Automated construction and analysis of political networks via open government and media sources

We present a tool to generate real world political networks from user provided lists of politicians and news sites. Additional output includes visualizations, interactive tools and maps that allow a user to better understand the politicians and their surrounding environments as portrayed by the media. As a case study, we construct a comprehensive list of current Texas politicians, select news sites that convey a spectrum of political viewpoints covering Texas politics, and examine the results. We propose a ”Combined” co-occurrence distance metric to better reflect the relationship between two entities. A topic modeling technique is also proposed as a novel, automated way of labeling communities that exist within a politician’s ”extended” network.Peer ReviewedPostprint (author's final draft

Agis: heuristic search library & framework in haskell

There are currently few experiments that try to perform heuristic search in Haskell, even though the language provides a clean and modular syntax that can be specially useful for educational or research purposes in the field. Furthermore, functional programming provides a inherently concurrent way of writing code, which results in trivial parallelism using compiler flags. Also, due to the particular constraints imposed by the language, it is specially interesting to create a library of algorithms that solves the k best paths problem. Taking into account that it can be detrimental to the overall performance, the language’s nature allows the framework to return a list (that can theoretically be as long as infinite) containing all the solutions in the problem space, and use its lazy evaluation to only compute the k solutions asked by the user, without any kind of code modification. The aforementioned reasons are found as a motivation for developing a framework in Haskell, that allows the user to perform searches, as well as designing different algorithms and test them along with the ones provided for comparison. Haskell’s strong type system let us declare a set of types used by the library, declaring all needed constraints in them and ensuring that if the code provided by the user type checks the code will most likely behave as expected by the user. This thesis details all the steps that were needed in the process: from a software engineering approach to the design, to the generation of all needed artifacts to ensure the quality and intuition about the library; including the implementation step and all the reasoning behind it, and all formal verification of the models used in the library. The testing process also contains all the performance checks along with several low-level profile tests to spot a space leak in the library. All the organizational, legal and socioeconomic details of the project are also included in the document, along with an appendix containing all the generated documentation of the framework. The result is agis: a Haskell package that lets the user include in their own code a set of types to model and solve heuristic problems; design modular heuristic search algorithms (using intermediate functions provided by the library) or write them from scratch (using the types provided by the library) and be able to run them in several search domains provided in the framework or run several benchmarks using a criterion interface.Actualmente existen pocos ejemplos de búsqueda heurística en Haskell, a pesar de que el lenguaje ofrece una sintaxis modular y limpiar que lo hace especialmente interesante para fines educativos o de investigación en este campo. Además, la programación funcional ofrece una forma de escribir código intrínsecamente concurrente, lo que hace código de Haskell trivialmente paralelizable (tan solo es necesario activar ciertas opciones propuestas por el compilador). Además de todo ello, las restricciones impuestas por el lenguaje hacen una opción especialmente interesante que los algoritmos incluídos en la librería no tengan un comportamiento clásico, sino que resuelvan a su vez el problema de las k mejores soluciones: el algoritmo puede devolver una lista con todas las soluciones incluídas en el espacio de búsqueda (que puede ser infinita), y usar la evaluación perezosa del lenguaje para solo calcular las que el usuario realmente pida, sin ninguna modificación de código ni problema a la hora de evaluar dicha lista. Todas estas razones sirven de motivación para el desarrollo de un framework en Haskell, que permita al usuario tanto ejecutar búsquedas como diseñar distintos algoritmos y compararlos con otros ya existentes. El sistema de tipos de Haskell permite a la librería declarar un conjunto de tipos para que sean usados por el usuario a la hora de modelar problemas o diseñar algoritmos y asegurar de esta manera que si el código compila, es muy probable que el comportamiento del código sea el esperado. En este trabajo se recogen todos los pasos que se han seguido en este proceso: desde un diseño a nivel de ingeniería de software hasta la generación de todos los artefactos necesarios para asegurar un correcto diseño de la librería, para pasar a la implementación de dicho diseño. Esta implementación incluye todas las justificaciones necesarias así como la verificación formal de los modelos que así lo requiren. Se incluye una sección que define todas las pruebas realizadas que incluyen la medición de tiempos y recursos, así como varias pruebas de bajo nivel realizadas para encontrar el origen de una pérdida de espacio y desempeño encontrada en la librería. Todos los los detalles organizativos, legales y socioeconómicos se encuentran recogidos en este documento, así como la documentación generada por la librería en un apéndice a este. El resultado del trabajo es agis: un paquete de Haskell que permite al usuario incluir en su propio código un conjunto de tipos para modelar problemas y resolverlos usando distintos algoritmos de búsqueda, diseñar algoritmos de búsqueda modulares (usando funciones intermedias proporcionadas por el framework) o implementar uno de cero (usando los tipos de la librería), y ser así capaz de correrlos en distintos dominios de búsqueda incluidos en el framework o correr distintos benchmarks con la interfaz proporcionada al paquete criterion.Ingeniería Informátic

Ranking efficient DMUs using cooperative game theory

The problem of ranking Decision Making Units (DMUs) in Data Envelopment Analysis (DEA) has been widely studied in the literature. Some of the proposed approaches use cooperative game theory as a tool to perform the ranking. In this paper, we use the Shapley value of two different cooperative games in which the players are the efficient DMUs and the characteristic function represents the increase in the discriminant power of DEA contributed by each efficient DMU. The idea is that if the efficient DMUs are not included in the modified reference sample then the efficiency score of some inefficient DMUs would be higher. The characteristic function represents, therefore, the change in the efficiency scores of the inefficient DMUs that occurs when a given coalition of efficient units is dropped from the sample. Alternatively, the characteristic function of the cooperative game can be defined as the change in the efficiency scores of the inefficient DMUs that occurs when a given coalition of efficient DMUs are the only efficient DMUs that are included in the sample. Since the two cooperative games proposed are dual games, their corresponding Shapley value coincide and thus lead to the same ranking. The more an ef- ficient DMU impacts the shape of the efficient frontier, the higher the increase in the efficiency scores of the inefficient DMUs its removal brings about and, hence, the higher its contribution to the overall discriminant power of the method. The proposed approach is illustrated on a number of datasets from the literature and compared with existing methods

Plant surfaces as vehicles of Bacillus cereus responsible of human food poisoning

• Introduction A major concern in food safety is the contamination of fresh and stored food with spoiling bacteria that provoke human poisoning. Bacillus cereus is a common food-borne pathogen responsible of important poisoning outbreaks and severe bacteraemia and septicaemia. Poisoning caused by B. cereus is classified in two main categories: emetic and diarrheic. The emetic poisoning is correlated to the production of cereulide. This toxin is very heat stable, and it can be produced in the food contaminated by B. cereus cells. Diarrheic poisoning is provoked by the enterotoxin hemolysin BL, the non-hemolytic enterotoxin and the cytotoxin K. • Objective To study the interaction of B. cereus with plants as a bacteria reservoir, and in ready-to-eat fruits and vegetables. • Materials & Methods A collection of strains implicated in food-borne outbreaks were tested in vitro for a battery of phenotypes related to bacterial multicellular behaviour and thus interaction with host. 1. Solid or liquid media were used to study biofilm formation, motility or adhesion to surfaces. 2. Leaves, fruits and vegetables (melon leaf, cucumber leaf and fruit and endive) were used to study the persistence of B. cereus over time and their distribution and organization by electron microscopy. • Results All the strains behaved similarly in vitro, only some persisted on plant surfaces. Among them, the emetic strain AH187 was selected because bacterial cells persisted on a concentration of 104-105 CFU per gram of leaf, vegetable or fruit, with a sporulation rate of 40%. The electron microscopy images showed the organization of bacteria in well-developed biofilms with visible extracellular matrix. Finally, mass spectrometry analysis proved the presence of some isoforms of cereluide on the different surfaces. • Conclusion The fact that cells of B. cereus persist in leaf surface mainly as vegetative cells are indicative of their ability to adapt to the physico-chemical changeable phyllosphere, and thus to produce the emetic toxin cereulide. The presence of spores, and the formation of biofilms can be indicative of the versatile adhesive properties of this strain to diverse surfaces. Altogether are supportive of the importance of plant surfaces either as reservoir of bacterial cells or as vehicles for further contamination and food poisoning.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

From farmers to bioengineers: Sowing genes, harvesting molecules

Twenty-first-century agriculture faces major challenges that urgently need to be answered. In the last decade, new breeding technologies have been developed that can help meet these challenges. These technologies are not only more accurate and efficient, but are also simpler and more accessible, which will facilitate the progressive democratisation of agricultural biotechnology. In this text we discuss future agricultural development in terms of technological democratisation and regulatory relaxation. In this scenario one would expect an increase in the diversity of cultivated varieties and species, the strong development of biofactory crops and, in the long term, the emergence of increasingly fit «smart» crops

Extracellular matrix components are required to protect bacillus subtilis from pseudomonas invasion and co-colonization of plants

Plants are colonized by a vast variety of microbes. Among them, bacteria are the most predominant and are able to adapt to environmental changes and interact with other microorganisms using a wide array of molecules, metabolic plasticity and secretion systems. One way bacteria have evolved to succeed in this competitive scenario is the formation of biofilms which provides protection to the cells, modulates the flux of signals and controls cellular differentiation. Thus, efforts are encouraged to really determine the functionality of the bacterial extracellular matrix. In this study, we have employed microbiological and microscopic techniques to study the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We demonstrate the important role of the extracellular matrix in protecting B. subtilis colonies from infiltration by Pseudomonas. Furthermore, time-lapse confocal laser scanning microscopy (CLSM) analyses of the bacterial interactions have permitted to complete the study of the bacterial behaviors and to measure bacterial expansion rates. Surprising, we find that the Pseudomonas type VI secretion system (T6SS) is required in the cell-to-cell contact with matrix-impaired B. subtilis cells, revealing a novel role for T6SS against Gram-positive bacteria. In response to P. chlororaphis infiltration, we find that B. subtilis activates sporulation and expresses motility-related genes. Confocal microscopy of the bacterial interactions using plant organs highlights the functional importance of these different bacterial strategies in their coexistence as stable bacterial communities. The findings further our understanding of the functional role played by biofilms in mediating bacterial social interactions.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Analysis of the molecular machinery implicated in multicellularity in bacillus cereus

Introduction: Bacillus cereus is a Gram-positive bacterium usually implicated in food poisoning outbreaks and human infections that sometimes result fatal. These events are closely related to the assembly of a biofilm that serves as a reservoir of cells, a nest for sporulation and protection from environmental stresses, host defenses or chemotherapy. Objectives: To perform a comprehensive comparative study of biofilm and planktonic cells to: i) delineate the molecular machinery implicated in the different steps of the biofilm life cycle, and ii) define new genes dedicated to biofilm formation. Materials & methods: Bacteria were grown under biofilm inducing conditions. Biofilm cells were separated from planktonic cells at different times and their whole mRNA was isolated, sequenced and analyzed. Results: Our results reveal a high number of genes associated to biofilm, many of them with unknown function, but highly conserved in others bacterial species. Besides, we found global changes in cell wall synthesis, metabolism and interspecies interaction molecules. ​ Conclusions: The interaction of B. cereus with other bacteria is conditioned by secondary metabolites, which are apparently overexpressed in biofilm. On the other hand, toxins are mainly expressed in planktonic cells, which are more oriented to interact with its hosts. These results reveal the defense and attacking positions of B. cereus in biofilm vs planktonic states.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Shotgun Phage Display of Lactobacillus casei BL23 Against Collagen and Fibronectin

7 pages, 4 figures.-- First published online 23 November 2010Lactobacilli are normal constituents of the intestinal microbiota, and some strains show the capacity to bind to extracellular matrix proteins and components of the mucosal layer, which represents an adaptation to persist in this niche. A shotgun phage-display library of Lactobacillus casei BL23 was constructed and screened for peptides able to bind to fibronectin and collagen. Clones showing binding to these proteins were isolated, which encoded overlapping fragments of a putative transcriptional regulator (LCABL_29260), a hypothetical protein exclusively found in the L. casei/rhamnosus group (LCABL_01820), and a putative phage-related endolysin (LCABL_13470). The construction of different glutathione S-transferase (GST) fusions confirmed the binding activity and demonstrated that the three identified proteins could interact with fibronectin, fibrinogen, and collagen. The results illustrate the utility of phage display for the isolation of putative adhesins in lactobacilli. However, it remains to be determined whether the primary function of these proteins actually is adhesion to mucosal surfaces.This work was supported by projects AGL2004-00176/ALI and Consolider Fun-c-Food CSD2007-00063 from the Spanish Ministry of Science and Innovation. Diego Muñoz-Provencio was the recipient of a research fellowship from the Instituto Danone.Peer reviewe

Diboson anomaly: Heavy Higgs resonance and QCD vector-like exotics

peer reviewedThe ATLAS collaboration (and also CMS) has recently reported an excess over Standard Model expectations for gauge boson pair production in the invariant mass region 1.8−2.2 TeV. In the light of these results, we argue that such signal might be the first manifestation of the production and further decay of a heavy CP-even Higgs resulting from a type-I Two Higgs Doublet Model. We demonstrate that in the presence of colored vector-like fermions, its gluon fusion production cross section is strongly enhanced, with the enhancement depending on the color representation of the new fermion states. Our findings show that barring the color triplet case, any QCD "exotic" representation can fit the ATLAS result in fairly large portions of the parameter space. We have found that if the diboson excess is confirmed and this mechanism is indeed responsible for it, then the LHC Run-2 should find: (i) a CP-odd scalar with mass below ∼2.3 TeV, (ii) new colored states with masses below ∼2 TeV, (iii) no statistically significant diboson events in the W±Z channel, (iv) events in the triboson channels W±W∓Z and ZZZ with invariant mass amounting to the mass of the CP-odd scalar