16,366 research outputs found
The computer simulation and prediction of rock fall
Get PDFThis thesis deals with the study of rock falls using a mathematical model, codified for computer use, entitled GeoFall. GeoFall, which was developed by the author, allows predictions to be made of rock fall trajectories, run out distances and kinetic energies for a rock of any arbitrary shape. Its main purpose is to assist in the design of remedial works. The mathematical model is based on rigid body mechanics, and analyses a fall in 2D space using a new theory of impact dynamics developed by Brach (1991). The main features and algorithms of the program are presented in this thesis. The performance of GeoFall was evaluated by comparing actual rock fall events described in several published papers with the output created by GeoFall. Also the output from GeoFall has been compared with the output from other rock fall simulation programs used to simulate the documented rockfalls. A new rock slope inventory system entitled the Rock Fall Risk Assessment System (RFRAS) has been developed by the author to determine the rock fall risk at specific rock fall sites. It consists of three phases of inspection, the slope survey, and the preliminary and detailed rating phases. The detailed rating phase uses 13 parameters that when assessed, evaluated and totalled, numerically differentiates slopes from the least to the most hazardous producing an overall rating in the range 21-1926. It not only allows the relative risk of rockfall between slopes to be assessed but it also categorises the rock fall risk and the potential number of future rockfalls. It has been tested on 18 slopes at ten locations in County Durham. The final part of the thesis details a new laboratory based procedure that can be used to determine the coefficients of restitution for any type of rock material. The normal coefficient of restitution has been determined for seven different types of rock, and the tangential coefficient of restitution has been determined for a local sandstone. Some tentative correlations between the normal coefficient of restitution and the rocks physical properties, such as its Unconfined Compressive Strength (UCS) have been presented
The rise and fall of the Labour league of youth
No full textThis thesis charts the rise and fall of the Labour Party’s first and most enduring youth organisation, the Labour League of Youth. The history of the League, from its birth in the early nineteen twenties to its demise in the late nineteen fifties, is placed in the context of the Labour Party’s subsequent fruitless attempts to establish and maintain a vibrant and functional youth organisation. A narrative is incorporated that illuminates the culture, organisation and political activism of the League and establishes it as a predominantly working class radical organisation. The reluctance on the part of the Labour Party to grant autonomy to its youth sections resulted in the history of the League of Youth being one of control, suppression and tension. This state of affairs ensured that subsequent youth groups, the Young Socialists and Young Labour, would be established in an atmosphere of reservation and scepticism.
The thesis places the prime responsibility for the failure of the party’s youth organisations with the party leadership but also considers the contributory factors of changing social and political circumstances. A number of themes are explored which include the impact of structure and agency factors, the power of the Parliamentary Labour Party, the political socialisation of leading figures within the party, the social context in which each of the groups emerged and the extent to which the youth groups were prey to intra-party factionalism.
The thesis redresses the balance of research where most accounts have focussed on the Young Socialists and traces the common characteristics that are prevalent in the way the party leadership has approached its relationship with its youth organisations. Use has been made of previously unpublished primary source material, the major source being the League of Youth members themselves whose recollections have helped to demonstrate the arguments put forward in this thesis
SOVAP v.1.3 : Soil Virome Analysis Pipeline
No full textSOVAP v.1.3: GitHub
Soil Virome Analysis Pipeline
Description
The study of viral communities in complex environmental samples, such as soil, can provide valuable insights into the diversity and functions of viral communities in the ecosystem. However, processing and analyzing of virome data can be a challenging task that requires the integration of various computational tools and techniques.
To address these challenges, we have developed SOVAP pipeline that utilizes a suite of state-of-the-art tools for processing, analysis, and annotation viromics and metagenomics data.
It utilizes various tools such as Fastp and Centrifuge for preprocessing and contamination removal, geNomad, Diamond and Megan for identification and annotation of viral contigs which are assembled and clustered using Megahit and CD-HIT. Additionally, this pipeline provides an estimate of the abundance of viral contigs, allowing for a more comprehensive understanding of the virome within the sample. The integration of these tools offers a reliable and effective means of taxonomy classification and annotation of viral contigs, aiding researchers in gaining insight into the composition and function of the virome within the analyzed sample.
By integrating the SOVAP pipeline with IMG/VR and geNomad, it is possible to identify a wider range of viruses, including those that were previously unknown.
The batch-mode script allows for the processing of multiple datasets using the SOVAP pipeline. This feature is particularly useful for large-scale analyses, such as those involving multiple environmental samples or large sequencing datasets.Diamond NCBI Genbank Viral database for SOVAP: https://doi.org/10.5281/zenodo.769752
L’application du séquençage à longue lecture en virologie de la vigne : du diagnostic aux interactions virus-hôte
Get PDFLa vigne (Vitis vinifera L.) est une culture d’une importance économique majeure, jouant un rôle clé dans l'industrie viticole mondiale. Cependant, la production viticole est menacée par plusieurs maladies virales émergentes et bien établies qui altèrent la qualité du raisin et réduisent les rendements. Le développement de technologies de séquençage de nouvelle génération a permis des avancées considérables dans l’identification et la caractérisation des virus de la vigne. Toutefois, ces approches présentent certaines limites, notamment en termes de coûts, de complexité et de longueur des fragments séquencés. Le séquençage à longue lecture, en particulier la technologie Nanopore, constitue une alternative innovante offrant une détection rapide et efficace des pathogènes viraux tout en permettant l’analyse des modifications post-transcriptionnelles et épigénétiques des génomes viraux. Dans cette thèse, nous avons exploré deux deux axes majeurs de l’application du séquençage Nanopore en virologie de la vigne : (1) le diagnostic des virus et viroïdes et l’optimisation d’un protocole de séquençage direct de l’ARN double brin (ARNdb) pour améliorer la détection des virus, et (2) l’analyse épigénomique et transcriptomique du grapevine red blotch virus (GRBV), un virus à ADN simple brin circulaire.
L'essor du séquençage de troisième génération a ouvert de nouvelles perspectives dans la surveillance et l’étude des maladies virales de la vigne. Contrairement aux technologies de séquençage de nouvelle génération (NGS) qui nécessitent des infrastructures lourdes et des protocoles de préparation d’échantillons complexes, la technologie Nanopore permet le séquençage direct de l’ARN et de l’ADN viraux sans amplification préalable. Dans cette étude, nous avons démontré que cette approche permet non seulement la détection de virus connus, mais également l'identification de virus émergents, ainsi que l’analyse des modifications post-transcriptionnelles des génomes viraux. Un des défis majeurs en virologie végétale est la détection précise et spécifique des agents pathogènes dans des environnements à forte complexité génomique. Nous avons donc développé un protocole de séquençage Nanopore basé sur l'extraction et l'analyse des ARN double-brin (ARNdb), qui constituent les intermédiaires réplicatifs des virus. En comparant cette approche au séquençage direct de l’ARN total après déplétion des ARN ribosomiques (ARNr), nous avons démontré que le séquençage des ARNdb permet une meilleure détection des virus, notamment dans les cas de co-infections. Cette méthode a également permis d’éliminer certains faux positifs causés par des annotations erronées de séquences issues du génome hôte. De plus, nous avons évalué différentes approches bioinformatiques pour l’analyse des données virales, en comparant les algorithmes DIAMOND/MEGAN et Centrifuge/Recentrifuge, mettant en évidence leurs avantages et leurs limites respectives pour la classification rapide des virus.
Le grapevine red blotch virus (GRBV) est un virus émergent causant des pertes économiques considérables dans le secteur viticole en raison de son impact sur la maturation des baies et la composition chimique du raisin. Bien que son génome code pour une protéine de la capside (CP), aucune particule virale n’a été observée à ce jour, suggérant un mécanisme alternatif de propagation du virus. Nous avons donc réalisé une analyse approfondie du profil de méthylation du génome viral et de la régulation de son expression génique afin d'expliquer cette observation. Nos résultats ont révélé que le gène CP présente une forte densité de méthylation, ce qui pourrait conduire à sa répression transcriptionnelle, expliquant ainsi l’absence de formation de virions. Par ailleurs, nous avons identifié 13 transcrits distincts, dont cinq nouveaux ARNm épissés et un long ARN non codant. Un nouveau transcrit, nommé V4, a été découvert au sein du gène V3, qui présente une expression différentielle entre les plantes symptomatiques et asymptomatiques. L’analyse fonctionnelle de V4 suggère qu’il pourrait jouer un rôle clé dans l'interaction virus-hôte et la formation de vésicules extracellulaires. Enfin, nous avons démontré expérimentalement que l'ADN viral du GRBV est présent dans des vésicules extracellulaires (VE), ce qui suggère un mécanisme alternatif de dissémination du virus indépendant des particules virales conventionnelles. Cette découverte ouvre la voie à de nouvelles hypothèses concernant la transmission du virus et ses interactions avec la cellule hôte.
L’ensemble de ces travaux met en évidence le potentiel du séquençage Nanopore pour une analyse intégrée des génomes viraux, de leur expression génique et de leurs modifications épigénétiques. Cette approche constitue un outil puissant pour le diagnostic des maladies virales de la vigne, l’étude de l’évolution des pathogènes et le développement de nouvelles stratégies de lutte contre les infections virales. Ces résultats ouvrent également de nouvelles perspectives quant à l'importance des vésicules extracellulaires dans la biologie des virus à ADN végétaux, un domaine encore peu exploré
Not a geography of what doesn't exist, but a counter-geography of what does: Rereading Giuseppe Dematteis' Le Metafore della Terra
No full textThe shaping of geography as a discipline has been the result of a combination of productive and successful communication and missed opportunities, of presence and absence, of fluid travels of ideas and projects, but also of closures, impediments, good lessons that got lost. This paper suggests that using a counterfactual approach to draw attention to specific geographies that remained unfulfilled and poorly known helps to think beyond linear genealogies. By discussing a particular book called Le Metafore della Terra by Giuseppe Dematteis, published in Italian in 1985 but largely unknown in English-language geography, we reflect on what happened when it was published - and also specifically what did not happen and, cautiously, what might have happened. In his book, Dematteis took issue with geography and geographers' past and contemporary mistakes, suggesting that the depoliticization of geographical knowledge had served merely powerful interests, rendering the imagining of alternative worlds impossible. He picked apart sacred tenets of the geographical tradition: escapist fantasies of exploration and conquest, the poorly problematized use of scale, the faith in the power of cartographic reason, the metaphysics of organicism, and the magical belief in the power of the market. Here, by extending the idea of counterfactual histories to look inwards to the discipline of geography itself, we choose to engage with what might have happened if this particular critical approach to geography had become better known, exploring why this radical project for the discipline was cast aside, including by the author himself. In so doing, we consider how scholars are located in so-called peripheral' places of production of geographical knowledge, discussing how this helps to understand the circulation and non-circulation of certain ideas. We use these alternatively rewritten geographies to show how dominant linear narratives of the emerging of critical thinking in the 1980s tell us an incomplete story, suggesting instead a tangled, multiple history of the discipline. We are interested in how scientific knowledge is communicated and received, how this exposes both the multi-sited nature of knowledge production and circulation, and cultural and national differences in the reception of science, and what this says about the possibility of critical thinking and progressive ideas having real impact
On the Castelnuovo-Mumford regularity of ideals, in dimension 2
No full text5 pagesWe give a bound on the Castelnuovo-Mumford regularity of a homogeneous ideals I, in a polynomial ring A, in terms of number of variables and the degrees of generators, when the dimension of A/I is at most two. This bound improves the one obtained by Caviglia and Sbarra in this case. In the continuation of the examples constructed by Clare D'Cruz and the first author, we use families of monomial curves to construct homogeneous ideals showing that these bounds are quite sharp
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