The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

CLEAR: a credible method to evaluate website archivability

Web archiving is crucial to ensure that cultural, scientific and social heritage on the web remains accessible and usable over time. A key aspect of the web archiving process is optimal data extraction from target websites. This procedure is difficult for such reasons as, website complexity, plethora of underlying technologies and ultimately the open-ended nature of the web. The purpose of this work is to establish the notion of Website Archivability (WA) and to introduce the Credible Live Evaluation of Archive Readiness (CLEAR) method to measure WA for any website. Website Archivability captures the core aspects of a website crucial in diagnosing whether it has the potentiality to be archived with completeness and accuracy. An appreciation of the archivability of a web site should provide archivists with a valuable tool when assessing the possibilities of archiving material and in- uence web design professionals to consider the implications of their design decisions on the likelihood could be archived. A prototype application, archiveready.com, has been established to demonstrate the viabiity of the proposed method for assessing Website Archivability

Web-based visualization for 3D data in archaeology : The ADS 3D viewer

The solid geometry of archaeological deposits is fundamental to the interpretation of their chronological sequence. However, such stratigraphic sequences are generally viewed as static two-dimensional diagrammatic representations which are difficult to manipulate or to relate to real layers. The ADS 3D Viewer is a web-based resource for the management and analysis of archaeological data. The viewer was developed to take advantage of recent developments in web technology, namely the adoption of WebGL (Web Graphics Library) by current web browsers. The ADS 3D Viewer combines the potential of the 3D Heritage Online Presenter (3DHOP), a software package for the web-based visualization of 3D geometries, with the infrastructure of the Archaeology Data Service (ADS) repository, in the attempt to create a platform for the visualization and analysis of 3D data archived by the ADS. Two versions of the viewer have been developed to answer the needs of different users. The first version, the Object Level 3D Viewer, was implemented to extend the browsing capability of ADS project archives by enabling the visualization of single 3D models. The second version, the Stratigraphy 3D Viewer, is an extension which allows the exploration of a specific kind of aggregated data: the multiple layers of an archaeological stratigraphic sequence. This allows those unable to participate directly in the fieldwork to access, analyse and re-interpret the archaeological context remotely. This has the potential to transform the discipline, allowing inter-disciplinary, cross-border and ‘at-distance’ collaborative workflows, and enabling easier access to and analysis of archaeological data

New Challenges on Web Architectures for the Homogenization of the Heterogeneity of Smart Objects in the Internet of Things

Aquesta tesi tracta de dues de les noves tecnologies relacionades amb la Internet of Things (IoT) i la seva integració amb el camp de les Smart Grids (SGs); aquestes tecnologies son la Web of Things (WoT) i la Social Internet of Things (SIoT). La WoT és una tecnologia que s’espera que proveeixi d’un entorn escalable i interoperable a la IoT usant la infraestructura web existent, els protocols web y la web semàntica. També s’espera que la SIoT contribueixi a solucionar els reptes d’escalabilitat i capacitat de descobriment creant una xarxa social d’agents (objectes i humans). Per explorar la sinergia entre aquestes tecnologies, l’objectiu és el de proporcionar evidència pràctica i empírica, generalment en forma de prototips d’implementació i experimentació empírica. En relació amb la WoT i les SGs, s’ha creat un prototip per al Web of Energy (WoE) que té com a objectiu abordar els desafiaments presents en el domini les SGs. El prototip és capaç de proporcionar interoperabilitat i homogeneïtat entre diversos protocols. El disseny d’implementació es basa en el Model d’Actors, que també proporciona escalabilitat del prototip. L’experimentació mostra que el prototip pot gestionar la transmissió de missatges per a aplicacions de les SGs que requereixen que la comunicació es realitzi sota llindars de temps crítics. També es pren una altra direcció d’investigació similar, menys centrada en les SGs, però per a una gamma més àmplia de dominis d’aplicació. S’integra la descripció dels fluxos d’execució com a màquines d’estats finits utilitzant ontologies web (Resource Description Framework (RDF)) i metodologies de la WoT (les accions es realitzen basant-se en peticions Hyper-Text Transfer Protocol/Secure (HTTP/S) a Uniform Resource Locators (URLs)). Aquest flux d’execució, que també pot ser un plantilla per a permetre una configuració flexible en temps d’execució, s’implementa i interpreta com si fos (i mitjançant) un Virtual Object (VO). L’objectiu de la plantilla és ser reutilitzable i poder-se compartir entre múltiples desplegaments de la IoT dins el mateix domini d’aplicació. A causa de les tecnologies utilitzades, la solució no és adequada per a aplicacions de temps crític (llindar de temps relativament baix i rígid). No obstant això, és adequat per a aplicacions que no demanden resposta en un temps crític i que requereixen el desplegament de VOs similars en el que fa referència al flux d’execució. Finalment, el treball s’enfoca en una altra tecnologia destinada a millorar l’escalabilitat i la capacitat de descobriment en la IoT. La SIoT està sorgint com una nova estructura de la IoT que uneix els nodes a través de relacions significatives. Aquestes relacions tenen com a objectiu millorar la capacitat de descobriment; en conseqüència, millora la escalabilitat d’una xarxa de la IoT. En aquest treball s’aplica aquest nou paradigma per optimitzar la gestió de l’energia en el costat de la demanda a les SGs. L’objectiu és aprofitar les característiques de la SIoT per ajudar a la creació de Prosumer Community Groups (PCGs) (grups d’usuaris que consumeixen o produeixen energia) amb el mateix objectiu d’optimització en l’ús de l’energia. La sinergia entre la SIoT i les SGs s’ha anomenat Social Internet of Energy (SIoE). Per tant, amb la SIoE i amb el focus en un desafiament específic, s’estableix la base conceptual per a la integració entre la SIoT i les SGs. Els experiments inicials mostren resultats prometedors i aplanen el camí per a futures investigacions i avaluacions de la proposta. Es conclou que el WoT i la SIoT són dos paradigmes complementaris que nodreixen l’evolució de la propera generació de la IoT. S’espera que la propera generació de la IoT sigui un Multi-Agent System (MAS) generalitzat. Alguns investigadors ja estan apuntant a la Web i les seves tecnologies (per exemple, Web Semàntica, HTTP/S)—i més concretamente a la WoT — com a l’entorn que nodreixi a aquests agents. La SIoT pot millorar tant l’entorn com les relacions entre els agents en aquesta fusió. Les SGs també poden beneficiar-se dels avenços de la IoT, ja que es poden considerar com una aplicació específica d’aquesta última.  Esta tesis trata de dos de las novedosas tecnologías relacionadas con la Internet of Things (IoT) y su integración con el campo de las Smart Grids (SGs); estas tecnologías son laWeb of Things (WoT) y la Social Internet of Things (SIoT). La WoT es una tecnología que se espera que provea de un entorno escalable e interoperable a la IoT usando la infraestructura web existente, los protocolos web y la web semántica. También se espera que la SIoT contribuya a solucionar los retos de escalabilidad y capacidad de descubrimiento creando una red social de agentes (objetos y humanos). Para explorar la sinergia entre estas tecnologías, el objetivo es el de proporcionar evidencia práctica y empírica, generalmente en forma de prototipos de implementación y experimentación empírica. En relación con la WoT y las SGs, se ha creado un prototipo para la Web of Energy (WoE) que tiene como objetivo abordar los desafíos presentes en el dominio las SGs. El prototipo es capaz de proporcionar interoperabilidad y homogeneidad entre diversos protocolos. El diseño de implementación se basa en el Modelo de Actores, que también proporciona escalabilidad del prototipo. La experimentación muestra que el prototipo puede manejar la transmisión de mensajes para aplicaciones de las SGs que requieran que la comunicación se realice bajo umbrales de tiempo críticos. También se toma otra dirección de investigación similar, menos centrada en las SGs, pero para una gama más amplia de dominios de aplicación. Se integra la descripción de los flujos de ejecución como máquinas de estados finitos utilizando ontologías web (Resource Description Framework (RDF)) y metodologías de la WoT (las acciones se realizan basándose en peticiones Hyper-Text Transfer Protocol/Secure (HTTP/S) a Uniform Resource Locators (URLs)). Este flujo de ejecución, que también puede ser una plantilla para permitir una configuración flexible en tiempo de ejecución, se implementa e interpreta como si fuera (y a través de) un Virtual Object (VO). El objetivo de la plantilla es que sea reutilizable y se pueda compartir entre múltiples despliegues de la IoT dentro del mismo dominio de aplicación. Debido a las tecnologías utilizadas, la solución no es adecuada para aplicaciones de tiempo crítico (umbral de tiempo relativamente bajo y rígido). Sin embargo, es adecuado para aplicaciones que no demandan respuesta en un tiempo crítico y que requieren el despliegue de VOs similares en cuanto al flujo de ejecución. Finalmente, el trabajo se enfoca en otra tecnología destinada a mejorar la escalabilidad y la capacidad de descubrimiento en la IoT. La SIoT está emergiendo como una nueva estructura de la IoT que une los nodos a través de relaciones significativas. Estas relaciones tienen como objetivo mejorar la capacidad de descubrimiento; en consecuencia, mejora la escalabilidad de una red de la IoT. En este trabajo se aplica este nuevo paradigma para optimizar la gestión de la energía en el lado de la demanda en las SGs. El objetivo es aprovechar las características de la SIoT para ayudar en la creación de Prosumer Community Groups (PCGs) (grupos de usuarios que consumen o producen energía) con el mismo objetivo de optimización en el uso de la energía. La sinergia entre la SIoT y las SGs ha sido denominada Social Internet of Energy (SIoE). Por lo tanto, con la SIoE y con el foco en un desafío específico, se establece la base conceptual para la integración entre la SIoT y las SG. Los experimentos iniciales muestran resultados prometedores y allanan el camino para futuras investigaciones y evaluaciones de la propuesta. Se concluye que la WoT y la SIoT son dos paradigmas complementarios que nutren la evolución de la próxima generación de la IoT. Se espera que la próxima generación de la IoT sea un Multi-Agent System (MAS) generalizado. Algunos investigadores ya están apuntando a la Web y sus tecnologías (por ejemplo,Web Semántica, HTTP/S)—y más concretamente a la WoT — como el entorno que nutra a estos agentes. La SIoT puede mejorar tanto el entorno como las relaciones entre los agentes en esta fusión. Como un campo específico de la IoT, las SGs también pueden beneficiarse de los avances de la IoT.This thesis deals with two novel Internet of Things (IoT) technologies and their integration to the field of the Smart Grid (SG); these technologies are the Web of Things (WoT) and the Social Internet of Things (SIoT). The WoT is an enabling technology expected to provide a scalable and interoperable environment to the IoT using the existing web infrastructure, web protocols and the semantic web. The SIoT is expected to expand further and contribute to scalability and discoverability challenges by creating a social network of agents (objects and humans). When exploring the synergy between those technologies, we aim at providing practical and empirical evidence, usually in the form of prototype implementations and empirical experimentation. In relation to the WoT and SG, we create a prototype for the Web of Energy (WoE), that aims at addressing challenges present in the SG domain. The prototype is capable of providing interoperability and homogeneity among diverse protocols. The implementation design is based on the Actor Model, which also provides scalability in regards to the prototype. Experimentation shows that the prototype can handle the transmission of messages for time-critical SG applications. We also take another similar research direction less focused on the SG, but for a broader range of application domains. We integrate the description of flows of execution as Finite-State Machines (FSMs) using web ontologies (Resource Description Framework (RDF)) and WoT methodologies (actions are performed on the basis of calls Hyper Text Transfer Protocol/ Secure (HTTP/S) to a Uniform Resource Locator (URL)). This execution flow, which can also be a template to allow flexible configuration at runtime, is deployed and interpreted as (and through) a Virtual Object (VO). The template aims to be reusable and shareable among multiple IoT deployments within the same application domain. Due to the technologies used, the solution is not suitable for time-critical applications. Nevertheless, it is suitable for non-time-critical applications that require the deployment of similar VOs. Finally, we focus on another technology aimed at improving scalability and discoverability in IoT. The SIoT is emerging as a new IoT structure that links nodes through meaningful relationships. These relationships aim at improving discoverability; consequently, improving the scalability of an IoT network. We apply this new paradigm to optimize energy management at the demand side in a SG. Our objective is to harness the features of the SIoT to aid in the creation of Prosumer Community Group (PCG) (groups of energy users that consume or produce energy) with the same Demand Side Management (DSM) goal. We refer to the synergy between SIoT and SG as Social Internet of Energy (SIoE). Therefore, with the SIoE and focusing on a specific challenge, we set the conceptual basis for the integration between SIoT and SG. Initial experiments show promising results and pave the way for further research and evaluation of the proposal. We conclude that the WoT and the SIoT are two complementary paradigms that nourish the evolution of the next generation IoT. The next generation IoT is expected to be a pervasive Multi-Agent System (MAS). Some researchers are already pointing at the Web and its technologies (e.g. Semantic Web, HTTP/S) — and more concretely at the WoT — as the environment nourishing the agents. The SIoT can enhance both the environment and the relationships between agents in this fusion. As a specific field of the IoT, the SG can also benefit from IoT advancements

Multi-objective dynamic population shuffled frog-leaping biclustering of microarray data

<p>Abstract</p> <p>The structure of RiboNucleic Acid (RNA) has the potential to be altered by a Single Nucleotide Polymorphism (SNP). Disease-associated SNPs mapping to non-coding regions of the genome that are transcribed into RiboNucleic Acid (RNA) can potentially affect cellular regulation (and cause disease) by altering the structure of the transcript. We performed a large-scale meta-analysis of Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) data, which probes the structure of RNA. We found that several single point mutations exist that significantly disrupt RNA secondary structure in the five transcripts we analyzed. Thus, every RNA that is transcribed has the potential to be a “RiboSNitch;” where a SNP causes a large conformational change that alters regulatory function. Predicting the SNPs that will have the largest effect on RNA structure remains a contemporary computational challenge. We therefore benchmarked the most popular RNA structure prediction algorithms for their ability to identify mutations that maximally affect structure. We also evaluated metrics for rank ordering the extent of the structural change. Although no single algorithm/metric combination dramatically outperformed the others, small differences in AUC (Area Under the Curve) values reveal that certain approaches do provide better agreement with experiment. The experimental data we analyzed nonetheless show that multiple single point mutations exist in all RNA transcripts that significantly disrupt structure in agreement with the predictions.</p