unexpectedly, IL-18BP failed to neutralize the double mutant E42A plus K89A compared with WT IL-18. The K89A mutant was intermediate in being neutralized by IL-18BP, whereas neutralization of the E42A mutant was comparable to that in the WT IL-18. The identification of E42 and K89 in the mature IL-18 peptide is consistent with previous modeling studies of IL-18 binding to IL-18BP and explains the unusually high affinity of IL-18BP for IL-18.

X-ray structure of the human hyperplastic discs protein: An ortholog of the C-terminal domain of poly(A)-binding protein

The poly(A)-binding protein (PABP) recognizes the 3′ mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilization/degradation. PABP is a modular protein, with four N-terminal RNA-binding domains and an extensive C terminus. The C-terminal region of PABP is essential for normal growth in yeast and has been implicated in mediating PABP homo-oligomerization and protein–protein interactions. A small, proteolytically stable, highly conserved domain has been identified within this C-terminal segment. Remarkably, this domain is also present in the hyperplastic discs protein (HYD) family of ubiquitin ligases. To better understand the function of this conserved region, an x-ray structure of the PABP-like segment of the human HYD protein has been determined at 1.04-Å resolution. The conserved domain adopts a novel fold resembling a right-handed supercoil of four α-helices. Sequence profile searches and comparative protein structure modeling identified a small ORF from the Arabidopsis thaliana genome that encodes a structurally similar but distantly related PABP/HYD domain. Phylogenetic analysis of the experimentally determined (HYD) and homology modeled (PABP) protein surfaces revealed a conserved feature that may be responsible for binding to a PABP interacting protein, Paip1, and other shared interaction partners.