Analysis of different uncertainty activation cross section data libraries for LWR, ADS and DEMO neutron spectra

This work is aimed to present the main differences of nuclear data uncertainties among three different nuclear data libraries: EAF-2007, EAF-2010 and SCALE-6.0, under different neutron spectra: LWR, ADS and DEMO (fusion). To take into account the neutron spectrum, the uncertainty data are collapsed to onegroup. That is a simple way to see the differences among libraries for one application. Also, the neutron spectrum effect on different applications can be observed. These comparisons are presented only for (n,fission), (n,gamma) and (n,p) reactions, for the main transuranic isotopes (234,235,236,238U, 237Np, 238,239,240,241Pu, 241,242m,243Am, 242,243,244,245,246,247,248Cm, 249Bk, 249,250,251,252Cf). But also general comparisons among libraries are presented taking into account all included isotopes. In other works, target accuracies are presented for nuclear data uncertainties; here, these targets are compared with uncertainties on the above libraries. The main results of these comparisons are that EAF-2010 has reduced their uncertainties for many isotopes from EAF-2007 for (n,gamma) and (n,fission) but not for (n,p); SCALE-6.0 gives lower uncertainties for (n,fission) reactions for ADS and PWR applications, but gives higher uncertainties for (n,p) reactions in all applications. For the (n,gamma) reaction, the amount of isotopes which have higher uncertainties is quite similar to the amount of isotopes which have lower uncertainties when SCALE-6.0 and EAF-2010 are compared. When the effect of neutron spectra is analysed, the ADS neutron spectrum obtained the highest uncertainties for (n,gamma) and (n,fission) reactions of all libraries.

Testing JEFF-3.1.1 and ENDF/B-VII.1 Decay and Fission Yield Nuclear Data Libraries with Fission Pulse Neutron Emission and Decay Heat Experiments

The aim of this work is to test the present status of Evaluated Nuclear Decay and Fission Yield Data Libraries to predict decay heat and delayed neutron emission rate, average neutron energy and neutron delayed spectra after a neutron fission pulse. Calculations are performed with JEFF-3.1.1 and ENDF/B-VII.1, and these are compared with experimental values. An uncertainty propagation assessment of the current nuclear data uncertainties is performed.

Impact of Nuclear Data Uncertainties on Advanced Fuel Cycles and Their Irradiated Fuel - A comparison between Libraries

The uncertainties on the isotopic composition throughout the burnup due to the nuclear data uncertainties are analysed. The different sources of uncertainties: decay data, fission yield and cross sections; are propagated individually, and their effect assessed. Two applications are studied: EFIT (an ADS-like reactor) and ESFR (Sodium Fast Reactor). The impact of the uncertainties on cross sections provided by the EAF-2010, SCALE6.1 and COMMARA-2.0 libraries are compared. These Uncertainty Quantification (UQ) studies have been carried out with a Monte Carlo sampling approach implemented in the depletion/activation code ACAB. Such implementation has been improved to overcome depletion/activation problems with variations of the neutron spectrum.

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

Thermal Scattering Libraries Processing (F4E, Task 6.2)

Presentación del trabajo realizado en el marco del proyecto F4E, sobre el procesamiento de librerías de dispersión térmica de neutrones en formato ACE para su uso con el código MCNP. Se presentan tanto los métodos y procedimientos empleados, como los resultados y diferencias entre las distintas fuentes de datos.

Elementos peatonales de las ciudades medias españolas : tipos, orígenes, relaciones y articulaciones

A través de esta tesis se busca aportar un análisis de los elementos peatonales que cubren las necesidades y las infraestructuras de apoyo al peatón, siendo un campo poco desarrollado en nuestro país a diferencia de otros como Dinamarca, Reino Unido, Alemania y Holanda, donde las actuaciones peatonales ejecutadas son tradicionales y muy exitosas. Se trata por tanto de un tema poco estudiado pero que adquiere singular importancia en estos años de búsqueda de nuevos modelos urbanos que eviten el derroche de recursos, y avancen hacia formas de movilidad más adecuadas a un mundo limitado y vulnerable. La investigación tiene un carácter eminentemente descriptivo cuyo principal valor es documentar y analizar sistemáticamente una realidad poco conocida, aportándose datos para entender el origen y desarrollo de las actuaciones peatonales. El propósito es ayudar a cimentar este campo en nuestro país, definiendo con precisión el estado de la cuestión geográficamente y dejando para un futuro una cartografía temática completa. El objeto general es estudiar y comprender los elementos peatonales de un número limitado de ciudades medias españolas, marcándose como objetivos específicos los siguientes: - Identificar y describir los principales elementos que conforman la red peatonal de las ciudades. ‐ Estudiar las tipologías espaciales dominantes, sus características y orígenes, pudiendo distinguir de un lado, las desarrolladas en la ciudad consolidada, como las actuaciones en los cascos antiguos; y por otro, las ejecutadas en la ciudad nueva a través de fórmulas arquitectónicas generalmente residenciales con espacios peatonales adjuntos. ‐ Analizar los referidos elementos para comprobar si han conformado redes de uso peatonal, si se han constituido articulando la ciudad como en el caso de los ejes lineales en las ciudades con río o mar, o si han influenciado el carácter del entorno en el que se han realizado, centrando el interés en los cascos históricos peatonalizados. ‐ Comprobar si hay actuaciones complementarias a los procesos de urbanización y mejora urbanística, así como la aprobación de ayudas y subvenciones para afrontar las mismas. ‐ Finalmente, describir y evaluar los procesos y procedimientos mediante los que se produce la peatonalización de determinadas áreas urbanas, los orígenes, los instrumentos y fechas de su puesta en marcha, aportando una cronología peatonal. La metodología comienza con la acotación de 22 ciudades españolas, capitales de provincia con una población entre 100.000 y 500.000 habitantes según los datos del INE del año 2009. La distribución es equilibrada con la selección de ciudades de costa, de interior, con río/ría, con carácter patrimonial, ciudades en islas, etc. El análisis de los elementos peatonales de estas urbes se realiza gracias a la gran resolución de las bases cartográficas públicas y privadas que hay en la actualidad en internet, especialmente con el uso de las herramientas de Google Earth y Google Maps en su versión “street view”, softwares que permiten un paseo virtual de cada ciudad detallándose con gran precisión las actuaciones peatonales. Las ciudades elegidas son: ‐ 11 ciudades costeras: Alicante, Almería, Bilbao, Cádiz, Castellón de la Plana, Huelva, Las Palmas de Gran Canaria, Palma de Mallorca, Santander, San Sebastián y Tarragona. ‐ 11 ciudades de interior: Albacete, Burgos, Córdoba, León, Lérida, Logroño, Oviedo, Murcia, Pamplona, Valladolid y Vitoria. Finalmente, por tener los porcentajes mas elevados de las áreas peatonales de sus casco histórico, se eligen 3 casos de ciudades representativas para un desarrollo peatonal en profundidad, seleccionándose Burgos, San Sebastián y Pamplona. Otros aspectos metodológicos interesantes a destacar, es la extensa documentación adquirida a través de las fuentes de Internet, sobre todo a la hora de desarrollar el último capítulo “Procesos de peatonalización de las ciudades españolas” centrado en las 3 ciudades elegidas. Se consulta las hemerotecas de periódicos locales, los boletines oficiales, las actas de los plenos de los Ayuntamientos y los documentos de planificación (Planes Generales, Planes Especiales, Planes y Proyectos Municipales, Planes de Movilidad), adquiriéndose una precisa información en cuanto a la cronología de las fechas y extensión del trabajo. Se complementa la metodología con las entrevistas a actores claves en el proceso peatonal, como el personal técnico de los Ayuntamiento y los técnicos redactores de los proyectos; y con la colaboración directa de los técnicos de los consistorios de las 3 ciudades seleccionadas, aportando todo tipo de información demandada. En la tesis, se introduce los elementos peatonales mediante el estudio de los espacios peatonales y los procesos de peatonalización existentes, a través del análisis de la literatura consultada aportándose información valiosa en cuanto a la definición de los modelos peatonales, exponiéndose una breve historia de las peatonalizaciones. Destacan las publicaciones de los expertos europeos en la materia como los autores Carmen Hass-Klau, Rolf Monheim, Rob Krier y Collin Buchanan. En España, las actuaciones peatonales fueron tardías en el tiempo en comparación con el resto de Europa, con casi 40 años de retraso. Las referencias bibliográficas españolas en esta materia son escasas siendo las mas significativas las realizadas por Alfonso Sanz y por el profesor Julio Pozueta destacando una de sus últimas publicaciones “La ciudad paseable” describiéndose los elementos peatonales existentes en las ciudades, sirviendo como modelo y ejemplo para esta investigación. En base a lo anterior, se definen los elementos peatonales como aquellos espacios públicos libres de edificación que, por sus características y diseño, garantizan un confortable uso estancial, de tránsito peatonal y están expresamente reservados para ello. En la tesis se detectan y se especifican los siguientes elementos peatonales: las calles y plazas peatonales, las aceras y bulevares de una anchura superior a 8 metros, los paseos peatonales, los elementos de paso (tradicionales y mecánicos), espacios peatonales ligados a nuevas áreas residenciales, los soportales y pasajes peatonales con una anchura mínima de 4 metros, recintos feriales, espacios libres y zonas verdes y parques. Para cada una de las 22 ciudades seleccionadas se realiza un exhaustivo inventario de los anteriores elementos a través de fichas, aportando un gran número de proyectos individuales ejecutados en cada urbe. Esta información se recoge gráficamente en 2 fotoplanos, conformándose como herramientas fundamentales para esta investigación. El Fotoplano 1 se hace sobre la base de la ciudad del Google Earth diferenciándose las áreas peatonales y las zonas verdes. En el Fotoplano 2, y con el soporte anterior, se distinguen las tipologías persistentes y dominantes como son los grandes ejes peatonales, las redes peatonales locales y los elementos peatonales singulares. Finalmente, a partir de los 2 fotoplanos, se realiza la denominada “Huella peatonal” que destaca por su atractivo y pregnancia, algo de lo que el campo de lo peatonal es muy útil. A través de la huella se obtiene una rápida información al tener el plano dos colores, color naranja para lo peatonal (formado por las áreas peatonales y zonas verdes) y color negro para el resto el resto no peatonal. Toda esta documentación gráfica y descriptiva de los elementos peatonales de cada ciudad, queda ampliamente recogida en el Anexo de la tesis. La “Huella peatonal” se considera como el plano básico en la investigación obteniendo una percepción rápida, clara y visual del espacio peatonal de cada ciudad. Se arroja información morfológica con respecto a la distribución espacial, articulación, equilibrio, modulación, cohesión, concentración peatonal, etc. de cada una de las ciudades seleccionadas. A través de la huella se resuelve muchos de las cuestiones enmarcadas como objetivos de la tesis, comprobándose de forma general, que los elementos peatonales dentro de la trama urbana están desarticulados ya que no hay una estructura que module la ciudad como un conjunto cohesionado. Se localizan pequeñas redes conectadas entre sí, que de forma heterogénea, están dispersas por la ciudad. Se verifica que los elementos peatonales con mayor concentración y presencia en las ciudades analizadas son los ejes peatonales, los cascos históricos y los elementos peatonales en las nuevas áreas residenciales. En la investigación, además de estos 3 elementos mencionados, se analiza con mayor profundidad otros tipos que destacan por su persistencia y repetición en la “Huella peatonal” de cada una de las 22 ciudades, como son las plazas peatonales, los soportales y los elementos singulares peatonales: espacios tradicionales (recintos feriales, pasajes, puentes históricos), nuevos elementos peatonales (pasarelas peatonales, elementos mecánicos de paso), áreas peatonales entorno a edificios culturales y otros casos como los consistentes en la recuperación y transformación de edificaciones y construcciones urbanas de diferente uso y tipología, en nuevas áreas peatonales. Se aporta luz sobre su definición, localización, cronología, proporción, presencia y génesis, facilitando resultados de cada uno de ellos. De forma paralela, se obtiene información de índole cuantitativa a través de las mediciones de la huella, obteniéndose datos y porcentajes de extensión de la ciudad, de las zonas peatonales y de las zonas verdes, de los cascos históricos y de sus superficies peatonales, de los metros lineales de dichos cascos históricos y de sus calles peatonales. Se proporcionan ratios e índices que se consideran fundamentales para una mejor comprensión peatonal de cada urbe. Se establece una clasificación de las ciudades en cada uno de los ámbitos descritos, destacando las ciudades de Pamplona, San Sebastián y Burgos por arrojar las cifras peatonales más positivas encabezando la mayoría de las tablas clasificatorias. La peor ciudad valorada es Alicante, seguida según criterio, de Almería, Palma de Mallorca y Las Palmas de GC. En el capítulo final de la investigación, se eligen las ciudades de Burgos, San Sebastián y Pamplona como casos de estudio representativos. El objetivo es obtener un conocimiento más preciso en cuanto a su origen, cronología y procesos de las peatonalizaciones. Cada ciudad se compone de un cuadro cronológicos por etapas, desarrollándose de forma exhaustiva cada una de ellas, enunciadas normalmente, como instrumentos de planeamiento o proyectos de urbanización, acompañadas de los planos de las actuaciones peatonales. Al final de cada etapa se aportan datos de las cifras de las peatonalizaciones que se van realizando, con un cuadro numérico de localizaciones, superficie peatonal, superficie reurbanizada, longitud peatonal y el grado de peatonalización del casco histórico, además de los datos acumulados por etapa. De las conclusiones cruzadas de estas 3 ciudades, destaca la comprobación de la tendencia de ir peatonalizando los centros antiguos llegando incluso al 100% de calles peatonales en el caso de San Sebastián. No obstante, es difícil confirmar si el objetivo es una peatonalización global de los cascos, ya que son muchas las variables que afectan e influyen en el proceso peatonal de cada ciudad. Se coteja adicionalmente cómo se extiende la cultura peatonal desde el interior al exterior, mas allá de los cascos históricos hacia los ensanches próximos. En cuanto al origen de las peatonalizaciones, se concluye que no hay una concepción inicial y teórica marcada, a partir de la cual se va desarrollando la trama peatonal de cada ciudad. Se puede afirmar que los procesos peatonales ejecutados son variados y de diversa índole, sin poder precisar un hecho como causa principal. Según el momento y las circunstancias, las peatonalizaciones responden a distintas iniciativas promovidas por los comerciantes, por las administraciones locales o por los técnicos de planeamiento, con sus expertas aportaciones en los planes. Estos tres agentes actúan como impulsores de proyectos individuales peatonales que se van solapando en el tiempo. Como punto final de la tesis, se propone una serie de nuevas líneas de investigación que pueden servir como estudio adicional y complementario, respondiendo a aspectos tan relevantes como cuestiones de índole económica, social y de movilidad, fuertemente ligadas a las peatonalizaciones, tal y como se demuestra en la literatura consultada. ABSTRACT This thesis aims to analyse the pedestrian elements dealing with the needs and infrastructures that support pedestrians, as this is a field that is little developed in our country, in comparison to other regions such as Denmark, the United Kingdom, Germany and the Netherlands, where the pedestrian actions implemented are traditional and highly successful. Therefore, even though little research has been done about this topic, this field is increasingly important throughout these years of search for urban models intended to prevent the waste of resources and to develop new mobility ways, more adapted to a limited, vulnerable world. This research is essentially descriptive and it mainly aims to document and systematically analysed a scarcely known reality by providing data in order to understand the origin and development of pedestrian actions. This thesis intends to lay the foundations of this field in Spain, accurately defining the state of the art from a geographical point of view and preparing a full thematic map that may be used in the future. The overall aim is to study and understand the pedestrian elements of a limited number of Spanish medium-size cities, establishing the following specific goals: - To identify and describe the main elements comprising cities' pedestrian networks. - To study of special predominant typologies, their features and origins, with the possibility to, on the one hand, make a difference between the typologies developed in well-established cities, such as the actions in historic quarters, and, on the other hand, those implemented in new cities through generally residential architectural formulae with adjoining pedestrian areas. - To analyse the said elements in order to check whether they have resulted in pedestrian-use networks, whether they have been established by organising the city, such as the linear axes in coastal and riverside cities, or whether they have had an impact on the character of the areas where these elements have been implemented, focusing on pedestrian historic quarters. - Check whether there are actions supplementary to the urban development and urban improvement processes, as well as the approval of financial support and subventions to deal with these actions. - Finally, to describe and assess the processes and procedures by which the pedestrianisation of certain urban areas is carried out, the origins, the instruments and the date of their implementation, providing a pedestrian timeline. The methodology starts by defining 22 Spanish cities, province capitals with a population ranging from 100,000 to 500,000 inhabitants, according to the data recorded by the Spanish Statistics Institute (INE) in 2009. The distribution of coastal, riverside and interior cities, as well as of patrimonial cities and cities in islands, etc. is well balanced. The analysis of the pedestrian elements of these cities is made with the great resolution of the public and private map databases that can be accessed on the Internet, especially using the "street-view" version of tools such as Google Earth and Google Maps, software applications that allow to go for a virtual walk in each city, providing highly precise details about the pedestrian actions. The following cities have been chosen: ‐ 11 coastal cities: Alicante, Almería, Bilbao, Cádiz, Castellón de la Plana, Huelva, Las Palmas de Gran Canaria, Palma de Mallorca, Santander, San Sebastián and Tarragona. ‐ 11 interior cities: Albacete, Burgos, Córdoba, León, Lérida, Logroño, Oviedo, Murcia, Pamplona, Valladolid and Vitoria. Finally, as they have the highest percentages regarding the pedestrian areas found in the historic quarters, 3 cities representing a deep pedestrian development have been chosen: Burgos, San Sebastián and Pamplona. Other significant methodological aspects are the many documents found from online sources, especially when preparing the last chapter: “Processes for the pedestrianisation of Spanish cities”, which focuses on the 3 cities chosen. Local newspaper and periodical libraries, official gazettes, the minutes of plenary sessions of councils and the zoning regulation documents (General Zoning Plans, Special Zoning Plans, Municipal Plans and Projects, Mobility Plans, etc.) have been consulted, obtaining accurate information regarding the timeline and the extension of the works carried out. The methodology is supplemented by interviews with key players in the pedestrianisation process, such as the technical staff in councils and the officers drafting and designing the projects, as well as with the direct collaboration by the officers of the councils of the 3 cities chosen, who provided all the information requested. The thesis introduces the pedestrian elements by studying pedestrian areas and existing pedestrianisation processes through the analysis of the literature consulted, providing valuable information for the definition of pedestrian models and showing a brief history and background of the pedestrianisation process. Remarkable papers published by some European experts in the field, such as Carmen Hass-Klau, Rolf Monheim and Collin Buchanan, are covered in the thesis. In Spain, the pedestrianisation actions were late in time in comparison to the rest of Europe, with at least 40 years of delay. The Spanish literature references in this field are limited. The most significant papers are those published by Alfonso Sanz and by Professor Julio Pozueta, with a special mention of one of his last works "La ciudad paseable" (The Walkable City), which describes the pedestrian elements found in the cities and is used a model and an example for this research. Based on the elements above, pedestrian elements are defined as those construction-free public areas that, due to their features and design, ensure the comfortable, convenient use of the spaces, characterised by pedestrian traffic and specifically reserved for this purpose. The thesis detects and specifies the following pedestrian elements: pedestrian streets and squares, pavements (sidewalks) and boulevards with a width exceeding 8 metres, pedestrian promenades, crossing elements (traditional and mechanical), pedestrian spaces linked to new residential areas, colonnades and pedestrian passages or narrow streets with a minimum width of 4 metres, exhibition sites, free spaces and green areas and parks. For each of the 22 cities chosen, a thorough inventory of the elements mentioned above has been made by using worksheets, providing a significant number of individual projects developed in each city. This information is graphically collected and displayed on 2 photomaps, resulting in tools essential for this research. Photomap 1 is made based on the city displayed by Google Earth, making a difference between pedestrian areas and green areas. On Photomap 2, using the tool mentioned above, a difference can be made between persistent and predominant typologies, such as the big pedestrian axes, the local pedestrian networks and singular pedestrian elements. Finally, the 2 photomaps are used in order to establish the so-called "pedestrian footprint", which is highlighted by its attractiveness and appeal, concepts for which the pedestrian field is very useful. With the pedestrian footprint, quick information can be obtained, since the map shows two colours: orange for pedestrian elements (made up of pedestrian areas and green areas) and black for the other non-pedestrian elements. A significant part of these graphic, descriptive documents about each city's pedestrian elements can be found in the thesis appendix. The "Pedestrian Footprint" is regarded in the research as the basic map, obtaining a quick, clear and visual perception of each city's pedestrian space. This footprint provides morphological information regarding the space distribution, the organisation, the balance, the modulation, the cohesion, the pedestrian concentration, etc. in each of the cities chosen. The pedestrian footprint helps solve many of the questions established as the thesis goals, proving that, in general, the pedestrian elements are not organised in the urban plot, as there is no structure modulating the city as a properly linked set of elements. Small networks linked to each other and heterogeneously scattered all over the city are found. It has been verified that the pedestrian elements with the highest concentration and presence in the cities analysed are the pedestrian axes, the historic quarters and the pedestrian elements found in the new residential areas. Besides these 3 elements mentioned, the research analyses in depth other types that are remarkable due to their persistence and repetition in the "Pedestrian Footprint" of each of the 22 cities, such as the pedestrian squares, the colonnades and the singular pedestrian elements: traditional spaces (exhibition sites, passages, historic bridges), new pedestrian elements (pedestrian footbridges, mechanical crossing elements), pedestrian areas around cultural buildings and other cases such as those consisting of recovering and transforming building and urban constructions, intended for a wide range of purposes and of different types, into new pedestrian areas. This work puts light on the definition, location, timeline, proportion, presence and origin, providing results for each of these concepts. At the same time, quantitative information is obtained by measuring the footprint, getting data and percentages on the size of the city, the pedestrian areas and the green areas, the historic quarters and the pedestrian zones, the linear metres of such historic quarters and pedestrian streets. The footprint also provides ratios and rates that are considered as essential in order to better understand the pedestrian elements of each city. A classification of cities is established for each of the areas described, highlighting the cities of Pamplona, San Sebastián and Burgos, as they provide the most positive pedestrian figures and lead most of the classification tables or rankings. According to the criteria considered, the city with the worst values is Alicante, followed by Almería, Palma de Mallorca and Las Palmas de Gran Canaria. In the final chapter in the thesis, the cities of Burgos, San Sebastián and Pamplona are chosen as representative study cases. The aim is to gain more accurate knowledge regarding the pedestrianisation origin, timeline and processes. Each city comprises a chronological sequence made of stages, each of which is thoroughly developed and usually announced as zoning plans or urban development projects, accompanied by the plans of the pedestrian actions. At the end of each stage, data with the figures of the pedestrianisation projects are provided, including a numerical chart with locations, pedestrian area, redeveloped urban areas, pedestrian length and pedestrianisation degree in the historic quarter, as well as the data cumulated throughout each stage. In the crossed conclusions on the three cities, the trend of gradually pedestrianising the historic quarters (even reaching the 100% of the pedestrian streets as in San Sebastián) is verified. However, it is difficult to confirm whether the purpose is to reach an overall pedestrianisation of the historic quarters, since there are many variables that affect and influence each city's pedestrianisation process. In addition, the spread of the pedestrian culture from the internal areas to the external areas, beyond the historic quarters to the nearby expansion areas, is compared. Regarding the origin of pedestrianisations, the thesis comes to the conclusion that there is no initial or theoretical conception from which each city's pedestrian plot is developed. The pedestrian processes implemented are varied and diverse but no fact can be specified as the main cause. Based on the moment and circumstances, the pedestrianisation processes are due to different initiatives promoted by shopkeepers, by the local administrations or by the zoning officers, with their expert contributions to the plans. These three players promote and drive individual pedestrianisation projects that overlap in the course of time. Finally, new lines of research are put forwards, as they can be taken as an additional study and as a supplement to this research, dealing with aspects as significant as the economic, social and mobility factors, closely linked to the pedestrianisation processes, as proven in the literature consulted.

Isolation of recombinant antibody fragments (scFv) by phage display technology for detection of almond allergens in food products

Tree nut allergies are considered an important health issue in developed countries. To comply with the regulations on food labeling, reliable allergen detection methods are required. In this work we isolated almond-specific recombinant antibody fragments (scFv) from a commercial phage display library bypassing the use of live animals, hence being consistent with the latest policies on animal welfare. To this end an iterative selection procedure employing the Tomlinson I phage display library and a crude almond protein extract was carried out. Two different almond-specific scFv (named PD1F6 and PD2C9) were isolated after two rounds of biopanning, and an indirect phage ELISA was implemented to detect the presence of almond protein in foodstuffs. The isolated scFvs demonstrated to be highly specific and allowed detection of 40 ng mL?1 and 100 ng mL?1 of raw and roasted almond protein, respectively. The practical detection limit of the assay in almond spiked food products was 0.1 mg g?1 (110e120 ppm). The developed indirect phage ELISA was validated by analysis of 92 commercial food products, showing good correlation with the results obtained by a previously developed real-time PCR method for the detection of almond in foodstuffs. The selected phage clones can be affinity maturated to improve their sensitivity and genetically engineered to be employed in different assay formats.

Libraries Transforming Communities: The Value in an Academic Library Community at Lincoln University

Inman E. Page Library is coined as an, “Information Mall.” It houses special collections, archives, general reference services, computers, artistic programming, technological resources and space for different types of events. It is a modern academic library in the 21st century that was built on a legacy of scholarly opportunities for Lincoln University students, faculty, and our community in Jefferson City, MO and surrounding cities. The value that needs to be placed on this library is that it is an institution within an institution and should be given top priority as it pertains to continued funding, faculty support, and a place of higher learning that has a library etiquette. As well as, students need to understand the importance of how a library will affect their academic careers.

Creating Information Literacy Toolkits For HBCU Libraries

Information literacy is the set of research skills needed to access, retrieve, and analyze information. By creating an information literacy plan and an online toolkit that the entire campus uses for research purposes, faculty and students will be equipped with the necessary tools to become better researchers, understand the importance of citing information and the significance of searching for peer-reviewed articles.

A novel glutamine–RNA interaction identified by screening libraries in mammalian cells

The arginine-rich motif provides a versatile framework for RNA recognition in which few amino acids other than arginine are needed to mediate specific binding. Using a mammalian screening system based on transcriptional activation by HIV Tat, we identified novel arginine-rich peptides from combinatorial libraries that bind tightly to the Rev response element of HIV. Remarkably, a single glutamine, but not asparagine, within a stretch of polyarginine can mediate high-affinity binding. These results, together with the structure of a Rev peptide-Rev response element complex, suggest that the carboxamide groups of glutamine or asparagine are well-suited to hydrogen bond to G-A base pairs and begin to establish an RNA recognition code for the arginine-rich motif. The screening approach may provide a relatively general method for screening expression libraries in mammalian cells.

Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries

Transport of peptides across the membrane of the endoplasmic reticulum for assembly with MHC class I molecules is an essential step in antigen presentation to cytotoxic T cells. This task is performed by the major histocompatibility complex-encoded transporter associated with antigen processing (TAP). Using a combinatorial approach we have analyzed the substrate specificity of human TAP at high resolution and in the absence of any given sequence context, revealing the contribution of each peptide residue in stabilizing binding to TAP. Human TAP was found to be highly selective with peptide affinities covering at least three orders of magnitude. Interestingly, the selectivity is not equally distributed over the substrate. Only the N-terminal three positions and the C-terminal residue are critical, whereas effects from other peptide positions are negligible. A major influence from the peptide backbone was uncovered by peptide scans and libraries containing d amino acids. Again, independent of peptide length, critical positions were clustered near the peptide termini. These approaches demonstrate that human TAP is selective, with residues determining the affinity located in distinct regions, and point to the role of the peptide backbone in binding to TAP. This binding mode of TAP has implications in an optimized repertoire selection and in a coevolution with the major histocompatibility complex/T cell receptor complex.

RNA folding kinetics regulates translation of phage MS2 maturation gene

The gene for the maturation protein of the single-stranded RNA coliphage MS2 is preceded by an untranslated leader of 130 nt, which folds into a cloverleaf, i.e., three stem–loop structures enclosed by a long distance interaction (LDI). This LDI prevents translation because its 3′ moiety contains the Shine–Dalgarno sequence of the maturation gene. Previously, several observations suggested that folding of the cloverleaf is kinetically delayed, providing a time window for ribosomes to access the RNA. Here we present direct evidence for this model. In vitro experiments show that ribosome binding to the maturation gene is faster than refolding of the denatured cloverleaf. This folding delay appears related to special properties of the leader sequence. We have replaced the three stem–loop structures by a single five nt loop. This change does not affect the equilibrium structure of the LDI. Nevertheless, in this construct, the folding delay has virtually disappeared, suggesting that now the RNA folds faster than ribosomes can bind. Perturbation of the cloverleaf by an insertion makes the maturation start permanently accessible. A pseudorevertant that evolved from an infectious clone carrying the insertion had overcome this defect. It showed a wild-type folding delay before closing down the maturation gene. This experiment reveals the biological significance of retarded cloverleaf formation.

Altered 3′-terminal RNA structure in phage Qβ adapted to host factor-less Escherichia coli

The RNA phage Qβ requires for the replication of its genome an RNA binding protein called Qβ host factor or Hfq protein. Our previous results suggested that this protein mediates the access of replicase to the 3′-end of the Qβ plus strand RNA. Here we report the results of an evolutionary experiment in which phage Qβ was adapted to an Escherichia coli Q13 host strain with an inactivated host factor (hfq) gene. This strain initially produced phage at a titer ≈10,000-fold lower than the wild-type strain and with minute plaque morphology, but after 12 growth cycles, phage titer and plaque size had evolved to levels near those of the wild-type host. RNAs isolated from adapted Qβ mutants were efficient templates for replicase without host factor in vitro. Electron microscopy showed that mutant RNAs, in contrast to wild-type RNA, efficiently interacted with replicase at the 3′-end in the absence of host factor. The same set of four mutations in the 3′-terminal third of the genome was found in several independently evolved phage clones. One mutation disrupts the base pairing of the 3′-terminal CCCoh sequence, suggesting that the host factor stimulates activity of the wild-type RNA template by melting out its 3′-end.

The identification of CD4+ T cell epitopes with dedicated synthetic peptide libraries

For a large number of T cell-mediated immunopathologies, the disease-related antigens are not yet identified. Identification of T cell epitopes is of crucial importance for the development of immune-intervention strategies. We show that CD4+ T cell epitopes can be defined by using a new system for synthesis and screening of synthetic peptide libraries. These libraries are designed to bind to the HLA class II restriction molecule of the CD4+ T cell clone of interest. The screening is based on three selection rounds using partial release of 14-mer peptides from synthesis beads and subsequent sequencing of the remaining peptide attached to the bead. With this approach, two peptides were identified that stimulate the β cell-reactive CD4+ T cell clone 1c10, which was isolated from a newly diagnosed insulin-dependent diabetes mellitus patient. After performing amino acid-substitution studies and protein database searches, a Haemophilus influenzae TonB-derived peptide was identified that stimulates clone 1c10. The relevance of this finding for the pathogenesis of insulin-dependent diabetes mellitus is currently under investigation. We conclude that this system is capable of determining epitopes for (autoreactive) CD4+ T cell clones with previously unknown peptide specificity. This offers the possibility to define (auto)antigens by searching protein databases and/or to induce tolerance by using the peptide sequences identified. In addition the peptides might be used as leads to develop T cell receptor antagonists or anergy-inducing compounds.

Conditionally replicating mycobacteriophages: A system for transposon delivery to Mycobacterium tuberculosis

Transposon mutagenesis provides a direct selection for mutants and is an extremely powerful technique to analyze genetic functions in a variety of prokaryotes. Transposon mutagenesis of Mycobacterium tuberculosis has been limited in part because of the inefficiency of the delivery systems. This report describes the development of conditionally replicating shuttle phasmids from the mycobacteriophages D29 and TM4 that enable efficient delivery of transposons into both fast- and slow-growing mycobacteria. These shuttle phasmids consist of an Escherichia coli cosmid vector containing either a mini-Tn10(kan) or Tn5367 inserted into a nonessential region of the phage genome. Thermosensitive mutations were created in the mycobacteriophage genome that allow replication at 30°C but not at 37°C (TM4) or 38.5°C (D29). Infection of mycobacteria at the nonpermissive temperature results in highly efficient transposon delivery to the entire population of mycobacterial cells. Transposition of mini-Tn10(kan) occurred in a site-specific fashion in M. smegmatis whereas Tn5367 transposed apparently randomly in M. phlei, Bacille Calmette–Guérin (BCG), and M. tuberculosis. Sequence analysis of the M. tuberculosis and BCG chromosomal regions adjacent to Tn5367 insertions, in combination with M. tuberculosis genomic sequence and physical map data, indicates that the transpositions have occurred randomly in diverse genes in every quadrant of the genome. Using this system, it has been readily possible to generate libraries containing thousands of independent mutants of M. phlei, BCG, and M. tuberculosis.