EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/

Design of fault tolerant control system for individual blade control helicopters

This dissertation presents the development of a fault tolerant control scheme for helicopters fitted with individually controlled blades. This novel approach attempts to improve fault tolerant capabilities of helicopter control system by increasing control redundancy using additional actuators for individual blade input and software re-mixing to obtain nominal or close to nominal conditions under failure. An advanced interactive simulation environment has been developed including modeling of sensor failure, swashplate actuator failure, individual blade actuator failure, and blade delamination to support the design, testing, and evaluation of the control laws. This simulation environment is based on the blade element theory for the calculation of forces and moments generated by the main rotor. This discretized model allows for individual blade analysis, which in turn allows measuring the consequences of a stuck blade, or loss of the surface area of the blade itself, with respect to the dynamics of the whole helicopter. The control laws are based on non-linear dynamic inversion and artificial neural network augmentation, which is a mix of linear and nonlinear methods that compensates for model inaccuracies due to linearization or failure. A stability analysis based on the Lyapunov function approach has shown that bounded tracking error is guaranteed, and under specific circumstances, global stability is guaranteed as well. An analysis over the degrees of freedom of the mechanical system and its impact over the helicopter handling qualities is also performed to measure the degree of redundancy achieved with the addition of individual blade actuators as compared to a classic swashplate helicopter configuration. Mathematical analysis and numerical simulation, using reconfiguration of the individual blade control under failure have shown that this control architecture can potentially improve the survivability of the aircraft and reduce pilot workload under failure conditions

Exploiting natural selection to study adaptive behavior

The research presented in this dissertation explores different computational and modeling techniques that combined with predictions from evolution by natural selection leads to the analysis of the adaptive behavior of populations under selective pressure. For this thesis three computational methods were developed: EXPLoRA, EVORhA and SSA-ME. EXPLoRA finds genomic regions associated with a trait of interests (QTL) by explicitly modeling the expected linkage disequilibrium of a population of sergeants under selection. Data from BSA experiments was analyzed to find genomic loci associated with ethanol tolerance. EVORhA explores the interplay between driving and hitchhiking mutations during evolution to reconstruct the subpopulation structure of clonal bacterial populations based on deep sequencing data. Data from mixed infections and evolution experiments of E. Coli was used and their population structure reconstructed. SSA-ME uses mutual exclusivity in cancer to prioritize cancer driver genes. TCGA data of breast cancer tumor samples were analyzed.status: publishe

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis

Because of its clonal evolution a tumor rarely contains multiple genomic alterations in the same pathway as disrupting the pathway by one gene often is sufficient to confer the complete fitness advantage. As a result, many cancer driver genes display mutual exclusivity across tumors. However, searching for mutually exclusive gene sets requires analyzing all possible combinations of genes, leading to a problem which is typically too computationally complex to be solved without a stringent a priori filtering, restricting the mutations included in the analysis. To overcome this problem, we present SSA-ME, a network-based method to detect cancer driver genes based on independently scoring small subnetworks for mutual exclusivity using a reinforced learning approach. Because of the algorithmic efficiency, no stringent upfront filtering is required. Analysis of TCGA cancer datasets illustrates the added value of SSA-ME: well-known recurrently mutated but also rarely mutated drivers are prioritized. We show that using mutual exclusivity to detect cancer driver genes is complementary to state-of-the art approaches. This framework, in which a large number of small subnetworks are being analyzed in order to solve a computationally complex problem (SSA), can be generically applied to any problem in which local neighborhoods in a network hold useful information

Trincheras de retención / infiltración utilizadas como sistemas alternativos al drenaje urbano

El aumento de la urbanización ha traído como resultado la alteración del ciclo hidrológico natural de la zona. Como consecuencia a lo anterior, se incrementa la escorrentía superficial generando inundaciones, así como otros impactos negativos en las zonas aledañas. Para solucionar este problema se han venido desarrollando técnicas alternativas para el drenaje que simulen las condiciones naturales anteriores a la urbanización. Estas son comúnmente conocidas cómo Sistemas Urbanos de Drenaje Sostenible (SUDS), dentro de las cuales se encuentran las trincheras. Con el fin de promover la aplicabilidad de estas técnicas en Colombia, se realizó un documento que describiera y analizara los diferentes métodos para el diseño, construcción y mantenimiento de trincheras de retención e infiltración, como los propuestos por Azzout et al. (1994) y Woods-Ballard et al. (2007), entre otros. Además, se encontraron los pasos y recomendaciones para llevar a cabo la construcción y mantenimiento de estas y otras técnicas SUDS. Al estudiar los métodos de diseño se concluyó que las dimensiones de las trincheras son altamente dependientes de las condiciones hidrológicas de la zona. A partir de un ejercicio de aplicación a tres ciudades importantes de Colombia (Bogotá, Medellín y Cartagena), se estableció que es posible la aplicación de las técnicas en Colombia, en cuanto al diseño se refiere, debido a la poca información necesaria para el desarrollo las metodologías.The increase of the urban development has brought out the alteration of the natural hydrologic cycle of the area. As consequence, there is an increase in the surface runoff, generating floods, as well as others negative aspects of the bordering areas. To solve this problem, new alternative techniques have been developed for the drainage, which can simulate the natural conditions of the site prior the urbanization. These are commonly known as Sustainable Urban Drainage Systems (SUDS), which contains the trenches. In order to promote the applicability of these techniques in Colombia, a document was created that describes and analyzes the different methods for the design, construction and maintenance of the retention/infiltration trenches as proposed by Azzout et al. (1994) and Wood-Ballard et al. (2007), among others. The steps and recommendations were also developed to carry out the construction and maintenance of these and others SUDS techniques. With the study of the design methods, it was concluded that the dimensions of the trenches are highly dependent on the hydrologic conditions of the area. With the application of these trenches to three important cities of Colombia (Bogota, Medellin and Cartagena) it was established that these techniques are able to be applied in Colombia mainly in regard to the design due to the lack of information necessary for the development of the methodology.Ingeniero (a) CivilPregrad

Inspección eléctrica y lumínica de la Institución Educativa Luis Carlos González Mejía de Pereira

El siguiente trabajo tiene como objetivo principal realizar la inspección de la instalación eléctrica de la Institución Educativa Luis Carlos González Mejía. La cual consiste en detectar los posibles errores que pongan en riesgo la salud de las personas que realizan sus actividades en dicho lugar. Mediante la inspección se comprueba el cumplimiento de la Norma Técnica Colombiana NTC 2050, el Reglamento Técnico de Instalaciones Eléctricas RETIE, y a su vez lo establecido en el Reglamento Técnico de Iluminación y Alumbrado Público RETILAP

Combined burden and functional impact tests for cancer driver discovery using DriverPower

The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower's background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery

Identidades colectivas y patrimonio cultural. Una perspectiva sobre la modernidad urbana

El proceso de privatización, ya generalizado, que reduce la participación del Estado en ramas importantes de la economía y en áreas que anteriormente estaban destinadas al bienestar social, ha traído consigo la reanimación de valores, algunos muy tradicionales y conservadores que dan predominio a la condición privada sobre la pública, al individualismo sobre la colectividad, a la persona, aislada de la dinámica social. Estos valores se han aplicado poco a poco en casi todos los campos donde concurre el comportamiento humano: en el arte, en la tecnología, en la vida cotidiana y en la ciudad, y es precisamente, en esta última donde se ubica el con texto de la disertación de este trabajo, que se ocupa de describir la forma como los grupos sociales de escasos recursos han reconstruido una identidad colectiva distinta, a través de prácticas comunicativas cotidianas y de la forma de apropiación del espacio físico, que tiene como resultado un renovado espíritu ciudadano. Debo advertir, no obstante, que sería un error suponer que este nuevo carácter ciudadano proyectarla una actitud meramente individualista, o al contrario exclusivamente comunitaria, pues reflejaría, más bien de manera nítida, la particular y combinada visión de lo público y lo privado

La teoría de la ciudadanía en los estudios urbanos: estado y sociedad civil, derechos ciudadanos y movimientos sociales

El presente trabajo intenta profundizar en algunos aspectos sobre la teoría de la ciudadanía que recogen una visión tanto histórica como cultural, con el fin de contribuir al debate sobre la formación de la ciudadanía en general, y que además pueda ser útil para entender su práctica específica en las ciudades latinoamericanas. Durante el curso de este trabajo, podremos profundizar en el debate de diferentes puntos de vista sobre ciudadanía. Esta discusión teórica nos mostrará, en sí misma, por qué no podemos definir la ciudadanía de una única forma. La confrontación teórica, por lo tanto, ayudará a delinear la forma en que diferentes fuerzas sociales han considerado los componentes de la ciudadanía y cómo esas fuerzas se relacionan y luchan entre sí para encontrar la transición a la democracia

Autonomía, redes de significación e impacto institucional de los movimientos sociales

Comentario al libro Leslie Serna, ¡Aquí nos quedaremos! Testimonios de la Coordinadora. Única de Damnificados. El libro ¡Aquí nos quedaremos! no pretende ser un análisis teórico de la experiencia de damnificados, la pretensión es únicamente contribuir a la construcción de la memoria escrita de los movimientos sociales en nuestro país, no obstante, en su verdadera esencia el libro nos permite estructurar muy bien las etapas de nacimiento, consolidación y transformación del Movimiento de damnificados