Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections.

Identifying the semantics of eligibility criteria of clinical trials based on relevant medical ontologies

An important objective of the INTEGRATE project1 is to build tools that support the efficient execution of post-genomic multi-centric clinical trials in breast cancer, which includes the automatic assessment of the eligibility of patients for available trials. The population suited to be enrolled in a trial is described by a set of free-text eligibility criteria that are both syntactically and semantically complex. At the same time, the assessment of the eligibility of a patient for a trial requires the (machineprocessable) understanding of the semantics of the eligibility criteria in order to further evaluate if the patient data available for example in the hospital EHR satisfies these criteria. This paper presents an analysis of the semantics of the clinical trial eligibility criteria based on relevant medical ontologies in the clinical research domain: SNOMED-CT, LOINC, MedDRA. We detect subsets of these widely-adopted ontologies that characterize the semantics of the eligibility criteria of trials in various clinical domains and compare these sets. Next, we evaluate the occurrence frequency of the concepts in the concrete case of breast cancer (which is our first application domain) in order to provide meaningful priorities for the task of binding/mapping these ontology concepts to the actual patient data. We further assess the effort required to extend our approach to new domains in terms of additional semantic mappings that need to be developed.

DIMETER: a haptic master device for tremor diagnosis in neurodegenerative diseases

In this study, a device based on patient motion capture is developed for the reliable and non-invasive diagnosis of neurodegenerative diseases. The primary objective of this study is the classification of differential diagnosis between Parkinson's disease (PD) and essential tremor (ET). The DIMETER system has been used in the diagnoses of a significant number of patients at two medical centers in Spain. Research studies on classification have primarily focused on the use of well-known and reliable diagnosis criteria developed by qualified personnel. Here, we first present a literature review of the methods used to detect and evaluate tremor; then, we describe the DIMETER device in terms of the software and hardware used and the battery of tests developed to obtain the best diagnoses. All of the tests are classified and described in terms of the characteristics of the data obtained. A list of parameters obtained from the tests is provided, and the results obtained using multilayer perceptron (MLP) neural networks are presented and analyzed.

Analysis of the suitability of existing medical ontologies for building a scalable semantic interoperability solution supporting multi-site collaboration in oncology

Semantic interoperability is essential to facilitate efficient collaboration in heterogeneous multi-site healthcare environments. The deployment of a semantic interoperability solution has the potential to enable a wide range of informatics supported applications in clinical care and research both within as ingle healthcare organization and in a network of organizations. At the same time, building and deploying a semantic interoperability solution may require significant effort to carryout data transformation and to harmonize the semantics of the information in the different systems. Our approach to semantic interoperability leverages existing healthcare standards and ontologies, focusing first on specific clinical domains and key applications, and gradually expanding the solution when needed. An important objective of this work is to create a semantic link between clinical research and care environments to enable applications such as streamlining the execution of multi-centric clinical trials, including the identification of eligible patients for the trials. This paper presents an analysis of the suitability of several widely-used medical ontologies in the clinical domain: SNOMED-CT, LOINC, MedDRA, to capture the semantics of the clinical trial eligibility criteria, of the clinical trial data (e.g., Clinical Report Forms), and of the corresponding patient record data that would enable the automatic identification of eligible patients. Next to the coverage provided by the ontologies we evaluate and compare the sizes of the sets of relevant concepts and their relative frequency to estimate the cost of data transformation, of building the necessary semantic mappings, and of extending the solution to new domains. This analysis shows that our approach is both feasible and scalable.

WCSPH viscosity diffusion processes in vortex flows

The aim of this paper is to clarify the role played by the most commonly used viscous terms in simulating viscous laminar flows using the weakly compressible approach in the context of smooth particle hydrodynamics (WCSPH). To achieve this, Takeda et al. (Prog. Theor. Phys. 1994; 92(5):939–960), Morris et al. (J. Comput. Phys. 1997; 136:214–226) and Monaghan–Cleary–Gingold's (Appl. Math. Model. 1998; 22(12):981–993; Monthly Notices of the Royal Astronomical Society 2005; 365:199–213) viscous terms will be analysed, discussing their origins, structures and conservation properties. Their performance will be monitored with canonical flows of which related viscosity phenomena are well understood, and in which boundary effects are not relevant. Following the validation process of three previously published examples, two vortex flows of engineering importance have been studied. First, an isolated Lamb–Oseen vortex evolution where viscous effects are dominant and second, a pair of co-rotating vortices in which viscous effects are combined with transport phenomena. The corresponding SPH solutions have been compared to finite-element numerical solutions. The SPH viscosity model's behaviour in modelling the viscosity related effects for these canonical flows is adequate

Theoretical Analysis of the No-Slip Boundary Condition Enforcement in SPH Methods

The aim of the present work is to provide an in-depth analysis of the most representative mirroring techniques used in SPH to enforce boundary conditions (BC) along solid profiles. We specifically refer to dummy particles, ghost particles, and Takeda et al. [Prog. Theor. Phys. 92 (1994), 939] boundary integrals. The analysis has been carried out by studying the convergence of the first- and second-order differential operators as the smoothing length (that is, the characteristic length on which relies the SPH interpolation) decreases. These differential operators are of fundamental importance for the computation of the viscous drag and the viscous/diffusive terms in the momentum and energy equations. It has been proved that close to the boundaries some of the mirroring techniques leads to intrinsic inaccuracies in the convergence of the differential operators. A consistent formulation has been derived starting from Takeda et al. boundary integrals (see the above reference). This original formulation allows implementing no-slip boundary conditions consistently in many practical applications as viscous flows and diffusion problems.

Segmentation of RV in 4D Cardiac MR Volumes using region-merging graph cuts

Non-invasive quantitative assessment of the right ventricular anatomical and functional parameters is a challenging task. We present a semi-automatic approach for right ventricle (RV) segmentation from 4D MR images in two variants, which differ in the amount of user interaction. The method consists of three main phases: First, foreground and background markers are generated from the user input. Next, an over-segmented region image is obtained applying a watershed transform. Finally, these regions are merged using 4D graph-cuts with an intensity based boundary term. For the first variant the user outlines the inside of the RV wall in a few end-diastole slices, for the second two marker pixels serve as starting point for a statistical atlas application. Results were obtained by blind evaluation on 16 testing 4D MR volumes. They prove our method to be robust against markers location and place it favourably in the ranks of existing approaches.

Semantic neology in the domain of videogames in Spanish

The aim of this paper is to discuss the meaning of five neologisms in the domain of videogames in Spanish: título, aventura, personaje, plataforma, and rol. Our study focuses on a special type of neologism since the Spanish terms we deal with here are not strictly new words; they are what have been called sense neologisms or neosemanticisms, that is, old words taking a new sense in a different domain. These words were identified as new concepts after a process of analysis based on contextual evidence. This study of neology is based on the analysis of a corpus of press articles evaluating videogames published by the Spanish newspaper El País from 1998 to 2008. The analysis of the instances of use of domain specific terms in the corpus revealed that they acquired new senses different to those they have in other domains where they are also used. The paper explains the process of discovering the specialized meaning these words have developed in the domain of videogames and how the analysis of collocational behavior helps in the process of discovering the new sense and in the design of the definition provided.

Probabilistic meta-analysis of risk from the exposure to Hg in artisanal gold mining communities in Colombia

Colombia is one of the largest per capita mercury polluters in the world as a consequence of its artisanal gold mining activities. The severity of this problem in terms of potential health effects was evaluated by means of a probabilistic risk assessment carried out in the twelve departments (or provinces) in Colombia with the largest gold production. The two exposure pathways included in the risk assessment were inhalation of elemental Hg vapors and ingestion of fish contaminated with methyl mercury. Exposure parameters for the adult population (especially rates of fish consumption) were obtained from nation-wide surveys and concentrations of Hg in air and of methyl-mercury in fish were gathered from previous scientific studies. Fish consumption varied between departments and ranged from 0 to 0.3 kg d?1. Average concentrations of total mercury in fish (70 data) ranged from 0.026 to 3.3 lg g?1. A total of 550 individual measurements of Hg in workshop air (ranging from menor queDL to 1 mg m?3) and 261 measurements of Hg in outdoor air (ranging from menor queDL to 0.652 mg m?3) were used to generate the probability distributions used as concentration terms in the calculation of risk. All but two of the distributions of Hazard Quotients (HQ) associated with ingestion of Hg-contaminated fish for the twelve regions evaluated presented median values higher than the threshold value of 1 and the 95th percentiles ranged from 4 to 90. In the case of exposure to Hg vapors, minimum values of HQ for the general population exceeded 1 in all the towns included in this study, and the HQs for miner-smelters burning the amalgam is two orders of magnitude higher, reaching values of 200 for the 95th percentile. Even acknowledging the conservative assumptions included in the risk assessment and the uncertainties associated with it, its results clearly reveal the exorbitant levels of risk endured not only by miner-smelters but also by the general population of artisanal gold mining communities in Colombia.

Semantic Neology in the Domain of Videogames in Spanish.

The aim of this paper is to discuss the meaning of five neologisms in the domain of videogames in Spanish: título, aventura, personaje, plataforma, and rol. Our study focuses on a special type of neologism since the Spanish terms we deal with here are not strictly new words; they are what have been called sense neologisms or neosemanticisms, that is, old words taking a new sense in a different domain. These words were identified as new concepts after a process of analysis based on contextual evidence. This study of neology is based on the analysis of a corpus of press articles evaluating videogames published by the Spanish newspaper El País from 1998 to 2008. The analysis of the instances of use of domain specific terms in the corpus revealed that they acquired new senses different to those they have in other domains where they are also used. The paper explains the process of discovering the specialized meaning these words have developed in the domain of videogames and how the analysis of collocational behavior helps in the process of discovering the new sense and in the design of the definition provided. RESUMEN: En este trabajo se presentan cinco neologismos del ámbito del videojuego en español: “título”, “aventura”, “personaje”, “plataforma” y “rol”. Se trata de un tipo especial de neologismo, conocido también como “neologismo semántico” o “neosemanticismo”, ya que son palabras ya existentes en la lengua que adquieren un nuevo significado. Los nuevos significados que adquieren estos términos en el ámbito del videojuego se establecieron tras el análisis del contexto de uso en un corpus periodístico de críticas de videojuegos. Este corpus recoge las críticas de videojuegos publicadas por el periódico El País entre 1998 y 2008. El análisis de los casos de uso de los términos en el corpus de videojuegos reveló que adquirían un nuevo significado diferente al de su uso en otros ámbitos o en el lenguaje general. El artículo describe cada uno de los neologismos y el proceso de análisis contextual que conduce a descubrir el nuevo significado y elaborar su definición.

The Spreading of Christianity and the introduction of Modern Architecture in Shannxi, China (1840-1949): Christian churches and traditional Chinese architecture

La arquitectura china ha experimentado grandes cambios a lo largo de un extenso proceso histórico. El hito de mayor importancia es el que da paso al denominado Tiempo Moderno, periodo en el cual irrumpe por vez primera en China la arquitectura occidental, que comienza a tener una influencia muy activa y significativa sobre los rasgos y la identidad de la arquitectura tradicional china, hasta ese momento el único estilo o forma de hacer –muy diferente, en cuanto a su concepción y fisonomía, de los planteamientos occidentales- que había sobrevivido sin desvíos significativos, configurando un panorama milenario bastante homogéneo en los aspectos técnicos y artísticos en el desarrollo de esa arquitectura. Por un cúmulo de complejas razones, la mayor parte de la arquitectura china del periodo feudal -es decir el que forman todos los años anteriores a 1849- ha desaparecido. Sin embargo, desde la fecha indicada hasta la Revolución de 1949 (el denominado periodo semicolonial o semifeudal), sí se conservan muchas edificaciones, que fueron mejor construidas y mantenidas luego, destacando por su importancia en ese sentido las iglesias cristianas. Dichos templos representan cronológicamente, no sólo la primera irrupción de la arquitectura clásica occidental en China, sino el inicio de un proceso de modernización de la profundamente enraizada y, en buena medida, estancada arquitectura vernácula, combinando técnicas y estilos de ambos planteamientos, para dar como resultado originales edificaciones de un singular eclecticismo que caracterizarían buena parte de la arquitectura de dicha etapa semicolonial. En términos generales, últimamente se ha ido prestando cada vez más atención a esta arquitectura de los tiempos modernos, aunque las iglesias cristianas de la provincia de Shaanxi no han sido objeto de estudio específico, a pesar de que su tipología es muy representativa de las construcciones de esta clase en otras regiones del interior de China. La investigación que desarrolla la presente tesis doctoral sale al paso de esa deficiencia, abriendo puertas a la continuación del trabajo referido, extendido a otras zonas o arquitecturas, y, por extensión, a la profundización analítica de la hibridación arquitectónica y cultural entre China y Occidente. Sobre las bases de investigación documental, estudios de campo y dibujo, la tesis plantea un estudio aclaratorio de los rasgos y raíces de la arquitectura tradicional china, al que sigue otro histórico y tipológico de los templos cristianos en la provincia de Shaanxi, deteniéndose en sus características fundamentales, situación (uso) actual y estado de conservación. Se ha considerado imprescindible añadir al trabajo, como apéndice, un elaborado glosario conceptual ilustrado de términos básicos arquitectónicos y constructivos, en chino, inglés y español. ABSTRACT The Chinese architecture has gone through great changes during the long process of history. The tremendous changing period was the named Modern Times of China when, for the very first time, the western architecture was introduced into China and became to influence majorly on the traditional Chinese architecture. Before that, the traditional Chinese architecture which has its own, yet totally different system from the occidental architecture system was the only architectural style could be found in China. Although, due to many historical, conceptual and architectural characteristic reasons, large amount of the ancient Chinese architecture built in the feudal China was not preserved, there are a lot of buildings of semi-feudal China that was well constructed and conserved. The most important architectural type of the semi-feudal China is the Christian Churches. It was not only the first western architectural form that was brought into and well developed in China, but also was the beginner of the modernization process of Chinese architecture. Because of the deep root of the 2000-year traditional Chinese architecture, all the Christian Churches built in China during the semi-colonial society has a combined style of both the traditional Chinese architecture and the classic western churches. They are a priceless asset of the Chinese architectural history. Recently, more and more attention had been paid on the Chinese Modern Times architecture, however, the Christian Churches in Shaanxi Province, the province which has a unique history with the Christian, but less economically developed have never been researched yet. The Christian Churches of Shaanxi Province reflect the general feature of developing history of the Christian Churches of common inner-land regions in China. The research opens the door to further study on other Christian Churches and related buildings, and also for the further study on the Chinese-western architectural and culture communication. On the base of document research, field survey and mapping, in this thesis, an in-depth study had been done on the general history of the features and roots of the traditional Chinese architecture, the developing history of the Christian Churches of Shaanxi Province and the architectural types, examples, characteristics, present situation and conservation status. By comparing the Christian Churches of the cities in Shaanxi province to the Christian Churches in other more developed cities, and by comparing the Christian Churches in China to the classic western churches, the architectural combination feature of the Christian Churches in China are highlighted. The thesis is a fundamental research on which many further studies about the architectural developing history, characteristics and conservation of the Christian Churches in China could be done. It is considered essential to add to the work, as an appendix, an elaborate conceptual illustrated glossary of architectural and construction terms in Chinese, English and Spanish.

Numerical study of ultrasound induced non-linear shape and size bubble oscillations in viscoelastic media

The theoretical study of forced bubble oscillations is motivated by the importance of cavitation bubbles and oscillating encapsulated microbubbles (i.e. contrast agents) in medical sciences. In more details,theoretical studies on bubble dynamics addressing the sound-bubble interaction phenomenon provide the basis for understanding the dynamics of contrast agent microbubbles used in medical diagnosis and of non-linearly oscillating cavitation bubbles in the case of high-intensity ultrasound therapy. Moreover, the inclusion of viscoelasticity is of vital importance for an accurate theoretical analysis since most biological tissues and fluids exhibit non-Newtonian behavior.

Electron transport and azimuthal oscillations in hall thrusters

The Hall Effect Thruster (HET) is a type of satellite electric propulsion device initially developed in the 1960’s independently by USA and the former USSR. The development continued in the shadow during the 1970’s in the Soviet Union to reach a mature status from the technological point of view in the 1980’s. In the 1990’s the advanced state of this Russian technology became known in western countries, which rapidly restarted the analysis and development of modern Hall thrusters. Currently, there are several companies in USA, Russia and Europe manufacturing Hall thrusters for operational use. The main applications of these thrusters are low-thrust propulsion of interplanetary probes, orbital raising of satellites and stationkeeping of geostationary satellites. However, despite the well proven in-flight experience, the physics of the Hall Thruster are not completely understood yet. Over the last two decades large efforts have been dedicated to the understanding of the physics of Hall Effect thrusters. However, the so-called anomalous diffusion, short name for an excessive electron conductivity along the thruster, is not yet fully understood as it cannot be explained with classical collisional theories. One commonly accepted explanation is the existence of azimuthal oscillations with correlated plasma density and electric field fluctuations. In fact, there is experimental evidence of the presence of an azimuthal oscillation in the low frequency range (a few kHz). This oscillation, usually called spoke, was first detected empirically by Janes and Lowder in the 1960s. More recently several experiments have shown the existence of this type of oscillation in various modern Hall thrusters. Given the frequency range, it is likely that the ionization is the cause of the spoke oscillation, like for the breathing mode oscillation. In the high frequency range (a few MHz), electron-drift azimuthal oscillations have been detected in recent experiments, in line with the oscillations measured by Esipchuk and Tilinin in the 1970’s. Even though these low and high frequency azimuthal oscillations have been known for quite some time already, the physics behind them are not yet clear and their possible relation with the anomalous diffusion process remains an unknown. This work aims at analysing from a theoretical point of view and via computer simulations the possible relation between the azimuthal oscillations and the anomalous electron transport in HET. In order to achieve this main objective, two approaches are considered: local linear stability analyses and global linear stability analyses. The use of local linear stability analyses shall allow identifying the dominant terms in the promotion of the oscillations. However, these analyses do not take into account properly the axial variation of the plasma properties along the thruster. On the other hand, global linear stability analyses do account for these axial variations and shall allow determining how the azimuthal oscillations are promoted and their possible relation with the electron transport.

Diseño e implementación de un módulo para la estructuración de notas clínicas

El presente Trabajo Fin de Grado (TFG) surge de la necesidad de disponer de tecnologías que faciliten el Procesamiento de Lenguaje Natural (NLP) en español dentro del sector de la medicina. Centrado concretamente en la extracción de conocimiento de las historias clínicas electrónicas (HCE), que recogen toda la información relacionada con la salud del paciente y en particular, de los documentos recogidos en dichas historias, pretende la obtención de todos los términos relacionados con la medicina. El Procesamiento de Lenguaje Natural permite la obtención de datos estructurados a partir de información no estructurada. Estas técnicas permiten un análisis de texto que genera etiquetas aportando significado semántico a las palabras para la manipulación de información. A partir de la investigación realizada del estado del arte en NLP y de las tecnologías existentes para otras lenguas, se propone como solución un módulo de anotación de términos médicos extraídos de documentos clínicos. Como términos médicos se han considerado síntomas, enfermedades, partes del cuerpo o tratamientos obtenidos de UMLS, una ontología categorizada que agrega distintas fuentes de datos médicos. Se ha realizado el diseño y la implementación del módulo así como el análisis de los resultados obtenidos realizando una evaluación con treinta y dos documentos que contenían 1372 menciones de terminología médica y que han dado un resultado medio de Precisión: 70,4%, Recall: 36,2%, Accuracy: 31,4% y F-Measure: 47,2%.---ABSTRACT---This Final Thesis arises from the need for technologies that facilitate the Natural Language Processing (NLP) in Spanish in the medical sector. Specifically it is focused on extracting knowledge from Electronic Health Records (EHR), which contain all the information related to the patient's health and, in particular, it expects to obtain all the terms related to medicine from the documents contained in these records. Natural Language Processing allows us to obtain structured information from unstructured data. These techniques enable analysis of text generating labels providing semantic meaning to words for handling information. From the investigation of the state of the art in NLP and existing technologies in other languages, an annotation module of medical terms extracted from clinical documents is proposed as a solution. Symptoms, diseases, body parts or treatments are considered part of the medical terms contained in UMLS ontology which is categorized joining different sources of medical data. This project has completed the design and implementation of a module and the analysis of the results have been obtained. Thirty two documents which contain 1372 mentions of medical terminology have been evaluated and the average results obtained are: Precision: 70.4% Recall: 36.2% Accuracy: 31.4% and F-Measure: 47.2%.