UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists

As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.

The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool

Essays on the Application and Improvement of the Geographical Economics Models to Policy Analysis: The Case of Road Infrastructure in Central America

The novel models of Geographical Economy have analyzed the effects on the distribution of economic activity over the area of a given region, generated by different socio-economic shocks. For example, the costs of migrating from one place to another, as shown in Desmet et al. (2018). A key advantage of such models is that, given the structural definition of the market interactions, they can first create counterfactual scenarios based on the economic fundamentals. And second, a broad set of variables can account for that impact. These dynamic spatial general equilibrium models embody features such as measures for amenities, trade and transportation costs, productivity, and GDP that allow for multiple applications and uses. One of those is the design and evaluation of specific policies, such as the investment in infrastructure. This dissertation analyzes the application of the model to the case of the Pacific Corridor. It is a highway from Mexico City to Panama City, passing through six countries over 1.300 miles. This corridor is critical to the economic integration of that region. Desmet et al. (2018) model can account for the potential benefits of improving such infrastructure. In the first Chapter, I show how to adapt the model to create the necessary counterfactuals. The benefits are favorable for the locations near the project. In the second Chapter, I introduce an improvement to the model’s transportation costs matrix. It consists of the possibility to account for the effects of the administrative border controls (customs) on transportation costs. I used data on travel times in five regional countries to calibrate the model’s matrix. It matches the observed increase in transportation time cost due to border delays. The impact of removing such delay is more significant than the effect of the corridor on economic activity. Finally, I provide policy recommendations and the future steps of this research

Psychobiology of creativity, emotions and creative attitude

La creatividad como fenómeno psicológico implica procesos moleculares, en el sentido estricto del término, así como procesos globales que pueden contemplar interacción social o cultural. El estudio de la creatividad, desde las neurociencias, ha arrojado hallazgos que van desde lo genético hasta lo neuroanatómico. Sin embargo, es probable que tales hallazgos tengan una comprensión incompleta, o incluso errónea, si no se consideran la mediación de otras variables. El objetivo del presente trabajo es vincular el procesamiento emocional y la actitud creativa con las variables psicobiológicas asociadas a la creatividad. Para ello, se hace una revisión de la literatura en la que se destacan algunas aproximaciones a la creatividad desde las neurociencias. Se consideró que fueran trabajos meta-analíticos o de revisión crítica, así como trabajos empíricos, que en ambos casos estuvieran indizados en Web of Science y que tuvieran al menos dos citas por año, salvo los estudios de 2017. Como resultado del análisis de estudios genéticos, de neurotransmisión y otros a nivel de neuroimagen y electroencefalografía se señalan posibles vínculos con hallazgos de trabajos sobre procesamiento emocional. La actitud creativa a su vez, al orientar los desempeños creativos, da un sentido más comprehensivo a tal vinculación. Finalmente se discuten los hallazgos de la neurociencia en términos la necesidad de brindar marcos de referencia más acotados que permitan mejores explicacionesCreativity as a psychological phenomenon implies molecular processes, in the strict sense of the term, as well as global processes that can contemplate social or cultural interaction. The study of creativity, from the neurosciences perspective, has yielded findings that range from the genetic to the neuroanatomical. However, such findings are likely to have incomplete, or even erroneous, understanding if mediation of other variables is not considered. The objective of this work is to link emotional processing and creative attitude with the psychobiological variables associated with creativity. To do this, a review of the literature is made in which some approaches to creativity from the neurosciences are highlighted. It was considered that they were meta-analytic or critical review works, as well as empirical studies, which in both cases were indexed in Web of Science and had at least two citations per year, except for studies of 2017. As a result of the analysis of genetic studies, neurotransmission and others at the level of neuroimaging and electroencephalography, possible links to findings of work on emotional processing are indicated. The creative attitude, in turn, guiding the creative performances, gives a more comprehensive sense to such linkage. Finally, the findings of neuroscience are discussed in terms of the need to provide more limited frameworks that allow better explanation

El proceso de representaciones sobre las FARC. 1964. Los inicios

Este artículo presenta una parte de la investigación concerniente al procesode construcción de representaciones en la prensa nacional e internacionalsobre las Fuerzas Armadas Revolucionarias de Colombia-Ejército del Pueblo–FARC-EP– durante un periodo que comprende su inicio como grupo guerrilleroen 1964 y su consolidación como un ejército que puso en vilo al Estadocolombiano en 1996. Este ensayo se enfoca de manera exclusiva en el primeraño de origen de esta guerrilla, enfáticamente en el año de 196

OFDM comparison with FFT and DWT processing for DVB-T2 wireless channels

Introduction− Recent studies on the FFT processing (Fast Fourier Transform) or DWT (Discrete Wavelet Transform) of the OFDM signal (Orthogonal Frequency Division Multiplexing) have shown pros and cons for DVB-T2 (Digital Video Broadcasting-Second Generation Terrestrial) radio communications; however, the benefits of both types of processing have yet to be compared for the same scenario. Objective− The objective of this research is to compare the response of the wireless channel with AWGN noise (Additive White Gaussian Noise Channel) and Rayleigh and Rician fading in the UHF (Ultra High Frequency) bandMethodology−The transmission of DVB-T2 information with OFDM modulation and FFT and DWT processing was simulated in Matlab®, specifically in Simulink. Results− The results of the study proved to be more ef-ficient for DWT system than FFT system, due to the low rate of erroneous bits, spectral efficiency and reduction of the Peak-to-Average Power Ratio (PAPR), for Eb / No relations greater than 10dB. Conclusions−In this article, we present the designs of both systems and the results of the research experience; likewise, the practical applicability of these systems is discussed, and improvements are suggested for future work.Introducción− Recientes estudios sobre el procesado FFT (Fast Fourier Transform) o DWT (Discrete Wavelet Transform) de la señal OFDM (Orthogonal Frequency Di-vision Multiplexing) han demostrado pros y contras para comunicaciones de radio DVB-T2 (Digital Video Broad-casting – Second Generation Terrestrial); sin embargo, aún falta comparar las prestaciones de ambos tipos de procesamiento para el mismo escenario. Objetivo− El objetivo de esta investigación es comparar la respuesta del canal inalámbrico con ruido AWGN (Ad-ditive White Gaussian Noise Channel) y desvanecimiento Rayleigh y Rician en la banda de UHF (Ultra High Fre-quency).Metodología− Se simuló en Matlab®, específicamente en Simulink, la transmisión de información DVB-T2 con modulación OFDM y procesado FFT y DWT. Resultados− Los resultados del estudio demostraron ser más eficientes para el sistema DWT en comparación con el Sistema FFT, por la baja tasa de bits errados, eficiencia espectral y reducción del cociente entre la potencia pico a promedio (PAPR: Peak-to-Average Power Ratio), para relaciones Eb/No mayores a 10dB. Conclusiones− En este artículo se presentan los diseños de ambos sistemas y los resultados de la experiencia de investigación; así mismo, se discute la aplicabilidad práctica de estos sistemas y se sugieren mejoras para trabajos futuros

Comparación OFDM con procesado FFT y DWT para canales inalámbricos DVB-T2

Introduction: Recent studies on the FFT processing (Fast Fourier Transform) or DWT (Discrete Wavelet Transform) of the OFDM signal (Orthogonal Frequency Division Multiplexing) have shown pros and cons for DVB-T2 (Digital Video Broadcasting-Second Generation Terrestrial) radio communications; however, the benefits of both types of processing have yet to be compared for the same scenario. Objective: The objective of this research is to compare the response of the wireless channel with AWGN noise (Additive White Gaussian Noise Channel) and Rayleigh and Rician fading in the UHF (Ultra High Frequency) band. Methodology: The transmission of DVB-T2 information with OFDM modulation and FFT and DWT processing was simulated in Matlab®, specifically in Simulink. Results: The results of the study proved to be more efficient for DWT system than FFT system, due to the low rate of erroneous bits, spectral efficiency and reduction of the Peak-to-Average Power Ratio (PAPR), for Eb / No relations greater than 10dB. Conclusions: In this article, we present the designs of both systems and the results of the research experience; likewise, the practical applicability of these systems is discussed, and improvements are suggested for future work.Introducción: Recientes estudios sobre el procesado FFT (Fast Fourier Transform) o DWT (Discrete Wavelet Transform) de la señal OFDM (Orthogonal Frequency Division Multiplexing) han demostrado pros y contras para comunicaciones de radio DVB-T2 (Digital Video Broadcasting – Second Generation Terrestrial); sin embargo, aún falta comparar las prestaciones de ambos tipos de procesamiento para el mismo escenario. Objetivo: El objetivo de esta investigación es comparar la respuesta del canal inalámbrico con ruido AWGN (Additive White Gaussian Noise Channel) y desvanecimiento Rayleigh y Rician en la banda de UHF (Ultra High Frequency). Metodología: Se simuló en Matlab®, específicamente en Simulink, la transmisión de información DVB-T2 con modulación OFDM y procesado FFT y DWT. Resultados: Los resultados del estudio demostraron ser más eficientes para el sistema DWT en comparación con el Sistema FFT, por la baja tasa de bits errados, eficiencia espectral y reducción del cociente entre la potencia pico a promedio (PAPR: Peak-to-Average Power Ratio), para relaciones Eb/No mayores a 10dB. Conclusiones: En este artículo se presentan los diseños de ambos sistemas y los resultados de la experiencia de investigación; así mismo, se discute la aplicabilidad práctica de estos sistemas y se sugieren mejoras para trabajos futuros

La construcción de la memoria de un lugar en la prensa. Urabá en la Revista Semana (1980-2002)

El documento parte del concepto teórico de la prensa como fuente y referente deconstrucción significativa de memoria de un lugar, en este caso Urabá, Colombia.Hace el análisis de treinta artículos de la Revista Semana publicados entre los años1980 y 2002 y los compara con algunas obras historiográficas que abordan el temade Urabá. Se concluye que la Revista Semana elabora una narración centrada en elconflicto armado construida de manera reduccionista, sin contexto y simplista dellugar y que esto afecta la construcción de la memoria y la imagen de Urabá, haciéndolaver como una zona tórrida, violenta y sin esperanz

Metodología avanzada para la captura de LPS en biofluidos

ABSTRACT: Lipopolysaccharide (LPS), or endotoxin, is the main component of the outer membrane of Gram-negative bacteria where lipid A is the responsible segment for its toxicity. It poses a serious risk when detected both in different industries and environments and when is present in human bloodstream as it can lead to sepsis, an exaggerated response to LPS that triggers immune suppression, organ dysfunction or even death. Unfortunately, alternative methods for contaminant removal through extracorporeal blood detoxification processes present drawbacks that make endotoxin detection/removal a crucial challenge to achieve safe and effective detoxification processes. In this regard, magnetofluidic devices deserve special attention and involve two main steps: the sequestration of LPS on suitably functionalized magnetic nanoparticles (MNPs) and, the removal of the MNPs-LPS complex from the biological fluid. Consequently, this dissertation provides an integrated methodology to advance the design of the LPS sequestration step to promote its separation from biofluids through the synthesis of an antilipopolysaccharide (LALF) protein from Limulus polyphemus species using genetic engineering techniques in addition to the quantification of the binding strength of the LALF protein to LPS through a newly approach and addressing the variables that affect the formation of the complex. In addition, in order to contribute to the development of an application for continuous LPS capture, as a first approach, homogeneous and heterogeneous L-L separation of aqueous anions (chromate) in microdevices is addressed experimentally and by means of a theoretical model developed with ANSYS FLUENT, laying the foundations to continue with the microfluidic design for L-S separation and finally, its application to LPS capture.RESUMEN: El lipopolisacárido (LPS), o endotoxina, es el principal componente de la membrana externa de las bacterias Gram negativas donde el lípido A es el segmento responsable de su toxicidad. Su presencia supone un grave riesgo tanto en diferentes industrias y entornos como cuando llega al torrente sanguíneo pudiendo conducir a la sepsis, una respuesta exagerada al LPS que desencadena una supresión inmunitaria, una disfunción orgánica o incluso la muerte. Lamentablemente, los métodos alternativos para la eliminación de contaminantes a través de procesos de detoxificación extracorpórea de la sangre presentan inconvenientes que hacen que la detección/eliminación de endotoxinas sea un reto crucial para lograr procesos de detoxificación seguros y eficaces. En este sentido, los dispositivos magnetofluídicos merecen especial atención e implican dos etapas principales; el secuestro de LPS en nanopartículas magnéticas (MNPs) convenientemente funcionalizadas y, la eliminación del complejo MNPs-LPS del fluido biológico. En consecuencia, esta disertación aporta una metodología integrada para avanzar en el diseño de la etapa de secuestro de LPS para promover su separación de los biofluidos a través de la síntesis de una proteína antilipopolisacáridos (LALF) procedente de la especie Limulus polyphemus mediante técnicas de ingeniería genética además de la cuantificación de la fuerza de unión de la proteína LALF al LPS mediante un nuevo enfoque y teniendo en cuenta las variables que afectan a la formación del complejo. Además, con el objeto de contribuir al desarrollo de una aplicación para la captura de LPS en continuo, como primera aproximación, se aborda para la separación homogénea y heterogénea L-L de aniones acuosos (cromato) en microdispositivos experimentalmente y mediante un modelo teórico desarrollado con ANSYS FLUENT, sentando las bases para continuar con el diseño microfluidico para la separación L-S y finalmente, su aplicación a la captura de LPS.The research described in this dissertation was conducted at the Advanced Separation Processes research group of the Department of Chemical and Biomolecular Engineering at the University of Cantabria. The research was financially supported by the Ministry of Economy and Competitiveness of the Spanish Government through the R&D project RTI2018-093310-B-I00 (MINECO / FEDER, UE)