Intestinal microbiome in chronic intestinal failure and associations with intestinal failure associated liver disease

Background and Aims: Intestinal dysbiosis has been described in children with chronic intestinal failure (CIF) and in adults with short bowel syndrome (SBS), mostly with jejunocolic anastomosis (SBS-2) and jejuno-ileal anastomosis (SBS-3), linked to generic data with the pathogenesis of Intestinal Failure Associated Liver Disease (IFALD). Little is known about gut microbiome of adults with end-jejunostomy (SBS-1) and in CIF other than SBS and any specific associations with the onset of IFALD. We aimed to describe the fecal microbiome of adult patients with different mechanisms of CIF and any possible associations with the development of IFALD. Material and methods: Fecal samples from 61 patients with benign CIF. Phylogenetic characterization of the microbiome by amplification of the hypervariable regions V3 and V4 of the bacterial gene encoding 16S rRNA, and subsequent grouping of sequences in amplicon sequence variants (ASVs). Patient samples comparison to microbiome sequences from 61 healthy subjects, matched for sex and age, selected from the healthy subjects library of the Laboratory of the Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, of the University of Bologna. IFALD was assessed by the diagnostic criteria of IFALD-cholestasis, IFALD-steatosis, IFALD-fibrosis. Results: Decreased bacterial α-diversity in CIF patients (increase of Proteobacteria and Actinobacteria and decrease in Bacteroidetes). Identification of microbial family-level signatures specific for CIF mechanisms (increase in Actinomycetaceae and Streptococcaceae in SBS-1, Bifidobacteriaceae and Lactobacillaceae in SBS-2, Bacteroidaceae and Porphyromonadaceae in dysmotility). Abundance of Lactobacillus and Lactobacillaceae strongly associated with IFALD-cholestasis and IFALD–fibrosis for SBS-1; Peptostreptococcus, Prevotellaceae (Prevotella) and Pasteurellaceae (Haemophilus) significantly increased in IFALD-fibrosis for other CIF mechanisms. Conclusions: CIF patients had a marked intestinal dysbiosis with microbial family-level signatures specific to the pathophysiological mechanism. Specific characteristics of microbiome may contribute to the pathogenesis of IFALD. Intestinal microbiome could become a therapeutic target in patients with CIF.

Cosmology from probe combination: synergies between the number counts of galaxy clusters and cosmic voids

This Thesis work concerns the complementary study of the abundance of galaxy clusters and cosmic voids identified in cosmological simulations, at different redshifts. In particular, we focus our analyses on the combination of the cosmological constraints derived from these probes, which can be considered statistically independent, given the different aspects of Universe density field they map. Indeed, we aim at showing the orthogonality of the derived cosmological constraints and the resulting impressive power of the combination of these probes. To perform this combination we apply three newly implemented algorithms that allow us to combine independent probes. These algorithms represent a flexible and user-friendly tool to perform different techniques for probe combination and are implemented within the environment provided by the large set of free software C++/Python CosmoBolognaLib. All the new implemented codes provide simple and flexible tools that will be soon applied to the data coming from currently available and next-generation wide-field surveys to perform powerful combined cosmological analyses.

Investigation of clusters of giardiasis using GIS and a spatial scan statistic

Affiliation: Pascal Michel : Département de pathologie et microbiologie, Faculté de médecine vétérinaire

Fossil associations from the middle and upper Eocene strata of the Pamplona Basin and surrounding areas (Navarre, western Pyrenees)

Fossil associations from the middle and upper Eocene (Bartonian and Priabonian) sedimentary succession of the Pamplona Basin are described. This succession was accumulated in the western part of the South Pyrenean peripheral foreland basin and extends from deep-marine turbiditic (Ezkaba Sandstone Formation) to deltaic (Pamplona Marl, Ardanatz Sandstone and Ilundain Marl formations) and marginal marine deposits (Gendulain Formation). The micropalaeontological content is high. It is dominated by foraminifera, and common ostracods and other microfossils are also present. The fossil ichnoasssemblages include at least 23 ichnogenera and 28 ichnospecies indicative of Nereites, Cruziana, Glossifungites and ?Scoyenia-Mermia ichnofacies. Body macrofossils of 78 taxa corresponding to macroforaminifera, sponges, corals, bryozoans, brachiopods, annelids, molluscs, arthropods, echinoderms and vertebrates have been identified. Both the number of ichnotaxa and of species (e. g. bryozoans, molluscs and condrichthyans) may be considerably higher. Body fossil assemblages are comparable to those from the Eocene of the Nord Pyrenean area (Basque Coast), and also to those from the Eocene of the west-central and eastern part of South Pyrenean area (Aragon and Catalonia). At the European scale, the molluscs assemblages seem endemic from the Pyrenean area, although several Tethyan (Italy and Alps) and Northern elements (Paris basin and Normandy) have been recorded. Palaeontological data of studied sedimentary units fit well with the shallowing process that throughout the middle and late Eocene occurs in the area, according to the sedimentological and stratigraphical data.

A VLT/FLAMES survey for massive binaries in Westerlund 1 III. The WC9d binary W239 and implications for massive stellar evolution

Context. There is growing evidence that a treatment of binarity amongst OB stars is essential for a full theory of stellar evolution. However the binary properties of massive stars - frequency, mass ratio & orbital separation - are still poorly constrained. Aims. In order to address this shortcoming we have undertaken a multiepoch spectroscopic study of the stellar population of the young massive cluster Westerlund 1. In this paper we present an investigation into the nature of the dusty Wolf-Rayet star and candidate binary W239. Methods. To accomplish this we have utilised our spectroscopic data in conjunction with multi-year optical and near-IR photometric observations in order to search for binary signatures. Comparison of these data to synthetic non-LTE model atmosphere spectra were used to derive the fundamental properties of the WC9 primary. Results. We found W239 to have an orbital period of only similar to 5.05 days, making it one of the most compact WC binaries yet identified. Analysis of the long term near-IR lightcurve reveals a significant flare between 2004-6. We interpret this as evidence for a third massive stellar component in the system in a long period (> 6 yr), eccentric orbit, with dust production occuring at periastron leading to the flare. The presence of a near-IR excess characteristic of hot (similar to 1300 K) dust at every epoch is consistent with the expectation that the subset of persistent dust forming WC stars are short (< 1 yr) period binaries, although confirmation will require further observations. Non-LTE model atmosphere analysis of the spectrum reveals the physical properties of the WC9 component to be fully consistent with other Galactic examples. Conclusions. The simultaneous presence of both short period Wolf-Rayet binaries and cool hypergiants within Wd 1 provides compelling evidence for a bifurcation in the post-Main Sequence evolution of massive stars due to binarity. Short period O+OB binaries will evolve directly to the Wolf-Rayet phase, either due to an episode of binary mediated mass loss - likely via case A mass transfer or a contact configuration - or via chemically homogenous evolution. Conversely, long period binaries and single stars will instead undergo a red loop across the HR diagram via a cool hypergiant phase. Future analysis of the full spectroscopic dataset for Wd 1 will constrain the proportion of massive stars experiencing each pathway; hence quantifying the importance of binarity in massive stellar evolution up to and beyond supernova and the resultant production of relativistic remnants.

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/

Theory for Optical Absorption in Small Clusters: Dependence on Atomic Structure and Cluster Size

We present a theory which permits for the first time a detailed analysis of the dependence of the absorption spectrum on atomic structure and cluster size. Thus, we determine the development of the collective excitations in small clusters and show that their broadening depends sensitively on the tomic structure, in particular at the surface. Results for Hg_n^+ clusters show that the plasmon energy is close to its jellium value in the case of spherical-like structures, but is in general between w_p/ \wurzel{3} and w_p/ \wurzel{2} for compact clusters. A particular success of our theory is the identification of the excitations contributing to the absorption peaks.

Adsorption of NO on the Rh-13, Pd-13, Ir-13, and Pt-13 Clusters: A Density Functional Theory Investigation

The adsorption of NO on transition-metal (TM) surfaces has been widely studied by experimental and theoretical techniques; however, our atomistic understanding of the interaction of nitrogen monoxide (NO) with small TM clusters is far from satisfactory, which compromises a deep understanding of real catalyst devices. In this study, we report a density functional theory study of the adsorption properties of NO on the TM13 (TM = Rh, Pd, Ir, Pt) clusters employing the projected augmented wave method. We found that the interaction of NO with TM13 is much more complex than that for NO/TM(111). In particular, for low symmetry TM13 clusters, there is a strong rearrangement of the electronic charge density upon NO adsorption and, as a consequence, the adsorption energy shows a very complex dependence even for adsorption sites with the same local effective coordination. We found a strong enhancement of the binding energy of NO to the TM13 clusters compared with the TM(111) surfaces, as the antibonding NO states are not occupied for NO/TM13, and the general relationship based on the d-band model between adsorption energy and the center of gravity of the occupied d-states does not hold for the studied TM13 clusters, in particular, for clusters with low symmetry. In contrast with the adsorption energy trends, the geometric NO/TM13 parameters and the vibrational N-O frequencies for different coordination sites follow the same trend as for the respective TM(111) surfaces, while the changes in the frequencies between different surfaces and TM13 clusters reflect the strong NO-TM13 interaction.

Digital library of historical cartography: open access to cultural heritage and public good

This paper describes the integration of information between Digital Library of Historical Cartography and Bibliographical Database (DEDALUS), both of the University of São Paulo (USP), to guarantee open, public access by Internet to the maps in the collection and make them available to users everywhere. This digital library was designed by Historical Cartography Studies Laboratory team (LECH/USP), and provides maps images on the Web, of high resolution, as well as such information on these maps as technical-scientific data (projection, scale, coordinates), printing techniques and material support that have made their circulation and cultural consumption possible. The Digital Library of Historical Cartography is accessible not only to the historical cartography researchers, but also to students and the general public. Beyond being a source of information about maps, the Digital Library of Historical Cartography seeks to be interactive, exchanging information and seeking dialogue with different branches of knowledge

Procesos configurativos: de la trama a la noción de campo en los "mat buildings"

La presente tesis aborda el estudio sobre los llamados mat buildings, que surgen entre los años cincuenta y sesenta del pasado siglo. Los mat buildings, también llamados “edificios esteras” o “edificios alfombras”, nacen en gran parte como consecuencia de los desacuerdos e insatisfacciones de los CIAM con el reduccionismo funcionalista y los principios de compartimentación funcional. Estos nuevos modelos remplazan el modelo de ciudad entendido como una colección de edificios individuales por una concepción de un patrón urbano. No es la suma de la longitud, la altura y el ancho sino más bien una densa alfombra bi-dimensional, con una configuración de formas que ofrece al mismo tiempo un orden repetitivo y una infinita diversidad de secuencias con infinitas posibilidades de adaptación donde el hombre vive y se desplaza. Estas características que irán apareciendo en la obras de muchos de los arquitectos que forman parte del grupo Team X son los que Alison Smithson empieza a revelar en su artículo, con la ambición de manifestar una nueva sensibilidad y una nueva forma de entender y ver la arquitectura. Los mat buildings y los cluster serán los códigos utilizados por diferentes miembros del Team X para pensar una arquitectura y un urbanismo alternativo al propuesto por los CIAM. Mediante ellos encuentran el camino para una nueva estética de la conexión con un desplazamiento desde una concepción determinista de la forma arquitectónica (una forma cerrada y en general definida a priori) hacia una actitud más libre, más abierta, fundamentada no tanto en la entereza de la forma global sino en cuanto a la intensidad de sus redes internas y de sus diferentes niveles de asociación. La tesis tiene como propósito final cuestionar si esta tipología de edificios, cuyo principio de base es siempre una matriz geométrica abierta (trama, retícula, malla), con crecimiento ilimitado, puede redefinir la frontera entre ciudad y edificio y, por tanto, entre público y privado, individual y colectivo, estructural e infraestructural, permanente y variable. Por ello, se presenta un estudio histórico y crítico en profundidad sobre los mat buildings, analizando detenidamente y por orden cronológico cinco de sus obras más paradigmáticas: el Orfanato en Ámsterdam de Aldo Van Eyck, la Universidad Libre en Berlín de Candilis, Josic y Woods, el Hospital de Venecia de Le Corbusier y Guillermo Jullián de la Fuente, el edificio administrativo de la Centraal Beheer en Apeldoorn de Herman Hertzberger, y por último el MUSAC en León, realizado por Mansilla y Tuñon. Las cuatro primeras obras pertenecen al periodo Team X y son precursoras de muchos otros proyectos que aparecerán a posteriori. La última obra analizada, el MUSAC, es estudiada conjuntamente con algunas obras del arquitecto japonés Sou Fujimoto y otros casos contemporáneos con la intención de manifestar cómo arquitectos de horizontes muy diferentes vuelven a recurrir a estos modelos de crecimientos ilimitados. Mediante el estudio de varios ejemplos contemporáneos se examinan las repercusiones, transformaciones y evoluciones que estos modelos han tenido. La exploración contrastada permite apreciar adecuadamente la pertinencia de estos modelos y los cambios de modalidades y de procesos que advienen con la aparición en el panorama contemporáneo de la noción de campo y los cambios de paradigma que conlleva. Estos nuevos modelos abren nuevos procesos y forma de abordar la arquitectura basada en las relaciones, flujos, movimientos y asociaciones que son caracterizados por diferentes patrones que vienen a alimentar todo el proceso del proyecto arquitectónico. El estudio de estos nuevos modelos nos indica las cualidades que puede ofrecer la revisión de estos métodos para empezar a tratar nuevas cuestiones que hoy en día parecen ser, permanentemente, parte de la condición urbana. XII ABSTRACT This thesis deals with the study of the so-called mat buildings which emerged between the fifties and sixties of the last century. Mat, or carpet, buildings appeared largely as a result of the CIAM’s disagreement and dissatisfaction with functionalist reductionism and the principles of functional compartmentalisation. These new models replaced the model of the city, seen as a collection of individual buildings, with the concept of an urban pattern. It is not the sum of the length, height and width but rather a dense, two- dimensional mat with a configuration of forms offering both a repetitive order and an infinite diversity of sequences with endless possibilities for adaptation, where man lives and circulates. These characteristics, which appeared in the works of many of the architects who formed part of Team X, are those that Alison Smithson started to reveal in her article with the aim of manifesting a new sensibility and a new way of understanding and seeing architecture. Mat buildings and clusters were the codes used by different members of Team X to plan an alternative architecture and urbanism to that proposed by the CIAM. With them, they found the path for a new aesthetic of connection, with a shift from a deterministic concept of the architectural form (closed and generally defined a priori) towards a more free, more open attitude based not so much on the integrity of the overall form but on the intensity of its internal networks and different levels of association. The end purpose of this thesis is to question whether this type of building, the basic principle of which is always an open geometric matrix (grid, recticle, network) with unlimited growth, can redefine the boundary between city and building and, thus, between public and private, individual and collective, structural and infrastructural, and permanent and variable. To this end, an in-depth historical and critical study of mat buildings is presented, analysing carefully and in chronological order five of the most paradigmatic works of this style: the Orphanage in Amsterdam, by Aldo Van Eyck; the Free University of Berlin, by Candilis, Josic and Woods; Venice Hospital, by Le Corbusier and Guillermo Jullián de la Fuente; the Centraal Beheer administration building in Apeldoorn, by Herman Hertzberger; and lastly, the MUSAC (Contemporary Art Museum) in León, designed by Mansilla and Tuñon. The first four works are from the Team X period and were the precursors to many other projects that would appear later. The last work analysed, the MUSAC, is studied together with some works by Japanese architect Sou Fujimoto and other contemporary cases to show how architects with very different perspectives revert to these models of limitless growth. Through the study of several contemporary examples we examine the repercussions, transformations and evolutions these models have had. The contrasted research XIII allows us to properly appreciate the importance of these models and the changes in forms and processes that came with the emergence of the idea of field in the contemporary arena and the paradigm shifts it entailed. These new models opened up new processes and a way of approaching architecture based on relationships, flows, movements and associations characterised by different patterns that feed the entire process of the architectural project. The study of these new models shows us the benefits that a review of these methods can contribute to addressing new issues that today appear to be a permanent part of the urban condition.

Competition, competitive advantage, and clusters:the ideas of Michael Porter

Comprehensive coverage of all aspects of Michael Porter's works Contributions from leading authorities across the disciplines Contains response from Porter Harvard professor, Michael Porter has been one of the most influential figures in strategic management research over the last three decades. He infused a rigorous theoretical framework of industrial organization economics with the then still embryonic field of strategic management and elevated it to its current status as an academic discipline. Porter's outstanding career is also characterized by its cross-disciplinary nature. Following his most important work on strategic management, he then made a leap to the policy side and dealt with a completely different set of analytical units. More recently he has made a foray into inner city development, environmental regulations, and health care services. Throughout these explorations Porter has maintained his integrative approach, seeking a road that links management case studies and the general model building of mainstream economics. With expert contributors from a range of disciplines including strategic management, economic development, economic geography, and planning, this book assesses the contribution Michael Porter has made to these respective disciplines. It clarifies the sources of tension and controversy relating to all the major strands of Porter's work, and provides academics, students, and practitioners with a critical guide for the application of Porter's models. The book highlights that while many of the criticisms of Porter's ideas are valid, they are almost an inevitable outcome for a scholar who has sought to build bridges across wide disciplinary valleys. His work has provided others with a set of frameworks to explore in more depth the nature of competition, competitive advantage, and clusters from a range of vantage points.

Bacteria and tumours: causative agents or opportunistic inhabitants?

Associations between different bacteria and various tumours have been reported in patients for decades. Studies involving characterisation of bacteria within tumour tissues have traditionally been in the context of tumourigenesis as a result of bacterial presence within healthy tissues, and in general, dogma holds that such bacteria are causative agents of malignancy (directly or indirectly). While evidence suggests that this may be the case for certain tumour types and bacterial species, it is plausible that in many cases, clinical observations of bacteria within tumours arise from spontaneous infection of established tumours. Indeed, growth of bacteria specifically within tumours following deliberate systemic administration has been demonstrated for numerous bacterial species at preclinical and clinical levels. We present the available data on links between bacteria and tumours, and propose that besides the few instances in which pathogens are playing a pathogenic role in cancer, in many instances, the prevalent relationship between solid tumours and bacteria is opportunistic rather than causative, and discuss opportunities for exploiting tumour-specific bacterial growth for cancer treatment.

Source Provenance of Pre-Historic Granitic Grindstones: The Case Study of the Cogotas I Archaeological Site of Arroyo Mucientes/San Lázaro (Castronuño, Valladolid) and a Proposal on the General Methodological Flow Process

The occurrence of hand grindstones at the Cogotas I archaeological sites is considered to be a common feature. Given that a distant-provenance raw material is frequently involved, determination of its source is a basic factor in the search for a better understanding of resource management and for any Political Economy approach. To progress in these directions an overall study should be planned, using selected grindstones with a view to covering diverse sub-zones of the Cogotas I dispersal area, especially because of its considerable distance from the granite basement source. Such a study may today includes diverse analytical procedures combining successive geographic, petrographic, mineralogical and geochemical criteria. To check the plausibility of the proposed methodology, a preliminary test has been carried out on two granite grindstones, obtained at the archaeological excavation at the Castronuño (Valladolid) Cogotian site, which is fifty km away from an inferred source area that was presumably located at Peñausende (Zamora). The result obtained validates the proposed operational process, yielding a generalizable knowledge to other similar situations.

Standardization in the Pre-Columbian Pottery from El Caño, Panama: Specialization, Productivity and Consumption

The pottery found in the burials of El Cano is uniform in style to these made in the coclesanos valleys between 700 and 1000 AD. The coefficient of variability of the different pottery forms, evidence diverse standardizations values for polychrome and non-polychrome ceramics. Moreover, data of funerary contexts from the Cano recently excavated, suggest that elite has controlled ceramic production. This control over the production of certain goods reveals that these were important in the support or proper operational of the chiefdoms in Panama and mark the phase of splendour of this culture.

Motivation and Vocabulary Breadth in CLIL and EFL Contexts. Different age, Same Time of Exposure

Numerous studies have found a positive connection between learners’ motivation towards foreign language and foreign language achievement. The present study examines the role of motivation in receptive vocabulary breadth (size) of two groups of Spanish learners of different ages, but all with 734 hours of instruction in English as a Foreign Language (EFL): a CLIL (Content and Language Integrated Learning) group in primary education and a non-CLIL (or EFL) group in secondary education. Most students in both groups were found to be highly motivated. The primary CLIL group slightly overcame the secondary non-CLIL group with respect to the mean general motivation but this is a non-significant difference. The secondary group surpass significantly the primary group in receptive vocabulary size. No relationship between the receptive vocabulary knowledge and general motivation is found in the primary CLIL group. On the other hand, a positive significant connection, although a very small one, is identified for the secondary non-CLIL group. We will discuss on the type of test, the age of students and the type of instruction as variables that could be influencing the results.