Assessing the patterns of colorectal cancer treatment, adherence to treatment guidelines and survival in Texas

Colorectal cancer (CRC) is the third leading cancer in both incidence and mortality in Texas. This study investigated the adherence of CRC treatment to standard treatment guidelines and the association between standard treatment and CRC survival in Texas. The author used Texas Cancer Registry (TCR) and Medicare linked data to study the CRC treatment patterns and factors associated with standard treatment in patients who were more than 65 years old and were diagnosed in 2001 through 2007. We also determined whether adherence to standard treatment affect patients' survival. Multiple logistic regression and Cox regression analysis were used to analyze our data. Both regression models are adjusted for demographic characteristics and tumor characteristics. We found that for the 3977 regional colon cancer patients 80 years old or younger, 60.2% of them received chemotherapy, in adherence to the recommended treatment guidelines. People with younger age, female gender, higher education and lower comorbidity score are more likely adherent to this surgery guideline. Patients' adherence to chemotherapy in this cohort have better survival compared to those who are not (HR: 0.76, 95% CI: 0.68-0.84). For the 12709 colon cancer patients treated with surgery, 49.3% have more than 12 lymph nodes removed, in adherence to the treatment guidelines. People with younger age, female gender, higher education, regional stage, lager tumor size and lower comorbidity score are more likely to adherent to this surgery guideline. Patients with more than 12 lymph nodes removed in this cohort have better survival (HR: 0.86, 95% CI: 0.82-0.91). For the 1211 regional rectal cancer patients 80 years old or younger, 63.2% of them were adherent to radiation treatment. People with smaller tumor size and lower comorbidity score are more likely to adherent to this radiation guideline. There is no significant survival difference between radiation adherent patients and non-adherent patients (HR: 1.03, 95% CI: 0.82-1.29). For the 1122 regional rectal cancer patients 80 years old or younger who were treated with surgery, 76.0% of them received postoperative chemotherapy, in adherence to the treatment guidelines. People with younger age and smaller comorbidity score are related with higher adherence rate. Patients adherent with adjuvant chemotherapy in this cohort have better survival than those were not adherent (HR: 0.60, 95% CI: 0.45-0.79).^

Map4rdf - Faceted Browser for Geospatial Datasets

Recently we have seen a large increase in the amount of geospatial data that is being published using RDF and Linked Data principles. Eorts such as the W3C Geo XG, and most recently the GeoSPARQL initiative are providing the necessary vocabularies to pub- lish this kind of information on the Web of Data. In this context it is necessary to develop applications that consume and take advantage of these geospatial datasets. In this paper we present map4rdf, a faceted browsing tool for exploring and visualizing RDF datasets enhanced with geospatial information.

A Metadirectory of Web Components for Mashup Composition

Because of the growing availability of third-party APIs, services, widgets and any other reusable web component, mashup developers now face a vast amount of candidate components for their developments. Moreover, these components quite often are scattered in many different repositories and web sites, which makes difficult their selection or discovery. In this paper, we discuss the problem of component selection in Service-Oriented Architectures (SOA) and Mashup-Driven Development, and introduce the Linked Mashups Ontology (LiMOn), a model that allows describing mashups and their components for integrating and sharing mashup information such as categorization or dependencies. The model has allowed the building of an integrated, centralized metadirectory of web components for query and selection, which has served to evaluate the model. The metadirectory allows accessing various heterogeneous repositories of mashups and web components while using external information from the Linked Data cloud, helping mashup development.

Modelos de métrica para sistemas electrónicos de adquisición de datos y de procesamiento para investigación clínica con dispositivos cardiacos implantables

RESUMEN Las enfermedades cardiovasculares constituyen en la actualidad la principal causa de mortalidad en el mundo y se prevé que sigan siéndolo en un futuro, generando además elevados costes para los sistemas de salud. Los dispositivos cardiacos implantables constituyen una de las opciones para el diagnóstico y el tratamiento de las alteraciones del ritmo cardiaco. La investigación clínica con estos dispositivos alcanza gran relevancia para combatir estas enfermedades que tanto afectan a nuestra sociedad. Tanto la industria farmacéutica y de tecnología médica, como los propios investigadores, cada día se ven involucrados en un mayor número de proyectos de investigación clínica. No sólo el incremento en su volumen, sino el aumento de la complejidad, están generando mayores gastos en las actividades asociadas a la investigación médica. Esto está conduciendo a las compañías del sector sanitario a estudiar nuevas soluciones que les permitan reducir los costes de los estudios clínicos. Las Tecnologías de la Información y las Comunicaciones han facilitado la investigación clínica, especialmente en la última década. Los sistemas y aplicaciones electrónicos han proporcionado nuevas posibilidades en la adquisición, procesamiento y análisis de los datos. Por otro lado, la tecnología web propició la aparición de los primeros sistemas electrónicos de adquisición de datos, que han ido evolucionando a lo largo de los últimos años. Sin embargo, la mejora y perfeccionamiento de estos sistemas sigue siendo crucial para el progreso de la investigación clínica. En otro orden de cosas, la forma tradicional de realizar los estudios clínicos con dispositivos cardiacos implantables precisaba mejorar el tratamiento de los datos almacenados por estos dispositivos, así como para su fusión con los datos clínicos recopilados por investigadores y pacientes. La justificación de este trabajo de investigación se basa en la necesidad de mejorar la eficiencia en la investigación clínica con dispositivos cardiacos implantables, mediante la reducción de costes y tiempos de desarrollo de los proyectos, y el incremento de la calidad de los datos recopilados y el diseño de soluciones que permitan obtener un mayor rendimiento de los datos mediante la fusión de datos de distintas fuentes o estudios. Con este fin se proponen como objetivos específicos de este proyecto de investigación dos nuevos modelos: - Un modelo de recuperación y procesamiento de datos para los estudios clínicos con dispositivos cardiacos implantables, que permita estructurar y estandarizar estos procedimientos, con el fin de reducir tiempos de desarrollo Modelos de Métrica para Sistemas Electrónicos de Adquisición de Datos y de Procesamiento para Investigación Clínica con Dispositivos Cardiacos Implantables de estas tareas, mejorar la calidad del resultado obtenido, disminuyendo en consecuencia los costes. - Un modelo de métrica integrado en un Sistema Electrónico de Adquisición de Datos (EDC) que permita analizar los resultados del proyecto de investigación y, particularmente del rendimiento obtenido del EDC, con el fin de perfeccionar estos sistemas y reducir tiempos y costes de desarrollo del proyecto y mejorar la calidad de los datos clínicos recopilados. Como resultado de esta investigación, el modelo de procesamiento propuesto ha permitido reducir el tiempo medio de procesamiento de los datos en más de un 90%, los costes derivados del mismo en más de un 85% y todo ello, gracias a la automatización de la extracción y almacenamiento de los datos, consiguiendo una mejora de la calidad de los mismos. Por otro lado, el modelo de métrica posibilita el análisis descriptivo detallado de distintos indicadores que caracterizan el rendimiento del proyecto de investigación clínica, haciendo factible además la comparación entre distintos estudios. La conclusión de esta tesis doctoral es que los resultados obtenidos han demostrado que la utilización en estudios clínicos reales de los dos modelos desarrollados ha conducido a una mejora en la eficiencia de los proyectos, reduciendo los costes globales de los mismos, disminuyendo los tiempos de ejecución, e incrementando la calidad de los datos recopilados. Las principales aportaciones de este trabajo de investigación al conocimiento científico son la implementación de un sistema de procesamiento inteligente de los datos almacenados por los dispositivos cardiacos implantables, la integración en el mismo de una base de datos global y optimizada para todos los modelos de dispositivos, la generación automatizada de un repositorio unificado de datos clínicos y datos de dispositivos cardiacos implantables, y el diseño de una métrica aplicada e integrable en los sistemas electrónicos de adquisición de datos para el análisis de resultados de rendimiento de los proyectos de investigación clínica. ABSTRACT Cardiovascular diseases are the main cause of death worldwide and it is expected to continue in the future, generating high costs for health care systems. Implantable cardiac devices have become one of the options for diagnosis and treatment of cardiac rhythm disorders. Clinical research with these devices has acquired great importance to fight against these diseases that affect so many people in our society. Both pharmaceutical and medical technology companies, and also investigators, are involved in an increasingly number of clinical research projects. The growth in volume and the increase in medical research complexity are contributing to raise the expenditure level associated with clinical investigation. This situation is driving health care sector companies to explore new solutions to reduce clinical trial costs. Information and Communication Technologies have facilitated clinical research, mainly in the last decade. Electronic systems and software applications have provided new possibilities in the acquisition, processing and analysis of clinical studies data. On the other hand, web technology contributed to the appearance of the first electronic data capture systems that have evolved during the last years. Nevertheless, improvement of these systems is still a key aspect for the progress of clinical research. On a different matter, the traditional way to develop clinical studies with implantable cardiac devices needed an improvement in the processing of the data stored by these devices, and also in the merging of these data with the data collected by investigators and patients. The rationale of this research is based on the need to improve the efficiency in clinical investigation with implantable cardiac devices, by means of reduction in costs and time of projects development, as well as improvement in the quality of information obtained from the studies and to obtain better performance of data through the merging of data from different sources or trials. The objective of this research project is to develop the next two models: • A model for the retrieval and processing of data for clinical studies with implantable cardiac devices, enabling structure and standardization of these procedures, in order to reduce the time of development of these tasks, to improve the quality of the results, diminish therefore costs. • A model of metric integrated in an Electronic Data Capture system (EDC) that allow to analyze the results of the research project, and particularly the EDC performance, in order to improve those systems and to reduce time and costs of the project, and to get a better quality of the collected clinical data. As a result of this work, the proposed processing model has led to a reduction of the average time for data processing by more than 90 per cent, of related costs by more than 85 per cent, and all of this, through automatic data retrieval and storage, achieving an improvement of quality of data. On the other hand, the model of metrics makes possible a detailed descriptive analysis of a set of indicators that characterize the performance of each research project, allowing inter‐studies comparison. This doctoral thesis results have demonstrated that the application of the two developed models in real clinical trials has led to an improvement in projects efficiency, reducing global costs, diminishing time in execution, and increasing quality of data collected. The main contributions to scientific knowledge of this research work are the implementation of an intelligent processing system for data stored by implantable cardiac devices, the integration in this system of a global and optimized database for all models of devices, the automatic creation of an unified repository of clinical data and data stored by medical devices, and the design of a metric to be applied and integrated in electronic data capture systems to analyze the performance results of clinical research projects.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

Transparência governamental e accountability: uma análise comparativa da evolução dos portais de informações públicas no município de São Paulo

Impulsionados por mudanças na legislação e pelo contexto de favorecimento de medidas de publicidade, vários órgãos governamentais vêm ampliando o leque de informações divulgadas nos seus portais de transparência. Entretanto, esse movimento não é uniforme certos órgãos têm tendência maior de serem mais transparentes que outros. Este trabalho sugere a montagem de um modelo de avaliação desses portais em relação à variedade, qualidade e acessibilidade das informações públicas cuja divulgação é exigida por lei e aplica-­o nos sites da Prefeitura de São Paulo, da Câmara Municipal e do Tribunal de Contas do Município. Foi verificada uma diferença significa na avaliação dos portais entre 2008 e 2013, também desigual de acordo com o órgão. Entrevistas com funcionários dos três órgãos indicam que fatores institucionais específicos como a accountability vertical, a receptividade em relação ao escrutínio público e a fiscalização por órgãos de controle são essenciais para entender a diferença nos estímulos para se ampliar a transparência governamental.

Aplicación de tecnologías de procesamiento de lenguaje natural y tecnología semántica en Brand Rain y Anpro21

Este artículo presenta la aplicación y resultados obtenidos de la investigación en técnicas de procesamiento de lenguaje natural y tecnología semántica en Brand Rain y Anpro21. Se exponen todos los proyectos relacionados con las temáticas antes mencionadas y se presenta la aplicación y ventajas de la transferencia de la investigación y nuevas tecnologías desarrolladas a la herramienta de monitorización y cálculo de reputación Brand Rain.

Integrazione di contenuti multimediali in basi di conoscenza strutturate: il caso DBpedia

Viene presentato l’approccio Linked Data, che si serve di descrizioni scritte in linguaggio RDF per rendere espliciti ai calcolatori i legami semantici esistenti tra le risorse che popolano il Web. Si descrive quindi il progetto DBpedia, che si propone di riorganizzare le informazioni disponibili su Wikipedia in formato Linked Data, così da renderle più facilmente consultabili dall’utente e da rendere possibile l’esecuzione di query complesse. Si discute quindi della sfida riguardante l’integrazione di contenuti multimediali (immagini, file audio, video…) su DBpedia e si analizzano tre progetti rivolti in tal senso: Multipedia, DBpedia Commons e IMGpedia. Vengono infine sottolineate l’importanza e le potenzialità legate alla creazione di un Web Semantico.

Studies in coordinate indexing.

v.4.The mechanization of data retrieval.--v.5.Emerging solutions for mechanizing the storage and retrieval of information.--v.6.The coming age of information technology.

Pulse Pressure magnifies the effect of COMT Val158Met on 15 Year Episodic Memory Trajectories

We investigated whether a physiological marker of cardiovascular health, pulse pressure (PP), and age magnified the effect of the functional COMT Val158Met (rs4680) polymorphism on 15-years cognitive trajectories [episodic memory (EM), visuospatial ability, and semantic memory] using data from 1585 non-demented adults from the Betula study. A multiple-group latent growth curve model was specified to gauge individual differences in change, and average trends therein. The allelic variants showed negligible differences across the cognitive markers in average trends. The older portion of the sample selectively age-magnified the effects of Val158Met on EM changes, resulting in greater decline in Val compared to homozygote Met carriers. This effect was attenuated by statistical control for PP. Further, PP moderated the effects of COMT on 15-years EM trajectories, resulting in greater decline in Val carriers, even after accounting for the confounding effects of sex, education, cardiovascular diseases (diabetes, stroke, and hypertension), and chronological age, controlled for practice gains. The effect was still present after excluding individuals with a history of cardiovascular diseases. The effects of cognitive change were not moderated by any other covariates. This report underscores the importance of addressing synergistic effects in normal cognitive aging, as the addition thereof may place healthy individuals at greater risk for memory decline.

A multiresolution terrain model for efficient visualization query processing

Multiresolution Triangular Mesh (MTM) models are widely used to improve the performance of large terrain visualization by replacing the original model with a simplified one. MTM models, which consist of both original and simplified data, are commonly stored in spatial database systems due to their size. The relatively slow access speed of disks makes data retrieval the bottleneck of such terrain visualization systems. Existing spatial access methods proposed to address this problem rely on main-memory MTM models, which leads to significant overhead during query processing. In this paper, we approach the problem from a new perspective and propose a novel MTM called direct mesh that is designed specifically for secondary storage. It supports available indexing methods natively and requires no modification to MTM structure. Experiment results, which are based on two real-world data sets, show an average performance improvement of 5-10 times over the existing methods.

Direct mesh: A multiresolution approach to terrain visualization

Terrain can be approximated by a triangular mesh consisting millions of 3D points. Multiresolution triangular mesh (MTM) structures are designed to support applications that use terrain data at variable levels of detail (LOD). Typically, an MTM adopts a tree structure where a parent node represents a lower-resolution approximation of its descendants. Given a region of interest (ROI) and a LOD, the process of retrieving the required terrain data from the database is to traverse the MTM tree from the root to reach all the nodes satisfying the ROI and LOD conditions. This process, while being commonly used for multiresolution terrain visualization, is inefficient as either a large number of sequential I/O operations or fetching a large amount of extraneous data is incurred. Various spatial indexes have been proposed in the past to address this problem, however level-by-level tree traversal remains a common practice in order to obtain topological information among the retrieved terrain data. A new MTM data structure called direct mesh is proposed. We demonstrate that with direct mesh the amount of data retrieval can be substantially reduced. Comparing with existing MTM indexing methods, a significant performance improvement has been observed for real-life terrain data.