Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

Reaching the unreached: An initiative to bridge the gap between the gap by active role of management institutes/schools

There are large numbers of business communities in India which neither had any formal education nor they took any professional training but still they contribute in successful business formation. Their presence can be felt in all areas of business. Still there is a big professional gap between the educational institutes, specially the B-Schools and this independent business community. With the help of this paper an effort is made to develop a Two-Way learning relationship for the mutual benefit of both entities. It will also highlight the role of an educational institute beyond academics for the well being of society. This may lead to derive and develop the exchange of innovative business ideas and framing the suitable policies for long term sustainability in today´s competitive arena. The study conducted by researcher with a sample size of 100 which includes a mix of well known academic professionals, MBA students and non academic business professionals has revealed that there is a need of an exchange program for the mutual benefits. There exists a big professional gap in this area which can be filled with the active and effective initiative by management institutes. An effort is made in this paper to highlight this gap and to suggest some framework to bridge the gap

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Sensitization profiles and cross-reactivity among plant allergens. Molecular mechanisms of food allergy development and the role of enhancers

La prevalencia de las alergias está aumentando desde mediados del siglo XX, y se estima que actualmente afectan a alrededor del 2-8 % de la población, pero las causas de este aumento aún no están claras. Encontrar el origen del mecanismo por el cual una proteína inofensiva se convierte en capaz de inducir una respuesta alérgica es de vital importancia para prevenir y tratar estas enfermedades. Aunque la caracterización de alérgenos relevantes ha ayudado a mejorar el manejo clínico y a aclarar los mecanismos básicos de las reacciones alérgicas, todavía queda un largo camino para establecer el origen de la alergenicidad y reactividad cruzada. El objetivo de esta tesis ha sido caracterizar las bases moleculares de la alergenicidad tomando como modelo dos familias de panalergenos (proteínas de transferencia de lípidos –LTPs- y taumatinas –TLPs-) y estudiando los mecanismos que median la sensibilización y la reactividad cruzada para mejorar tanto el diagnóstico como el tratamiento de la alergia. Para ello, se llevaron a cabo dos estrategias: estudiar la reactividad cruzada de miembros de familias de panalérgenos; y estudiar moléculas-co-adyuvantes que pudieran favorecer la capacidad alergénica de dichas proteínas. Para estudiar la reactividad cruzada entre miembros de la misma familia de proteínas, se seleccionaron LTPs y TLPs, descritas como alergenos, tomando como modelo la alergia a frutas. Por otra parte, se estudiaron los perfiles de sensibilización a alérgenos de trigo relacionados con el asma del panadero, la enfermedad ocupacional más relevante de origen alérgico. Estos estudios se llevaron a cabo estandarizando ensayos tipo microarrays con alérgenos y analizando los resultados por la teoría de grafos. En relación al estudiar moléculas-co-adyuvantes que pudieran favorecer la capacidad alergénica de dichas proteínas, se llevaron a cabo estudios sobre la interacción de los alérgenos alimentarios con células del sistema inmune humano y murino y el epitelio de las mucosas, analizando la importancia de moléculas co-transportadas con los alérgenos en el desarrollo de una respuesta Th2. Para ello, Pru p 3(LTP y alérgeno principal del melocotón) se selección como modelo para llevarlo a cabo. Por otra parte, se analizó el papel de moléculas activadoras del sistema inmune producidas por patógenos en la inducción de alergias alimentarias seleccionando el modelo kiwi-alternaria, y el papel de Alt a 1, alérgeno mayor de dicho hongo, en la sensibilización a Act d 2, alérgeno mayor de kiwi. En resumen, el presente trabajo presenta una investigación innovadora aportando resultados de gran utilidad tanto para la mejora del diagnóstico como para nuevas investigaciones sobre la alergia y el esclarecimiento final de los mecanismos que caracterizan esta enfermedad. ABSTRACT Allergies are increasing their prevalence from mid twentieth century, and they are currently estimated to affect around 2-8% of the population but the underlying causes of this increase remain still elusive. The understanding of the mechanism by which a harmless protein becomes capable of inducing an allergic response provides us the basis to prevent and treat these diseases. Although the characterization of relevant allergens has led to improved clinical management and has helped to clarify the basic mechanisms of allergic reactions, it seems justified in aspiring to molecularly dissecting these allergens to establish the structural basis of their allergenicity and cross-reactivity. The aim of this thesis was to characterize the molecular basis of the allergenicity of model proteins belonging to different families (Lipid Transfer Proteins –LTPs-, and Thaumatin-like Proteins –TLPs-) in order to identify mechanisms that mediate sensitization and cross reactivity for developing new strategies in the management of allergy, both diagnosis and treatment, in the near future. With this purpose, two strategies have been conducted: studies of cross-reactivity among panallergen families and molecular studies of the contribution of cofactors in the induction of the allergic response by these panallergens. Following the first strategy, we studied the cross-reactivity among members of two plant panallergens (LTPs , Lipid Transfer Proteins , and TLPs , Thaumatin-like Proteins) using the peach allergy as a model. Similarly, we characterized the sensitization profiles to wheat allergens in baker's asthma development, the most relevant occupational disease. These studies were performed using allergen microarrays and the graph theory for analyzing the results. Regarding the second approach, we analyzed the interaction of plant allergens with immune and epithelial cells. To perform these studies , we examined the importance of ligands and co-transported molecules of plant allergens in the development of Th2 responses. To this end, Pru p 3, nsLTP (non-specific Lipid Transfer Protein) and peach major allergen, was selected as a model to investigate its interaction with cells of the human and murine immune systems as well as with the intestinal epithelium and the contribution of its ligand in inducing an allergic response was studied. Moreover, we analyzed the role of pathogen associated molecules in the induction of food allergy. For that, we selected the kiwi- alternaria system as a model and the role of Alt a 1 , major allergen of the fungus, in the development of Act d 2-sensitization was studied. In summary, this work presents an innovative research providing useful results for improving diagnosis and leading to further research on allergy and the final clarification of the mechanisms that characterize this disease.

Considering cycling for commuting : the role of mode familiarity : an exploration on the (circular) relation between cycling behaviours and attitudes toward cycling in Vitoria-Gasteiz, Spain

¿La gente utiliza la bicicleta porque les gusta? ¿O es el propio hecho de usarla la razón por la que les gusta hacerlo? ¿O es una combinación de las dos? Este tipo de preguntas reflejan un problema que se puede llamar ‘el círculo de la consideración de la bicicleta’: para poder considerar el uso de la bicicleta en el conjunto de posibles opciones a escoger, un individuo tiene que tener creencias positivas sobre ella, sobre todo en el caso de ‘contextos de bajo uso’. Pero parece poco probable que se formen creencias positivas cuando hay bajos niveles de familiaridad al modo, es decir, con un bajo conocimiento de sus características, su funcionamiento y del imaginario asociado; al mismo tiempo, la familiaridad irá alcanzando niveles más altos conforme aumente el tiempo y la intensidad con la que se utilice la bicicleta a lo largo de la vida de los individuos. El problema parece un circulo recursivo huevo-gallina, ya que es difícil que alguien considere el usar la bicicleta en lugares donde su uso es una práctica poco extendida. En estos lugares, y dentro del conglomerado actual de tecnologías, infraestructuras, reglas, prácticas de los usuarios y preferencias culturales que se han desarrollado alrededor del automóvil (el actual "sistema socio-técnico de la movilidad urbana", Urry 2004; Geels 2005, 2012) usar la bicicleta es considerado por la mayoría como algo difícil, inseguro, y anormal. Como consecuencia, los procesos de aumento de familiaridad con la bicicleta permanecen inactivos. La tesis asume la familiaridad como una fuente de información e influencia sobre las creencias positivas sobre la bicicleta. En ‘contextos de bajo uso’, sin familiaridad al uso de la bicicleta, estas creencias sólo pueden surgir de ciertos rasgos personales (afecto, valores, identidades, voluntad, etc.). Tal como han evidenciado investigaciones recientes, en estos contextos la posibilidad de considerar el uso de la bicicleta (y su eventual adopción), se circunscribe principalmente a los ‘entusiastas’, a los que están dispuestos a “ir contra corriente” (Horton & Parkin 2012), limitando el alcance de las políticas de promoción. La investigación llevada a cabo en esta tesis ofrece un nuevo enfoque al problema del ‘círculo de la consideración de la bicicleta’. Para ello, plantea un modelo en el que se introduce a la familiaridad como un constructo que media entre el comportamiento final –qué modo de transporte elige el individuo– y el conjunto de constructos psicosociales que preceden la elección modal (creencias y actitudes). La familiaridad al uso de la bicicleta se concibe como una medida de la intensidad relativa del uso de una bicicleta, real y percibida (basándose en Diana & Mokhtarian 2009) que puede formarse de manera distinta según sus fines (utilitarios o no utilitarios). El constructo familiaridad con el modo bicicleta está relacionado con la cantidad de tiempo, la intensidad y la regularidad con la que un individuo ha hecho uso de la bicicleta a lo largo de su vida. La familiaridad se concibe así como una condición que permite definir adecuadamente el contexto en el que se toman las decisiones modales de los individuos, en línea con investigaciones que postulan patrones de causalidad alternativos entre los procesos cognitivos de elección y los comportamientos modales (Tardif 1977; Dobson et al. 1978; Golob et al. 1979; Golob 2001; Schwanen et al. 2012; Diana et al. 2009; Vij & Walker 2014). De este modo se plantea que el esquema unidireccional actitudesconductas podría no ser completamente valido en el caso de la consideración de la bicicleta, explorando la hipótesis que sean las propias conductas a influenciar la formación de las actitudes. En esta tesis, el constructo de familiaridad se articula teórica y metodológicamente, y se emplea un instrumento de diseño transversal para contrastarlo. Los resultados de una encuesta telefónica a una muestra representativa de 736 personas en la ciudad española de Vitoria-Gasteiz proveen evidencias que sugieren –aunque de forma preliminar– que la familiaridad juega un papel de mediadora en la relación entre la utilización de la bicicleta y la formación de las creencias y actitudes hacia el su uso. La tesis emplea mediciones para cada individuo con respecto tanto a su consideración como a su familiaridad al uso de la bicicleta. Éstas mediciones se definen haciendo uso del análisis factorial exploratorio (AFE). Por un lado, el AFE arroja una estructura del constructo ‘consideración’ formada por cuatro factores, tres de ellos asociados con elementos positivos y uno con elementos negativos: (1) de cómo el uso de la bicicleta se considera verde e inteligente (G&S); (2) sobre su carácter agradable y adecuado (P&S); (3) sobre su eficacia como modo de transporte para ir al trabajo (E); y (4) sobre los principales inconvenientes de su uso, es decir, las dificultades implícitas (sudoración y estar expuestos a las inclemencias del tiempo) y la sensación de inseguridad que genera (sentirse en riesgo de accidentes y estresarse por el tráfico) (D&T). Por otro lado, la familiaridad al uso de la bicicleta se mide en dos distintas variables ordinales (según se base en el uso utilitario o no utilitario). Como resultado, se puede hablar de que cada individuo se encuentra en una de las siguientes cuatro etapas en orden creciente hacia una familiaridad completa al modo: no familiarizados; apenas familiarizados; moderadamente familiarizados; totalmente familiarizados. El análisis de los datos de los cuatro grupos de sujetos de la muestra, –definidos de acuerdo con cada una de las cuatro etapas de familiaridad definidas– ha evidenciado la existencia de diferencias intergrupo estadísticamente significativas, especialmente para la medida relacionada con el uso utilitario. Asimismo, las personas en los niveles inferiores de familiaridad tienen una consideración menor de los aspectos positivos de la bicicleta y por el contrario presentan preocupaciones mayores hacia las características negativas respecto a aquellas personas que están más familiarizados en el uso utilitario. El uso, aunque esporádico, de una bicicleta para fines utilitarios (ir de compras, hacer recados, etc.), a diferencia de no usarla en absoluto, aparece asociado a unas puntuaciones significativamente más altas en los tres factores positivos (G&S, E, P&S), mientras que parece estar asociado a puntuaciones significativamente más bajas en el factor relacionado con las características negativas (D&U). Aparecen resultados similares cuando se compara un uso moderado, con uno esporádico, sobre todo con respecto a la consideración de las características negativas. Los resultados de esta tesis están en línea con la literatura anterior que se ha basado en variables similares (por ejemplo, de Geus et al. 2008; Stinson & Bhat 2003, 2004; Hunt & Abraham 2006; y van Bekkum et al. 2011a, entre otros), pero en este estudio las diferencias se observan en un contexto de bajo uso y se derivan de un análisis de toda la población de personas que se desplazan a su lugar de trabajo o estudio, lo cual eleva la fiabilidad de los resultados. La posibilidad de que unos niveles más altos de uso de la bicicleta para fines utilitarios puedan llevar a niveles más positivos de su consideración abre el camino a implicaciones teóricas y de políticas que se discuten en la tesis. Con estos resultados se argumenta que el enfoque convencional basado en el cambio de actitudes puede no ser el único y prioritario para lograr cambios a la hora de fomentar el uso de la bicicleta. Los resultados apuntan al potencial de otros esquemas de causalidad, basados en patrones de influencia más descentrados y distribuidos, y que adopten una mirada más positiva hacia los hábitos de transporte, conceptualizándolos como “inteligencia encarnada y pre-reflexiva” (Schwanen et al. 2012). Tales esquemas conducen a un enfoque más práctico para la promoción del uso de la bicicleta, con estrategias que podrían basarse en acciones de ‘degustación’ de su uso o de mayor ‘exposición’ a su uso. Is the fact that people like cycling the reason for them to cycle? Or is the fact that they do cycle the reason for them to like cycling? Or is a combination of the two? This kind of questions reflect a problem that can be called ‘the cycle of cycling consideration’: in order to consider cycling in the set of possible options to be chosen, an individual needs to have positive beliefs about it, especially in the case of ‘low-cycling contexts’. However, positive beliefs seem unlikely to be formed with low levels of mode familiarity, say, with a low acquaintance with mode features, functioning and images; at the same time, higher levels of familiarity are likely to be reached if cycling is practised over relative threshold levels of intensities and extensively across individual life courses. The problem looks like a chicken-egg recursive cycle, since the latter condition is hardly met in places where cycling is little practised. In fact, inside the current conglomerate of technologies, infrastructures, regulations, user practices, cultural preferences that have grown around the automobile (the current “socio-technical system of urban mobility”, Urry 2004; Geels 2005, 2012) cycling is commonly considered as difficult, unsafe, and abnormal. Consequently, the processes of familiarity forming remain disabled, and, as a result, beliefs cannot rely on mode familiarity as a source of information and influence. Without cycling familiarity, origins of positive beliefs are supposed to rely only on personal traits (affect, values, identities, willingness, etc.), which, in low-cycling contexts, confine the possibility of cycling consideration (and eventual adoption) mainly to ‘cycling enthusiasts’ who are willing to “go against the grain” (Horton & Parkin 2012), as it results from previous research. New research conducted by author provides theoretical insights for a different approach of the cycling consideration problem in which the presence of the new construct of cycling familiarity is hypothesised in the relationship between mode choice behaviour and the set of psychosocial constructs that are supposed to precede it (beliefs and attitudes). Cycling familiarity is conceived as a measure of the real and the perceived relative intensity of use of a bicycle (building upon Diana & Mokhtarian 2009) which may be differently formed for utilitarian or non-utilitarian purposes. The construct is assumed to be related to the amount of time, the intensity and the regularity an individual spends in using a bicycle for the two distinct categories of purposes, gaining in this way a certain level of acquaintance with the mode. Familiarity with a mode of transport is conceived as an enabling condition to properly define the decision-making context in which individual travel mode choices are taken, in line with rather disperse research efforts postulating inverse relationships between mode behaviours and mode choices (Tardiff 1977; Dobson et al. 1978; Golob et al. 1979; Golob 2001; Schwanen et al. 2012; Diana et al. 2009; Vij & Walker 2014). The new construct is built theoretically and methodologically, and a cross-sectional design instrument is employed. Results from a telephone survey in a representative sample of 736 commuters in the Spanish city of Vitoria-Gasteiz, provide suggestive –although preliminary– evidence on the role of mode familiarity as a mediator in the relationship between cycling use and the formation of beliefs and attitudes toward cycling. Measures of both cycling consideration and cycling familiarity are defined making use of exploratory factor analysis. On the one hand, four distinct cycling consideration measures are created, based on attitude expressions on four underlying factors relating to the cycling commuting behaviour: on how cycling commuting is considered green and smart (G&S); on its pleasant and suited character (P&S); on its efficiency as a mode of transport for commuting (E); and on the main drawbacks of its use, namely the difficulties implied (sweating and being exposed to adverse weather conditions) and the sense of unsafety it generates (feeling at risk of accidents and getting stressed by traffic) (D&U). On the other hand, dimensions of cycling familiarity are measured on two distinct ordinal variables (whether based on the utilitarian or non-utilitarian use) comprising four stages to a complete mode familiarity: not familiar; barely familiar; moderately familiar; fully familiar. For each of the four stages of cycling familiarity defined, statistical significant differences are found, especially for the measure related to the utilitarian use. Consistently, people at the lower levels of cycling familiarity have a lower consideration of the positive aspects of cycling and conversely they exhibit higher concerns towards the negative characteristics than those individuals that are more familiar in utilitarian cycling. Using a bicycle occasionally for practical purposes, as opposed to not using it at all, seems associated to significant higher scores in the three positive factors (G&S, E, P&S) while it appears to be associated to significant lower scores in the factor relating with the negative characteristics of cycling commuting (D&U). A same pattern also occurs with a moderate use, as opposed to an occasional one, especially for the consideration of the negative characteristics. The results are in line with previous literature based on similar variables (e.g. de Geus et al. 2008; Stinson & Bhat 2003, 2004; Hunt & Abraham 2006; and van Bekkum et al. 2011a, among others), but in this study the differences are observed in a low-cycling context and derive from an analysis of the entire population of commuters, which rises the reliability of results.