Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets

Since its first description, PCV2 has emerged as one of the most economically relevant diseases for the swine industry. Despite the introduction of vaccines effective in controlling clinical syndromes, PCV2 spread was not prevented and some potential evidences of vaccine immuno escape have recently been reported (“Complete genome sequence of a novel porcine circovirus type 2b variant present in cases of vaccine failures in the United States” (Xiao and Halbur, 2012) [1], “Genetic and antigenic characterization of a newly emerging porcine circovirus type 2b mutant first isolated in cases of vaccine failure in Korea” (Seo et al., 2014) [2]). In this article, we used a collection of PCV2 full genomes, provided in the present manuscript, and several phylogentic, phylodynamic and bioinformatic methods to investigate different aspects of PCV2 epidemiology, history and evolution (more thoroughly described in “PHYLODYNAMIC ANALYSIS of PORCINE CIRCOVIRUS TYPE 2 REVEALS GLOBAL WAVES of EMERGING GENOTYPES and the CIRCULATION of RECOMBINANT FORMS”[3]). The methodological approaches used to consistently detect recombiantion events and estimate population dymanics and spreading patterns of rapidly evolving ssDNA viruses are herein reported. Programs used are described and original scripts have been provided. Ensembled databases used are also made available. These consist of a broad collection of complete genome sequences (i.e. 843 sequences; 63 complete genomes of PCV2a, 310 of PCV2b, 4 of PCV2c, 217 of PCV2d, 64 of CRF01, 140 of CRF02 and 45 of CRF03.), divided in differnt ORF (i.e. ORF1, ORF2 and intergenic regions), of PCV2 genotypes and major Circulating Recombinat Forms (CRF) properly annotated with respective collection data and country. Globally, all of these data can be used as a starting point for further studies and for classification purpose

Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms

Since the first description of Porcine circovirus type 2 (PCV2), four genotypes (PCV2a, PCV2b, PCV2c and PCV2d) have been recognized and three of them have been shown to exhibit worldwide distribution. Here, the population dynamics of PCV2 has been reconstructed over time and the factors that have shaped its evolution determined. The results obtained confirm that PCV2 originated approximately at the beginning of the 20th century. The most recent common ancestor of genotypes PCV2a, PCV2b, PCV2c and PCV2d circulated in the 1950s, 1980s, 1960s and 1950s, respectively, and the population sizes of the individual genotypes remained low until the mid 90s, coinciding with the identification of PCV2 as a major pathogen of the pig industry. The population dynamics of PCV2 have been characterized by the appearance of periodic waves of distinct genotypes that, after an initial rise, spread following major swine commercial routes and were then superseded by subsequent emerging genotypes. Various recombinant forms displayed comparable population dynamics and spreading routes to those of major genotypes, suggesting that recombinant strains are able to compete with parental ones. The capsid gene is subjected to immune selection and evasion of the host immune response seems to be a major force for the emergence and spread of new genotypes. In contrast, the evolution of other genes appears to be constrained by the particular genomic organization of PCV2. In summary, obtained results suggest that changes in farming strategies, international trade, host population immunity, recombination and the constraints imposed by genome organization have all played a major role in the evolutionary dynamics of PCV2

The question of obedience and rebellion in Elizabeth Gaskell’s North and south

Treballs Finals del Grau d'Estudis Anglesos, Facultat de Filologia, Universitat de Barcelona, Curs: 2019-2020, Tutora: Ana Moya Gutiérrez[eng] The concept of obedience and, subsequently, of disobedience has been a common attraction for the human being throughout the centuries. Whereas the first concept has been always related to order and progress, the latter has been usually associated to chaos. Yet, without rebellion, the world we live in nowadays would not exist. In the Victorian Period, this topic was not at all ignored: writers, painters, philosophers and politicians worked on such a human matter, attracted by all the questions and contradictions it posed. In this paper, I will focus on how Elizabeth Gaskell explores the politics of obedience and disobedience in North and South (1855), one of her best known works, in terms of gender and class. To do this, the novel’s historical context regarding women, the working class and also her religion, which is basic in order to understand her writing, will be taken very much into account as well. Keywords: Victorian Period, Gaskell, obedience, gender, class[spa] El concepte d’obediència i, conseqüentment, de desobediència ha estat sovint una atracció pel ser humà a través dels segles. Mentre que el primer concepte sempre ha estat relacionat amb l’ordre i el progrés, l’últim s’ha associat més aviat amb el caos. D’altra banda, sense rebel·lió, el món que coneixem avui no existiria. Durant l’època victoriana, aquest tema tampoc no va ser passat per alt: pintors, escriptors, filòsofs i polítics van examinar aquest afer tant humà, atrets per totes les preguntes i contradiccions que ofereix. En aquest treball, el principal objectiu és veure com l’Elizabeth Gaskell explora la qüestió de l’obediència i desobediència en una de les seves novel·les més reconegudes, North and South (1855), especialment en termes de gènere i classe. Per fer-ho, el context històric de la novel·la pel que fa a la situació de les dones, la classe treballadora i la religió de la mateixa Gaskell, bàsica per entendre la seva producció literària, també es tindran en compte

Spike and wave identification algorithm for the detection of epileptic seizures

Els senyals electroencefalogràfics (EEG) son comunament utilitzats per investigar les funcions corticals. Una aplicació clínica rellevant és l'estudi de l'epilèpsia, una patologia del sistema nerviós central causada pel mal funcionament de neurones a l'escorça cerebral. Una senyal indicativa d'epilèpsia és la forma d’ona denominada com “spike-and-wave”. És un patró visible a l’EEG, l’anàlisi del qual permet obtenir una eina capaç de detectar convulsions de manera eficient, donant com a resultat un mètode de diagnòstic d’epilèpsia. Per tant, l'objectiu de l'estudi és obtenir un algorisme òptim i automatitzat per tal d'identificar els “spike-and-waves” a l'EEG de pacients epilèptics. S’estudia des d’una millora d'un model anterior implementat a Matlab, amb una selecció més precisa de prototips i nombroses proves basades en una àmplia base de dades. Els resultats s'han comparat amb un grup control i amb pacients amb trastorn per dèficit d'atenció i hiperactivitat (TDAH) per tal d'entendre com aquestes formes d’ona són característiques dels pacients epilèptics, però també poden aparèixer en subjectes amb TDAH, amb menys freqüència. A més, s'ha estudiat un mètode de prevenció; intentant trobar un llindar per alarmar el metge per tal de prevenir la crisi epilèptica, en funció del nombre i la freqüència de patrons detectats. L'estudi consta d'una breu introducció als conceptes bàsics, una descripció de la base de dades i del mètode utilitzat i dels resultats aconseguits, així com una discussió i conclusions posteriors de l'anàlisi realitzat.Una señal electroencefalográfica (EEG) se utiliza para investigar las funciones corticales. Una aplicación clínica relevante es el estudio de la epilepsia, una patología del sistema nervioso central causada por el mal funcionamiento de las neuronas de la corteza cerebral. Un evento patológico indicativo de epilepsia es el pico y onda, denominado como “spike-and-wave”. Se trata de patrones visibles en el EEG, que pueden ser analizados para obtener una herramienta capaz de detectarlos de manera eficiente, dando como resultado un método de diagnóstico de epilepsia y detección de convulsiones. Por tanto, el objetivo del estudio es obtener un algoritmo óptimo y automatizado para identificar picos y ondas en el EEG de pacientes epilépticos. El enfoque es a través de una mejora de un modelo anterior implementado en Matlab, con una selección más precisa de prototipos y numerosas pruebas basadas en una grande base de datos. Los resultados se han comparado con un grupo de control y con pacientes con trastorno por déficit de atención y hiperactividad (TDAH) para comprender cómo los picos y ondas son característicos de los pacientes epilépticos pero también pueden aparecer en sujetos con TDAH, con menos frecuencia. Además, se ha estudiado un método de prevención; tratando de encontrar un umbral para avisar al médico con el fin de prevenir una crisis epiléptica, en función del número y la frecuencia de los patrones detectados. El estudio consta de una breve introducción a los conceptos básicos, una descripción de la base de datos y el método utilizado y los resultados obtenidos, así como una discusión y conclusiones del análisis realizado.An electroencephalographic signal (EEG) is used in order to investigate cortical functions. A relevant clinical application is the study of epilepsy, a pathology in the central nervous system caused by the cerebral cortex neuron’s malfunction. A pathological event indicative of epilepsy is the spike-and-wave. These are visible patterns seen in the EEG which can be analyzed in order to obtain a tool capable of efficiently detecting them, resulting in a method of diagnosis of epilepsy and detection of seizures. Therefore, the objective of the study is to obtain an optimal and automated algorithm in order to identify spike-and-waves in the EEG of epileptic patients. The approach is through an improvement of a previous model implemented in Matlab, with a more precise selection of spike-and-wave prototypes and numerous tests based on a large dataset. The results have been compared to a control group and to recordings of attention deficit hyperactivity disorder (ADHD) patients in order to understand how spike-and-waves are characteristic of epileptic patients but can also appear in ADHD subjects, with less frequency. Moreover, a prevention method has been studied; attempting to find a threshold to alarm the doctor in order to prevent epileptic crisis, based on the number and frequency of firings. The study consists of a brief introduction to the basic concepts, a description of the dataset and the method used and the results achieved, as well as further discussion and conclusions to the analysis made throughout the study.Outgoin

Low levels of diversity among genomes of Porcine circovirus type 1 (PCV1) points to differential adaptive selection between Porcine circoviruses

AbstractSeveral features related with the evolutionary patterns among all the PCV1 genomes available at GenBank have been analyzed in the present work (diversity, number of genotypes, recombination, saturation, selection, evolutionary rate). The reported results point to low levels of nucleotide and amino acid diversity, low number of positively selected codons and a slow evolution rate. Compared with the other species of the Circoviridae family, the diversity is the lowest reported. This can be related with the fact that PCV1 is the single non-pathogenic member of the family. Overall, differential levels of adaptive evolution between PCV1 and PCV2 may explain the different diversity levels, and the different evolutionary and selection rates observed

Porcine Circovirus 2 Genotypes, Immunity and Vaccines: Multiple Genotypes but One Single Serotype

Identified for the first time in the 1990s, Porcine circovirus 2 (PCV-2) should not be considered an emerging virus anymore. Nevertheless, many aspects of its biology and epidemiology are still controversial. Particularly, its high evolutionary rate has caused the emergence of several variants and genotypes, alternating on the worldwide proscenium. The biological and practical implications of such heterogenicity are unfortunately largely unknown. The effectiveness of currently available vaccines against new genotypes that have emerged over time has been the topic of an intense debate and often inconclusive or contradictory results between experimental, field, and epidemiological studies have been gathered. The challenge in establishing an effective PCV-2 disease model, the peculiarities in experimental design and settings and the strains involved could justify the observed differences. The present work aims to summarize and critically review the available knowledge on PCV-2 genetic heterogeneity, immunity, and vaccine efficacy, organizing and harmonizing the available data from different sources, shedding light on this complex field and highlighting current knowledge gaps and future perspectives. So far, all vaccines in the market have shown great efficacy in reducing clinical signs associated to diseases caused by PCV-2, independently of the genotype present in the farm. Moreover, experimental data demonstrated the cross-protection of PCV-2a vaccines against the most widespread genotypes (PCV-2a, PCV-2b, and PCV-2d). Therefore, despite the significant number of genotypes described/proposed (PCV-2a to PCV-2i), it seems one single PCV-2 serotype would exist so far.info:eu-repo/semantics/publishedVersio

Arte gráfico y comunicación visual

The “Gutenberg effect” was, in the Books Arts, the fusion of Literature and Graphic Art of illustrators and engravers of the period, and the first technical media for visual communication and social spreading of Culture.El “efecto Gutenberg” constituyó la fusión de la literatura en las artes del libro, con el arte gráfico de los ilustradores y grabadores de la época, y el primer medio técnico de comunicación visual y difusión social de la cultura

Creatividad, invención e innovación

La creatividad es una aptitud de la inteligencia y de la imaginación en la que se incluye la capacidad de crear. La creatividad no es una creación libre, lúdica, gratuita: está supeditada a un brief o pliego de condiciones técnicas, y éste a su vez lo está a unos objetivos predeterminados por alguien que es ajeno a lo que será creado y a su creador. Para la invención, la creación y el descubrimiento no hay recetas, porque su campo es el de la imaginación y la fantasía. No es lo mismo para la creatividad.Creativity is a skill our intelligence and imagination provide in order to create something new. Creativity is not a random nor ludic activity: it depends on a brief that depends, at the same time, on certain aims someone claims outside the proper proccess of creation. There are no straight solutions for creation nor for invention since they belong to the field of fantasy and imagination. It is not the same for creativity