Educational activities for a gamified system

The objective of this dissertation is to analyze, design, and implement an activity module for a larger educational platform with the use of gamification techniques with the purpose to improve learning, pass rates, and feedback. The project investigates how to better incentivize student learning. A software requirement specification was delineated to establish the system guidelines and behavior. Following, a definition of the activities in the module was created. This definition encompassed a detailed description of each activity, together with elements that compose it, available customizations and the involved formulas. The activity high-level design process includes the design of the defined activities by use of the software methodology UWE (UML-based Web Engineering) for their future implementation, modeling requirements, content, navigation and presentation. The low-level design is composed of the database schema and types and the relating EER (Enhanced Entity-Relationship) diagram. After this, the implementation of the designed module began, together with testing in the later stages. We expect that by using the implemented activity module, students will become more interested in learning, as well as more engaged in the process, resulting in a continuous progress during the course.---RESUMEN---El objetivo de este trabajo es analizar, diseñar e implementar un módulo de actividades didácticas que formará parte de una plataforma educativa, haciendo uso de técnicas de gamificación con la finalidad de mejorar el aprendizaje, ratio de aprobados y retroalimentación para los alumnos. El proyecto investiga como incentivar mejor el aprendizaje estudiantil. Se trazó una especificación de requisitos de software para establecer las pautas del sistema y su comportamiento. A continuación, se definieron las actividades del módulo. Esta definición abarca una descripción detallada de cada actividad, junto a los elementos que la componen, las configuraciones disponibles y las formulas involucradas. El proceso de diseño de alto nivel incluye el diseño de las actividades definidas usando la metodología de software UWE (UML-based Web Engineering) para su futura implementación, requisitos de modelaje, contenido, navegación y presentación. El diseño de bajo nivel está compuesto por el esquema y tipos de la base de datos y el diagrama de entidad-relación correspondiente. Tras esto se realizó la implementación y pruebas de parte del sistema. Se espera que usando el módulo de actividades implementado, los estudiantes muestren un mayor interés por aprender, así como estar más involucrados en el proceso, resultando en un progreso más continuo durante el curso.

Desarrollo de un proceso de normalización semántica de bases de datos en ensayos clínicos

El trabajo se enmarca dentro de los proyecto INTEGRATE y EURECA, cuyo objetivo es el desarrollo de una capa de interoperabilidad semántica que permita la integración de datos e investigación clínica, proporcionando una plataforma común que pueda ser integrada en diferentes instituciones clínicas y que facilite el intercambio de información entre las mismas. De esta manera se promueve la mejora de la práctica clínica a través de la cooperación entre instituciones de investigación con objetivos comunes. En los proyectos se hace uso de estándares y vocabularios clínicos ya existentes, como pueden ser HL7 o SNOMED, adaptándolos a las necesidades particulares de los datos con los que se trabaja en INTEGRATE y EURECA. Los datos clínicos se representan de manera que cada concepto utilizado sea único, evitando ambigüedades y apoyando la idea de plataforma común. El alumno ha formado parte de un equipo de trabajo perteneciente al Grupo de Informática de la UPM, que a su vez trabaja como uno de los socios de los proyectos europeos nombrados anteriormente. La herramienta desarrollada, tiene como objetivo realizar tareas de homogenización de la información almacenada en las bases de datos de los proyectos haciendo uso de los mecanismos de normalización proporcionados por el vocabulario médico SNOMED-CT. Las bases de datos normalizadas serán las utilizadas para llevar a cabo consultas por medio de servicios proporcionados en la capa de interoperabilidad, ya que contendrán información más precisa y completa que las bases de datos sin normalizar. El trabajo ha sido realizado entre el día 12 de Septiembre del año 2014, donde comienza la etapa de formación y recopilación de información, y el día 5 de Enero del año 2015, en el cuál se termina la redacción de la memoria. El ciclo de vida utilizado ha sido el de desarrollo en cascada, en el que las tareas no comienzan hasta que la etapa inmediatamente anterior haya sido finalizada y validada. Sin embargo, no todas las tareas han seguido este modelo, ya que la realización de la memoria del trabajo se ha llevado a cabo de manera paralela con el resto de tareas. El número total de horas dedicadas al Trabajo de Fin de Grado es 324. Las tareas realizadas y el tiempo de dedicación de cada una de ellas se detallan a continuación:  Formación. Etapa de recopilación de información necesaria para implementar la herramienta y estudio de la misma [30 horas.  Especificación de requisitos. Se documentan los diferentes requisitos que ha de cumplir la herramienta [20 horas].  Diseño. En esta etapa se toman las decisiones de diseño de la herramienta [35 horas].  Implementación. Desarrollo del código de la herramienta [80 horas].  Pruebas. Etapa de validación de la herramienta, tanto de manera independiente como integrada en los proyectos INTEGRATE y EURECA [70 horas].  Depuración. Corrección de errores e introducción de mejoras de la herramienta [45 horas].  Realización de la memoria. Redacción de la memoria final del trabajo [44 horas].---ABSTRACT---This project belongs to the semantic interoperability layer developed in the European projects INTEGRATE and EURECA, which aims to provide a platform to promote interchange of medical information from clinical trials to clinical institutions. Thus, research institutions may cooperate to enhance clinical practice. Different health standards and clinical terminologies has been used in both INTEGRATE and EURECA projects, e.g. HL7 or SNOMED-CT. These tools have been adapted to the projects data requirements. Clinical data are represented by unique concepts, avoiding ambiguity problems. The student has been working in the Biomedical Informatics Group from UPM, partner of the INTEGRATE and EURECA projects. The tool developed aims to perform homogenization tasks over information stored in databases of the project, through normalized representation provided by the SNOMED-CT terminology. The data query is executed against the normalized version of the databases, since the information retrieved will be more informative than non-normalized databases. The project has been performed from September 12th of 2014, when initiation stage began, to January 5th of 2015, when the final report was finished. The waterfall model for software development was followed during the working process. Therefore, a phase may not start before the previous one finishes and has been validated, except from the final report redaction, which has been carried out in parallel with the others phases. The tasks that have been developed and time for each one are detailed as follows:  Training. Gathering the necessary information to develop the tool [30 hours].  Software requirement specification. Requirements the tool must accomplish [20 hours].  Design. Decisions on the design of the tool [35 hours].  Implementation. Tool development [80 hours].  Testing. Tool evaluation within the framework of the INTEGRATE and EURECA projects [70 hours].  Debugging. Improve efficiency and correct errors [45 hours].  Documenting. Final report elaboration [44 hours].

Diseño de una metodología CASE de desarrollo de software

En la actualidad existe una gran expectación ante la introducción de nuevas herramientas y métodos para el desarrollo de productos software, que permitirán en un futuro próximo un planteamiento de ingeniería del proceso de producción software. Las nuevas metodologías que empiezan a esbozarse suponen un enfoque integral del problema abarcando todas las fases del esquema productivo. Sin embargo el grado de automatización conseguido en el proceso de construcción de sistemas es muy bajo y éste está centrado en las últimas fases del ciclo de vida del software, consiguiéndose así una reducción poco significativa de sus costes y, lo que es aún más importante, sin garantizar la calidad de los productos software obtenidos. Esta tesis define una metodología de desarrollo software estructurada que se puede automatizar, es decir una metodología CASE. La metodología que se presenta se ajusta al modelo de ciclo de desarrollo CASE, que consta de las fases de análisis, diseño y pruebas; siendo su ámbito de aplicación los sistemas de información. Se establecen inicialmente los principios básicos sobre los que la metodología CASE se asienta. Posteriormente, y puesto que la metodología se inicia con la fijación de los objetivos de la empresa que demanda un sistema informático, se emplean técnicas que sirvan de recogida y validación de la información, que proporcionan a la vez un lenguaje de comunicación fácil entre usuarios finales e informáticos. Además, estas mismas técnicas detallarán de una manera completa, consistente y sin ambigüedad todos los requisitos del sistema. Asimismo, se presentan un conjunto de técnicas y algoritmos para conseguir que desde la especificación de requisitos del sistema se logre una automatización tanto del diseño lógico del Modelo de Procesos como del Modelo de Datos, validados ambos conforme a la especificación de requisitos previa. Por último se definen unos procedimientos formales que indican el conjunto de actividades a realizar en el proceso de construcción y cómo llevarlas a cabo, consiguiendo de esta manera una integridad en las distintas etapas del proceso de desarrollo.---ABSTRACT---Nowdays there is a great expectation with regard to the introduction of new tools and methods for the software products development that, in the very near future will allow, an engineering approach in the software development process. New methodologies, just emerging, imply an integral approach to the problem, including all the productive scheme stages. However, the automatization degree obtained in the systems construction process is very low and focused on the last phases of the software lifecycle, which means that the costs reduction obtained is irrelevant and, which is more important, the quality of the software products is not guaranteed. This thesis defines an structured software development methodology that can be automated, that is a CASE methodology. Such a methodology is adapted to the CASE development cycle-model, which consists in analysis, design and testing phases, being the information systems its field of application. Firstly, we present the basic principies on which CASE methodology is based. Secondly, since the methodology starts from fixing the objectives of the company demanding the automatization system, we use some techniques that are useful for gathering and validating the information, being at the same time an easy communication language between end-users and developers. Indeed, these same techniques will detail completely, consistently and non ambiguously all the system requirements. Likewise, a set of techniques and algorithms are shown in order to obtain, from the system requirements specification, an automatization of the Process Model logical design, and of the Data Model logical design. Those two models are validated according to the previous requirement specification. Finally, we define several formal procedures that suggest which set of activities to be accomplished in the construction process, and how to carry them out, getting in this way integrity and completness for the different stages of the development process.

Effektivisering av mjukvaruinstallationer : Genom automatiserad mjukvarudistribution

Software deployment, eller mjukvarudistribution översatt till svenska kan ses som processen där alla aktiviteter ingår för att göra en mjukvara tillgänglig för användare utan en manuell installation på användarens dator eller annan maskin. Det finns ett flertal software deployment-verktyg, som hanterar automatiska installationer, tillgängliga för företag på marknaden idag.  Avdelningen HVDC på ABB i Ludvika har behov att börja använda ett verktyg för automatiserade installationer av mjukvaror då installationer idag utförs manuellt och är tidsödande. Som Microsoftpartners vill ABB se hur Microsofts verktyg för mjukvarudistribution skulle kunna hjälpa för detta behov.  Vår studie syftade till att undersöka hur arbetet med installationer av mjukvara ser ut idag, samt hitta förbättringsmöjligheter för installationer som inte kan automatiseras i nuläget. I studien ingick även att ta fram ett generellt ramverk för hur verksamheter kan gå tillväga när de vill börja använda sig utav software deployment-verktyg. I ramverket ingår en utformad kravspecifikation som ska utvärderas mot Microsofts verktyg.  För att skapa en uppfattning om hur arbetet i verksamheten ser ut idag har vi utfört enkätundersökning och intervjuer med personal på HVDC. För att utveckla ett ramverk har vi använt oss av insamlade data från de intervjuer, enkätundersökning och gruppintervju som utförts, detta för att identifiera krav och önskemål från personalen hos ett software deployment-verktyg. Litteraturstudier utfördes för att skapa en teoretisk referensram att utgå ifrån vid utvecklande av ramverket och kravspecifikationen.  Studien har resulterat i en beskrivning av software deployment, förbättringsmöjligheter i arbetet med installationer av mjukvara samt ett generellt ramverk som beskriver hur verksamheter kan gå tillväga när de ska börja använda ett software deployment-verktyg. Ramverket innehåller också en kravspecifikation som använts för att utvärdera Microsofts verktyg för mjukvarudistribution. I vår studie har vi inte sett att någon tidigare har tagit fram ett generellt ramverk och kravspecifikation som verksamheter kan använda sig av som underlag när de ska börja använda ett software deployment-verktyg. Vårt resultat av studien kan täcka upp detta kunskapsgap.    

Retinoic acid signaling organizes endodermal organ specification along the entire antero-posterior axis

BACKGROUND: Endoderm organ primordia become specified between gastrulation and gut tube folding in Amniotes. Although the requirement for RA signaling for the development of a few individual endoderm organs has been established a systematic assessment of its activity along the entire antero-posterior axis has not been performed in this germ layer. METHODOLOGY/PRINCIPAL FINDINGS: RA is synthesized from gastrulation to somitogenesis in the mesoderm that is close to the developing gut tube. In the branchial arch region specific levels of RA signaling control organ boundaries. The most anterior endoderm forming the thyroid gland is specified in the absence of RA signaling. Increasing RA in anterior branchial arches results in thyroid primordium repression and the induction of more posterior markers such as branchial arch Hox genes. Conversely reducing RA signaling shifts Hox genes posteriorly in endoderm. These results imply that RA acts as a caudalizing factor in a graded manner in pharyngeal endoderm. Posterior foregut and midgut organ primordia also require RA, but exposing endoderm to additional RA is not sufficient to expand these primordia anteriorly. We show that in chick, in contrast to non-Amniotes, RA signaling is not only necessary during gastrulation, but also throughout gut tube folding during somitogenesis. Our results show that the induction of CdxA, a midgut marker, and pancreas induction require direct RA signaling in endoderm. Moreover, communication between CdxA(+) cells is necessary to maintain CdxA expression, therefore synchronizing the cells of the midgut primordium. We further show that the RA pathway acts synergistically with FGF4 in endoderm patterning rather than mediating FGF4 activity. CONCLUSIONS/SIGNIFICANCE: Our work establishes that retinoic acid (RA) signaling coordinates the position of different endoderm organs along the antero-posterior axis in chick embryos and could serve as a basis for the differentiation of specific endodermal organs from ES cells.

Specification and validation of process constraints for flexible workflows

Workflow systems have traditionally focused on the so-called production processes which are characterized by pre-definition, high volume, and repetitiveness. Recently, the deployment of workflow systems in non-traditional domains such as collaborative applications, e-learning and cross-organizational process integration, have put forth new requirements for flexible and dynamic specification. However, this flexibility cannot be offered at the expense of control, a critical requirement of business processes. In this paper, we will present a foundation set of constraints for flexible workflow specification. These constraints are intended to provide an appropriate balance between flexibility and control. The constraint specification framework is based on the concept of pockets of flexibility which allows ad hoc changes and/or building of workflows for highly flexible processes. Basically, our approach is to provide the ability to execute on the basis of a partially specified model, where the full specification of the model is made at runtime, and may be unique to each instance. The verification of dynamically built models is essential. Where as ensuring that the model conforms to specified constraints does not pose great difficulty, ensuring that the constraint set itself does not carry conflicts and redundancy is an interesting and challenging problem. In this paper, we will provide a discussion on both the static and dynamic verification aspects. We will also briefly present Chameleon, a prototype workflow engine that implements these concepts. (c) 2004 Elsevier Ltd. All rights reserved.

Development of the Minimum Information Specification for in situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)

We describe the creation process of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Modeled after the existing minimum information specification for microarray data, we created a new specification for gene expression localization experiments, initially to facilitate data sharing within a consortium. After successful use within the consortium, the specification was circulated to members of the wider biomedical research community for comment and refinement. After a period of acquiring many new suggested requirements, it was necessary to enter a final phase of excluding those requirements that were deemed inappropriate as a minimum requirement for all experiments. The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community. This paper is part of the special issue of OMICS on data standards.

RELAX:a language to address uncertainty in self-adaptive systems requirement

Self-adaptive systems have the capability to autonomously modify their behavior at run-time in response to changes in their environment. Self-adaptation is particularly necessary for applications that must run continuously, even under adverse conditions and changing requirements; sample domains include automotive systems, telecommunications, and environmental monitoring systems. While a few techniques have been developed to support the monitoring and analysis of requirements for adaptive systems, limited attention has been paid to the actual creation and specification of requirements of self-adaptive systems. As a result, self-adaptivity is often constructed in an ad-hoc manner. In order to support the rigorous specification of adaptive systems requirements, this paper introduces RELAX, a new requirements language for self-adaptive systems that explicitly addresses uncertainty inherent in adaptive systems. We present the formal semantics for RELAX in terms of fuzzy logic, thus enabling a rigorous treatment of requirements that include uncertainty. RELAX enables developers to identify uncertainty in the requirements, thereby facilitating the design of systems that are, by definition, more flexible and amenable to adaptation in a systematic fashion. We illustrate the use of RELAX on smart home applications, including an adaptive assisted living system.

Security specification and enforcement in mediation system

Mediation techniques provide interoperability and support integrated query processing among heterogeneous databases. While such techniques help data sharing among different sources, they increase the risk for data security, such as violating access control rules. Successful protection of information by an effective access control mechanism is a basic requirement for interoperation among heterogeneous data sources. ^ This dissertation first identified the challenges in the mediation system in order to achieve both interoperability and security in the interconnected and collaborative computing environment, which includes: (1) context-awareness, (2) semantic heterogeneity, and (3) multiple security policy specification. Currently few existing approaches address all three security challenges in mediation system. This dissertation provides a modeling and architectural solution to the problem of mediation security that addresses the aforementioned security challenges. A context-aware flexible authorization framework was developed in the dissertation to deal with security challenges faced by mediation system. The authorization framework consists of two major tasks, specifying security policies and enforcing security policies. Firstly, the security policy specification provides a generic and extensible method to model the security policies with respect to the challenges posed by the mediation system. The security policies in this study are specified by 5-tuples followed by a series of authorization constraints, which are identified based on the relationship of the different security components in the mediation system. Two essential features of mediation systems, i. e., relationship among authorization components and interoperability among heterogeneous data sources, are the focus of this investigation. Secondly, this dissertation supports effective access control on mediation systems while providing uniform access for heterogeneous data sources. The dynamic security constraints are handled in the authorization phase instead of the authentication phase, thus the maintenance cost of security specification can be reduced compared with related solutions. ^

Role for cell-to-cell communication in stem cell specification toward pancreatic progenitors: relevance to the design of novel therapies for diabetes.

Thesis (Ph.D.)--University of Washington, 2016-08

Specification of Supervisory Control Systems for Ventricular Assist Devices

One of the most important recent improvements in cardiology is the use of ventricular assist devices (VADs) to help patients with severe heart diseases, especially when they are indicated to heart transplantation. The Institute Dante Pazzanese of Cardiology has been developing an implantable centrifugal blood pump that will be able to help a sick human heart to keep blood flow and pressure at physiological levels. This device will be used as a totally or partially implantable VAD. Therefore, an improvement on device performance is important for the betterment of the level of interaction with patient`s behavior or conditions. But some failures may occur if the device`s pumping control does not follow the changes in patient`s behavior or conditions. The VAD control system must consider tolerance to faults and have a dynamic adaptation according to patient`s cardiovascular system changes, and also must attend to changes in patient conditions, behavior, or comportments. This work proposes an application of the mechatronic approach to this class of devices based on advanced techniques for control, instrumentation, and automation to define a method for developing a hierarchical supervisory control system that is able to perform VAD control dynamically, automatically, and securely. For this methodology, we used concepts based on Bayesian network for patients` diagnoses, Petri nets to generate a VAD control algorithm, and Safety Instrumented Systems to ensure VAD system security. Applying these concepts, a VAD control system is being built for method effectiveness confirmation.

Dietary lysine requirement of juvenile pacu Piaractus mesopotamicus (Holmberg, 1887)

Lysine is the reference essential amino acid in fish feeds and usually the most limiting amino acid in feedstuffs. The dietary lysine requirement of juvenile pacu Piaractus mesopotamicus (4.3 g) was determined using five isonitrogenous (32% CP) test diets containing graded levels of lysine (0.9, 1.17, 1.44, 1.69 and 1.96% of dry diet) fed three times a day to four groups of 18 fish for 74 days. Growth, body composition, nutrient retention and hematological parameters of pacu were analyzed. Analysis of variance showed that all growth performance parameters were significantly affected by dietary treatments. The lysine requirements estimated using regression analysis for maximum weight gain and feed efficiency were 1.45 and 1.51% of dry diet, respectively. Nitrogen retention efficiency increased with increasing levels of dietary lysine up to 1.43% (p<0.05). Whole-body protein increased (p<0.05) and whole-body lipid decreased (p<0.05) with increasing dietary lysine level. Thus, the lysine requirement of juvenile pacu was estimated as being 1.4-1.5% of dry diet or 4.4-4.7% of dietary protein. (c) 2009 Elsevier B.V. All rights reserved.

Estimating Amino Acid Requirement of Brazilian Freshwater Fish from Muscle Amino Acid Profile

Information on nutritional requirement of some Brazilian farmed fish species, especially essential amino acids (EAA) requirements, is scarce. The estimation of amino acids requirements based on amino acid composition of fish is a fast and reliable alternative. Matrinxa, Brycon amazonicus, and curimbata, Prochilodus lineatus, are two important Brazilian fish with potential for aquaculture. The objective of the present study was to estimate amino acid requirements of these species and analyze similarities among amino acid composition of different fish species by cluster analysis. To estimate amino acid requirement, the following formula was used: amino acid requirement = [(amount of an individual amino acid in fish muscle tissue) x (average totalEAA requirement among channel catfish, Ictalurus punctatus, Nile tilapia, Oreochromis niloticus, and common carp, Cyprinus carpio)]/(average fish muscle totalEAA). Most values found lie within the range of requirements determined for other omnivorous fish species, in exception of leucine requirement estimated for both species, and arginine requirement estimated for matrinxa alone. Rather than writing off the need for regular dose-response assays under the ideal protein concept to determine EAA requirements of curimbata and matrinxa, results set solid base for the study of tropical species dietary amino acids requirements.

Requirement for PLC gamma 2 in IL-3 and GM-CSF-Stimulated MEK/ERK Phosphorylation in Murine and Human Hematopoietic Stem/Progenitor Cells

Even though the involvement of intracellular Ca(2+) (Ca(i)(2+)) in hematopoiesis has been previously demonstrated, the relationship between Ca(i)(2+) signaling and cytokine-induced intracellular pathways remains poorly understood. Herein, the molecular mechanisms integrating Ca(2+) signaling with the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway in primary murine and human hematopoietic stem/progenitor cells stimulated by IL-3 and GM-CSF were studied. Our results demonstrated that IL-3 and GM-CSF stimulation induced increased inositol 1,4,5-trisphosphate (IP(3)) levels and Ca(i)(2+) release in murine and human hematopoietic stem/ progenitor cells. In addition, Ca(i)(2+) signaling inhibitors, such as inositol 1,4,5-trisphosphate receptor antagonist (2-APB), PKC inhibitor (GF109203), and CaMKII inhibitor (KN-62), blocked phosphorylation of MEK activated by IL-3 and GM-CSF, suggesting the participation of Ca(2+)-dependent kinases in MEK activation. In addition, we identify phospholipase C gamma 2 (PLC gamma 2) as a PLC gamma responsible for the induction of Ca(2+) release by IL-3 and GM-CSF in hematopoietic stem/progenitor cells. Furthermore, the PLCg inhibitor U73122 significantly reduced the numbers of granulocyte-macrophage colony-forming units after cytokine stimulation. Similar results were obtained in both murine and human hematopoietic stem/progenitor cells. Taken together, these data indicate a role for PLC gamma 2 and Ca(2+) signaling through the modulation of MEK in both murine and human hematopoietic stem/ progenitor cells. J. Cell. Physiol. 226: 1780-1792, 2011. (C) 2010 Wiley-Liss, Inc.