Compressed Text Indexes:From Theory to Practice!

A compressed full-text self-index represents a text in a compressed form and still answers queries efficiently. This technology represents a breakthrough over the text indexing techniques of the previous decade, whose indexes required several times the size of the text. Although it is relatively new, this technology has matured up to a point where theoretical research is giving way to practical developments. Nonetheless this requires significant programming skills, a deep engineering effort, and a strong algorithmic background to dig into the research results. To date only isolated implementations and focused comparisons of compressed indexes have been reported, and they missed a common API, which prevented their re-use or deployment within other applications. The goal of this paper is to fill this gap. First, we present the existing implementations of compressed indexes from a practitioner's point of view. Second, we introduce the Pizza&Chili site, which offers tuned implementations and a standardized API for the most successful compressed full-text self-indexes, together with effective testbeds and scripts for their automatic validation and test. Third, we show the results of our extensive experiments on these codes with the aim of demonstrating the practical relevance of this novel and exciting technology

Fitting and selecting scattering data

The main purpose of scattering experiments is to unveil the underlying structure of the colliding particles and their interaction. Typically one measures scattering observables (cross sections and polarizations) at discrete angles and energies and mutually consistent data may validate or falsify proposed theories or models. However, the accumulation of data from different laboratories while potentially improves the statistical significance it may sometimes generate mutually inconsistent data as a side-effect. Thus, some decision has to be made on what are the maximal amount of data which are mutually compatible. We show elastic $\pi N$ and $NN$ scattering as prominent examples where this selection is called for. We discuss how it can be done in a self-consistent manner invoking a principle of maximal consensus of the database and with the help of a sufficiently flexible model involving a minimal number of theoretical assumptions. In the NN case this has become possible with a combination of long distance field theoretical constraints at the hadronic level such as pion exchanges and electromagnetic effects and a coarse graining of the unknown interaction over the shortest de Broglie wavelength being probed in the scattering process.Comment: 7 pages, 5 figures, talk presented by ERA at XVII International Conference on Hadron Spectroscopy and Structure - Hadron2017, Salamanca, 25-29 September 201

Functional living biointerfaces to direct cell-material interaction

[EN] This thesis deals with the development of a living biointerface between synthetic substrates and living cells to engineer cell-material interactions for tissue engineering purposes. This living biointerface is made of Lactococcus lactis, a non-pathogenic lactic bacteria widely used as starter in the dairy industry and, recently, in the expression of heterologous proteins in applications such as oral vaccine delivery or membrane-bound expression of proteins. L. lactis has been engineered to display the III 7-10 fragment of the fibronectin fused to GFP as reporter protein. Fibronectin is a ubiquitous protein present in the extracellular matrix, a complex mesh of structural and adhesive proteins which serve as mechanical support and development niche for cells of a wide variety of tissues. This fragment contains two important sequences, RGD and PHSRN. RGD is an adhesive sequence that interacts with a wide range of integrins, membrane-bound receptors that play a role in cellular processes such as adhesion, migration, proliferation and differentiation. On the other hand, PHSRN binds synergistically with RGD to some integrins such as alpha-5-beta-1 and others, increasing the specificity of this interaction. Genetically engineered L. lactis has been thoroughly characterized to test its capabilities as a living interface. This strain was found to express the FNIII 7-10-GFP fragment covalently linked to the cell wall and biological activity and expression levels of this fragment was assessed with techniques such as Western blot, ELISA and immunofluorescence. Moreover, this strain still holds the ability to develop biofilms, communities of sessile, attached bacteria to abiotic surfaces which helps greatly in the generation of a stable monolayer of bacteria between synthetic substrates and mammalian cells. Mammalian cell behaviour in response to the expressed fibronectin fragment on L. lactis membrane was also assessed. Several cell lines were tested, such as Fn-/Fn- and NIH3T3 fibroblasts, C2C12 myoblasts and human bone-marrow derived mesenchymal cells. This living biointerface was found to trigger cell adhesion and FAK phosphorylation, a marker for intracellular integrin-mediated signalling in all of the tested cell lines. It also triggered myoblast-to-myotube differentiation on C2C12 cells. In hMSCs, the cell-wall exposed fibronectin fragment was found to enhance the phosphorylation of ERK1/2, a kinase involved in the MAPK pathway, which is deeply involved in a multitude of cellular processes related to differentiation, proliferation and migration. Nevertheless, this thesis is a proof of concept that this novel system can be further exploited to express almost any desired protein or small molecule to help in the development of new tissues from progenitor cells. These molecules can be either secreted in the medium or displayed in the membrane, and can also be constitutively expressed or in-demand, due to the great flexibility of L. lactis and the wide variety of expression systems available. This interface based on living bacteria establishes a new paradigm in surface functionalization for biomedical engineering applications.[ES] Esta tesis aborda el desarrollo de una biointerfase viviente entre materiales sintéticos y células vivas con el objetivo de dirigir la interacción célula-material en aplicaciones de ingeniería tisular. Esta biointerfase está compuesta de Lactococcus lactis, una bacteria láctica no patógena, ampliamente usada en la industria láctea como inóculo, y, recientemente, en la expresión heteróloga de proteínas para su uso como vacunas de administración oral o su expresión en membrana. L. lactis ha sido genéticamente modificado para expresar el fragmento III 7-10 de la fibronectina, unida a GFP como reporter. La fibronectina es una proteína presente de forma ubicua en la matriz extracelular, una compleja red de proteínas adhesivas y estructurales cuyo propósito es servir como soporte estructural y como nicho de desarrollo para diversos tejidos. Este fragmento contiene dos secuencias importantes, RGD y PHSRN. RGD es una secuencia adhesiva de unión que interacciona con una amplia variedad de integrinas, receptores de membrana que juegan muchos e importantes papeles en diferentes procesos celulares, como adhesión, proliferación, migración o diferenciación. Por otra parte, PHSRN se une a las integrinas de forma sinérgica con RGD facilitando aún más estos procesos y aumentando la especificidad de esta interacción. Esta cepa de L. lactis modificada ha sido ampliamente caracterizada para estudiar su idoneidad como interfaz funcional viviente. Se ha demostrado que L. lactis es capaz de expresar el fragmento FNIII7-10-GFP covalentemente anclado a la pared celular bacteriana, habiéndose caracterizado también su actividad biológica con técnicas como Western blot, ELISA e inmunofluorescencia. Esta cepa mantiene la capacidad de desarrollo de biofilms presente en la gran mayoría de microorganismos. Los biofilms son comunidades de bacterias sésiles adheridas a un sustrato que pueden ser usadas como interfase física entre células de mamífero y sustratos abióticos. También se ha estudiado la respuesta celular a la fibronectina expuesta en la membrana de L. lactis. Se estudiaron varias líneas celulares, como fibroblastos Fn-/Fn- y NIH3T3, mioblastos C2C12 y células mesenquimales humanas derivadas de médula ósea. Esta interfase viviente fue capaz de provocar respuesta celular en forma de adhesión en todas las líneas estudiadas, además de inducir diferenciación de mioblastos a miotubos en C2C12 y de provocar la fosforilación de FAK, un marcador de señalización celular mediada por integrinas. En células mesenquimales humanas se demostró la capacidad del fragmento de fibronectina expuesto para fosforilar ERK1/2, una kinasa perteneciente a la ruta de señalización MAPK, ruta que forma parte de muchos procesos celulares importantes como diferenciación, proliferación y migración. Pese a todo, esta tesis es sólo una prueba de concepto de un sistema que puede ser utilizado para expresar casi cualquier proteína o molécula pequeña deseada, que puede ser muy útil en el desarrollo de nuevos tejidos a partir de sus células progenitoras. Estas moléculas pueden ser secretadas en el medio o ancladas en la pared celular, de forma constitutiva o bajo demanda, debido a la flexibilidad y amplia variedad de sistemas de expresión disponibles para L. lactis. Esta biointerfase basada en bacterias vivas establece un nuevo paradigma en el campo de la funcionalización de superficies para aplicaciones de ingeniería biomédica.[CA] Aquesta tesi aborda el desenvolupament d'una interfase viva entre materials sintètics i cèl·lules vives amb l'objectiu de dirigir la interacció cèl·lula-material, per al seu ús en aplicacions d'enginyeria tissular. Aquesta interfase està composta de Lactococcus lactis, un bacteri làctic, no patogènic i àmpliament utilitzat en l'industria làctica com a inòcul, i, recentment, en l'expressió heteròloga de proteïnes per al seu ús com vacunes d'administració oral o per a la seva expressió en membrana. L. lactis ha sigut genèticament modificada per a expressar el fragment III7-10 de la fibronectina, unida a GFP com a reporter. La fibronectina és una proteïna present de forma ubiqua en la matriu extracel·lular, una complexa xarxa de proteïnes adhesives i estructurals que s'utilitzen com a suport estructural i com a nínxol de desenvolupament per a diversos teixits. Aquest fragment conté dos seqüències importants, RGD i PHSRN. RGD és una seqüència adhesiva d'unió a integrines, receptors de membrana que juguen molts i molt importants papers en diferents processos cel·lulars, com poden ser adhesió, proliferació, migració o diferenciació. Per altra banda, PHSRN s'uneix a les integrines de forma sinèrgica amb RGD facilitant encara més aquests processos i augmentant l'especificitat d'aquesta interacció. Aquesta modificació genètica de L. lactis ha estat àmpliament caracteritzada per provar les seves característiques com a interfase funcional vivent. S'ha demostrat que L. lactis és capaç d'expressar el fragment FNIII 7-10-GFP covalentment ancorat a la paret cel·lular bacteriana, havent-se caracteritzat també la seva activitat biològica amb tècniques com Western blot, ELISA i immunofluorescència. A més, aquest cep manté la capacitat de desenvolupament de biofilms, comunitats de bacteris sèssils adherits a un substrat que poden ser utilitzades com a interfase física entre cèl·lules de mamífer i substrats abiòtics. També s'ha estudiat la resposta cel·lular a la fibronectina expressada en la paret cel·lular de L. lactis. El estudi es va fer utilitzant diverses línies cel·lulars, com fibroblasts Fn-/Fn- i NIH3T3, mioblasts C2C12 i cèl·lules mesenquimals humanes derivades de medul·la òssia. Aquesta interfase vivent va ser capaç de provocar resposta cel·lular en forma d'adhesió a totes les línies estudiades, a més d'induir diferenciació de mioblasts a miotubs en C2C12 i de provocar la fosforilació de FAK, un marcador de senyalització cel·lular mediat per integrines, en les línies assajades. En cèl·lules mesenquimals humanes es va demostrar la capacitat del fragment de fibronectina exposat per fosforilar ERK1/2, una kinasa pertanyent a la ruta de senyalització MAPK, ruta que forma part de molts processos cel·lulars importants com diferenciació, proliferació i migració. Malgrat tot, aquesta tesi mostra només una prova de concepte d'un sistema que pot ser utilitzat per expressar gairebé qualsevol proteïna o molècula petita desitjada, que pot ser molt útil en el desenvolupament de nous teixits a partir de les seves cèl·lules progenitores. Aquestes molècules poden ser secretades en el medi o ancorades a la paret cel·lular, de manera constitutiva o sota demanda, a causa de la flexibilitat i àmplia varietat de sistemes d'expressió disponibles per L. lactis Aquesta biointerfase basada en bacteris vius estableix un nou paradigma en el camp de la funcionalització de superfícies per a aplicacions d'enginyería biomèdica.Rodrigo Navarro, A. (2015). Functional living biointerfaces to direct cell-material interaction [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/51461TESI

Microlensing events in the Galactic bulge

For the first time we detected microlensing events at zero latitude in the Galactic bulge using the VISTA Variables in the Via Lactea Survey (VVV) data. We have discovered a total sample of N = 630 events within an area covering 20.7 sq. deg. Using the near-IR color magnitude diagram we selected N = 291 red clump sources, allowing us to analyse the longitude dependence of microlensing across the central region of the Galactic plane. We thoroughly accounted for the photometric and sampling efficiency. The spatial distribution is homogeneous, with the number of events smoothly increasing toward the Galactic center. We find a slight asymmetry, with a larger number of events toward negative longitudes than positive longitudes, that is possibly related with the inclination of the bar along the line of sight. We also examined the timescale distribution which shows a mean on 17.4 +- 1.0 days for the whole sample, and 20.7 +- 1.0 for the Red Clump subsample.Comment: Proceedings of the Fifteenth Marcel Grossman Meeting on General Relativity Edited by Elia Battistelli, Robert T. Jantzen, and Remo Ruffini. 6 pages, 3 figures, to be published in Open access e-book proceedings World Scientific, Singapore, 201

Uncertainty quantification and falsification of Chiral Nuclear Potentials

Are chiral theories at present describing experimental NN scattering data satisfactorily ?. Will the chiral approach offer a framework where fitting and selecting the existing np and pp data can be done without theoretical bias ?. While predictive power in theoretical nuclear physics has been a major concern in the study of nuclear structure and reactions, the Effective Field Theory (EFT) based on chiral expansions has emerged after Weinberg as a model independent hierarchy for many body forces and much progress has been achieved over the last decades. We review some of the issues involved which point to being close to the solution, but also that work remains still to be done to validate the theory. We analyze several examples including zero energy NN scattering and perturbative counterterm -- free peripheral scattering where one would expect these methods to work best and unveil relevant systematic discrepancies when a fair comparison to the Granada-2013 NN-database and partial wave analysis (PWA) based on coarse graining the interaction is undertaken.Comment: Prepared for the special issue of "The tower of effective (field) theories and the emergence of nuclear phenomena"; 20 pages, 7 figure

Economic And Logistical Viability of Production of Freshwater Angelfish (Pterophyllum Scalare)

The Freshwater Angelfish stands out for being one of the most beautiful, best-selling and also most popular ornamental fish of tropical waters. Its cultivation is concentrated in the southeastern and southern regions of Brazil, so reproduction of this species in other areas can become a profitable venture. The present study analyzed the economic viability of the cultivation of the Freshwater Angelfish, Pterophyllum scalare, in a water recirculation system. To measure the market demand, an interview was conducted with the main tenants in the industry, adding to the estimate. The profitability of the venture was 2,65% in the first year and 11,95% in the second to the tenth year and the payback rate was 38 months or 3 years and 2 months. Small-scale farming proved to be economically viable, presenting attractive profitability indicators compared to other aquaculture enterprises.

Tropical Aquaponic Production of Medicinal Plants in Association with Goldfish

Aquaponics is an emerging technology that synergistically combines aquaculture and hydroponic production through nutrient cycling and water recycling. As aquaponics grows exponentially, studies that evaluate the technique by testing different species in these systems make this choice fundamental to result in a high productivity and profitability. Ornamental fish, as well as medicinal plants, are interesting options for a more in-depth analysis of aquaponic systems. In this context, the objective was to analyze the performance of four plant species: boldu chilanum, Peumus boldus; peppermint, Mentha x piperita; Brazilian joyweed, Alternanthera brasiliana; and oregano, Origanum vulgare, as well as the growth of goldfish, Carassius auratus, and physicochemical aspects of water quality in identical aquaponic systems installed in a greenhouse during 91 days of cultivation. The experimental design consisted in four treatments and four replications, using in all treatments a density of 21 fish.310L and four seedlings, in cuttings, of each plant species studied. The vegetable cultivation systems were composed of expanded clay sediments in a 0.25m² planters, using a density of 16 plants.m², repeated, each treatment, in four aquaponic systems, totaling 16 aquaponic systems analyzed. The results showed that, for the parameters of weight and height, of the four plant species studied, only oregano did not develop as expected, while boldu chilanum, peppermint and Brazilian joyweed showed a representative increase in the analyzed parameters. The goldfish also showed representative increase for weight, total and standard length in all treatments. The water quality parameters analyzed did not showed differences between treatments and were within the range recommended by reference authors, as well as for the well-being of the goldfish. The systems have demonstrated efficiency in vegetative and animal growth, and can help to add value to products from aquaponics, corroborating the evolution of technology.A aquaponia é uma tecnologia emergente que alia sinergicamente a produção aquícola e hidropônica, através da ciclagem de nutrientes e reciclagem de água. Como a aquaponia cresce exponencialmente, estudos que avaliam a técnica testando diferentes espécies nesses sistemas torna essa escolha fundamental para resultar em alta produtividade e lucratividade. Os peixes ornamentais, assim como as plantas medicinais são opções interessantes para uma análise mais aprofundada nos sistemas aquapônicos. Objetivou-se, nesse contexto, analisar o desempenho de quatro espécies vegetais: boldo do Chile, Peumus boldus; menta, Mentha x piperita; terramicina, Alternanthera brasiliana; e orégano, Origanum vulgare, assim como o crescimento de exemplares de goldfish, Carassius auratus, e aspectos físico-químicos da qualidade de água em sistemas aquapônicos idênticos instalados em estufa durante 91 dias de cultivo. O delineamento experimental foi composto de quatro tratamentos e quatro repetições, utilizando em todos os tratamentos densidade de 21 peixes.310L e quatro mudas, em estaca, de cada espécie vegetal estudada. Os sistemas de cultivo vegetal foram compostos por sedimentos de argila expandida em jardineiras de 0,25m², utilizando densidade de 16 plantas.m², repetidos, cada tratamento, em quatro sistemas aquapônicos, totalizando 16 sistemas aquapônicos analisados. Os resultados demonstraram que, para os parâmetros de peso e altura, das quatro espécies vegetais estudadas, apenas o orégano não se desenvolveu como o esperado, enquanto o boldo do Chile, menta e terramicina, apresentaram aumento representativo dos parâmetros analisados. O goldfish também demonstrou aumento significativo para o peso, comprimento total e comprimento padrão em todos os tratamentos. Os parâmetros de qualidade de água analisados não demonstraram diferenças estatísticas entre os tratamentos e estiveram dentro da faixa preconizada por autores de referência, assim como para o bem-estar dos goldfish. Os sistemas demonstraram eficiência no crescimento vegetativo e animal, podendo auxiliar a agregação de valor dos produtos oriundos da aquaponia corroborando com a evolução da tecnologia

Las técnicas sobre resoluciones de conflictos en educación secundaria: legislación y libros de texto de lengua y literatura españolas

En este artículo examinamos la legislación en vigor sobre educación secundaria en las materias de lengua y literatura españolas, para observar la importancia que concede a la resolución de conflictos mediante el diálogo. A pesar de que la resolución de conflictos figura entre los objetivos fundamentales y a pesar del papel que tiene la comunicación en los contextos y las situaciones en los que surgen desavenencias, se trata de un tema que no adquiere el desarrollo adecuado en la sección de lengua y literatura españolas, ni tampoco en los libros de texto. Llamamos la atención sobre este desajuste y estimamos que la explicación se encuentra, quizás, en el desconocimiento que existe sobre los avances realizados en las mediaciones y en las resoluciones de conflictos. Por este motivo, proporcionamos una serie de ejemplos que muestran cómo podemos trabajar en las clases de lengua y literatura españolas determinados aspectos lingüísticos, realizar prácticas de comunicación oral e instruir a los alumnos en estrategias comunicativas eficaces para solucionar conflictos de acuerdo con lo establecido en las normas legales.In this paper, we examine the legislation in force for secondary education in the subjects of Spanish language and literature, in order to observe the importance that it grants to the resolution of conflicts through dialogue. In spite of the fact that the resolution of conflicts appears among the fundamental aims and in spite of the role that the communication has in the contexts and situations in that disagreements arise, this topic have not an adequate development in the subject of Spanish language and literature, or in textbooks. We call attention on this mismatch, and we think that the explanation lies, probably, in the ignorance that exists on the advances realized in mediation and conflict resolutions. For this reason, we provide a number of examples that show how we can work some linguistic aspects on classes of Spanish language and literature, to practice oral communication and to instruct students in effective communicative strategies to resolve conflicts in accordance with the established in the legal procedure.Dans cet article nous examinons la législation en vigueur sur l´éducation secondaire dans les matières de Langue et littérature espagnoles, pour observer l´importance qu´elle accorde à la résolution de conflits moyennant le dialogue. Malgré le fait que la résolution de conflits figure parmi les objectifs fondamentaux et malgré le rôle joué par la communication dans les contextes et les situations dans lesquels un désaccord surgit, il s´agit d´un sujet qui n´acquiert pas le développement approprié dans la section de Langue et littérature espagnoles, et non plus dans les manuels scolaires. Nous attirons l´attention sur ce désajustement et nous estimons que l´explication se trouve, peut-être, dans l´ignorance qui existe sur les progrès réalisés dans les médiations et dans les résolutions de conflits. Pour ce motif, nous fournissons une série d´exemples qui montrent comment nous pouvons travailler dans les classes de Langue et littérature espagnoles certains aspects linguistiques, réaliser des pratiques de communication orale et instruire les élèves dans des stratégies communicatives efficaces pour résoudre des conflits conformément aux normes légales