Dissertations / Theses on the topic 'Prune'

Les insectes saproxylophages participent à la dégradation du bois mort. De nombreuses espèces de ce complexe sont menacées. Nous avons étudié l’écologie d’Osmoderma eremita, coléoptère saproxylophage qui se raréfie et disperse peu. Ses populations ont été suivies par capture-recapture et pistage-radio. Les capacités de vol ont été mesurées au laboratoire. Notre but était d’étudier la distribution de l’espèce dans un bocage, ses capacités de dispersion et des critères démographiques. L’ouverture du paysage, la densité de microhabitats et la persistance des habitats durant plusieurs décennies influencent la présence de l’espèce. Les capacités de dispersion mesurées sont trois fois supérieures à celles relevées in natura. Les capacités des femelles sont liées à leur condition. La sex-ratio est biaisée en fonction de la population et de l’année. Le sexe est donc un facteur qui devrait intervenir dans les analyses de viabilité permettant de proposer des mesures de conservation d’O. Eremita
Saproxylophagous Insects are involved in the degradation of dead wood. Many species of this complex are endangered. We studied the ecology Osmoderma eremita, a saproxylophagous beetle that is becoming scarce and is a short dispersal species. We monitored its populations by capture-recapture and radio-tracking. Fight capacities were measured in laboratory. Our goal was to explain the distribution of the species in an agricultural landscape, to study its dispersal capacities and some demographic characteristics. The landscape openness, the density of microhabitats and the persistence of the habitats during several decades have an influence on the species occurence. Dispersal capacities were three times greater than those observed in nature. The capacities of females were related to their condition. Sex-ratio was biased depending on population and year. Sex is a factor which should take place in viability analyses which would enable to propose conservation measures for O. Eremita

Fruit-tree borer, Maroga melanostigma (Wallengren), is a native Australian pest in many species of trees. It is of particular economic importance in prune (Prunus domestica) trees because the presence of this wood boring insect can reduce productivity by an average of 5% per tree. Large areas of orchards can be affected. There are currently no chemicals registered for control of this pest. Young, New South Wales is the second largest prune-growing district in Australia and the area most seriously affected by M. melanostigma. Prune growers in the district utilise integrated pest management and were supportive of a project to investigate biological control options for this economically damaging pest. The two main objectives of the project were 1) to understand the life cycle of M. melanostigma, so biological controls could be timed appropriately; and 2) to investigate biological control options for this pest. Life cycle studies were commenced in the first season (2003/04) using field cages and light trapping. These investigations continued throughout the project. In Young, moths were found to emerge from wood over a two month period (December and January). Oviposition was assumed to be during this period however, even after extensive searches of trees, no eggs were observed. Historical data were collated to determine locations and timings of moth emergence elsewhere in Australia. The data showed that M. melanostigma has been found in every state and territory Australia, with moths observed from October through to March. The biological control options reviewed were egg parasitoids (Trichogramma species only), entomopathogenic nematodes and entomopathogenic fungi. Trichogramma were favoured because of previous research undertaken against the same pest in pecans in Moree, NSW. Entomopathogenic nematodes were also investigated due to research indicating their effectiveness in cryptic situations, such as borer tunnels in trees. Fungi were considered but dismissed due to lack of literature supporting their effectiveness in reducing lepidopteran pest damage in trees. A major field trial was designed with the assistance of a biometrician and the trial blocks laid out based on this advice. There were three trial sites, each containing four blocks of approximately 200 trees (~800 trees/site). Two blocks were designated as release blocks and two as non-release blocks to correspond with the trial’s two treatments. In the first season (2003/04) an initial visual assessment of borer damage was undertaken after leaf fall on each of the trees in the trial. This information was used as baseline data, to compare against damage levels following biological control releases in the second and third years of the project. Natural parasitism in the field was assessed using cultured eggs of Helicoverpa armigera (Hübner) before and between Trichogramma carverae (Oatman and Pinto) releases. Temperature and relative humidity were recorded in each of the trial sites, for the duration of the trial, using commercially available data loggers. In the second season (2004/05), Trichogramma releases were made during the period of moth activity and H. armigera eggs were used to monitor parasitism in the trial orchards. Parasitised eggs were reared through and all parasitoids were identified as T. carverae. Damage assessments were again carried out after leaf fall to compare release versus non-release blocks, as well as to determine if there was any change in borer activity. Early instar larvae were collected from non-trial blocks and exposed to the entomopathogenic nematode Steinernema carpocapsae in a laboratory investigation. Results from this limited bioassay were inconclusive. In the third season (2005/06), Trichogramma releases were again made during the period of moth activity and H. armigera eggs were used to monitor parasitism in the trial orchards. Parasitised eggs were reared through to emergence. The emerged parasites were identified as T. carverae, T. pretiosum and T. nr brassicae. Damage assessments were again made of all the trees in the trial. Results were statistically analysed to detect any differences between treatments. There was no statistically significant evidence that the releases of T. carverae reduced damage from M. melanostigma over the duration of the trial. Although damage increased across both release and non-release treatments in most blocks during the trial investigations, the increase was slightly lower in trees in which Trichogramma had been released. It should be noted that the experiments were affected by serious drought conditions which prevailed during the three seasons of the trial.

Thesis (M.Sc.(Hons.)) -- University of Western Sydney, 2007.
A thesis submitted in fulfilment of the requirements for the degree of Master of Science (Hons) to the University of Western Sydney, College of Health and Science, Centre for Plant and Food Science. Includes bibliography.

Des modifications importantes de la structure cellulaire ont lieu pendant cette periode, correspondant successivement a la perte de permeabilite selective des membranes, au decollement du plasmalemme et a son alteration et enfin a la coagulation des constituants protoplasmiques et a leur prise en masse. A la desorganisation parietale sont associees d'importantes modifications biochimiques des constituants pectiques. Sous l'effet de l'elevation de la temperature, la teneur en pectines solubles augmente aux depens des protopectines, les differentes fractions pectiques (solubles a l'eau, a l'oxalate et a l'acide chlorhydrique) subissent une depolymerisation et une faible demethylation. La decompartimentation cellulaire conduit par ailleurs a une mise en contact d'enzymes et de substrats normalement separes dans la cellule vivante. C'est ainsi que l'acide chlorogenique, compose phenolique le plus abondant de la prune, est oxyde par les polyphenoloxydases a un taux dependant de la rapidite de denaturation thermique de ces enzymes. Les produits d'oxoydations des phenols participent a la degradation des anthocyanes par des reactions d'oxydations couplees dont on a etudie les mecanismes en solutions modeles. L'importance de ces transformations structurales et biochimiques discutees en les integrant dans leur contexte technologique

“Sem resumo feito pelo autor” - História da cultura - A amendoeira é uma das principais culturas arvenses a nível mundial. Esta árvore de fruto pertence à familia Posaceae e tem sido incluída por alguns botânicos no género Prunus devido à sua relação com outras espécies deste género (pessegueiro, ameixeira, cerejeira e damasqueiro), designando-a por Prunus dulcis (Miller) D. A. Webb syn. Prunus amygdalus Batsch. (Kester et al., 1986). No entanto, os primeiros botânicos classificavam-na como sendo um género distinto — Amygdalus - e utilizavam o termo communis para indicar as respectivas espécies cultivadas (Grasselly e Crossa-Raynaud, 1980 in Rugini, 1983). A amendoeira parece ter o centro de origem nas regiões montanhosas da Ásia Central (India, Irão e Paquistão), sendo provavelmente resultante do cruzamento entre as espécies Amygdalus fenziliana Fritsch e Amygdalus bucharica Korsch (Popov, 1929 in Rugini, 1983), ambas relacionadas com a Amygdalus communis L. Esta espécie foi dispersa pela Bacia do Mediterrâneo, e em cerca de 1700 a.C. era comum na Palestina (Woodroof, 1967 in Rugini,1983). A cultura da amendoeira, iniciada aproximadamente em 450 a.C., expandiu-se a partir da Grécia para a Costa Mediterrânica em áreas localizadas. Posteriormente, foi levada para a costa ocidental da América do Norte, onde agora constitui uma das mais importantes fruteiras dos Estados Unidos (Sousa, 1990). Actualmente, a cultura da amendoeira situa-se nos arredores do mar Mediterrâneo e Médio Oriente e na Califórnia - zonas onde se concentra mais de 90% da produção mundial - e em pequenas áreas que também apresentam o tipo de clima mediterrânico (Himalaia, Chile, Argentina, África do Sul e Austrália). Esta cultura é totalmente condicionada por este tipo de clima, em particular no que respeita ao regime de chuvas nestas zonas. Nesta espécie, as chuvas de Primavera não devem interferir com a polinização cruzada realizada pelas abelhas, porque as cultivares tradicionais são auto- -incompatíveis, enquanto que as chuvas de Outono não devem causar problemas à colheita e subsequente secagem dos frutos (Socias i Company,1997). - Características gerais da planta - A amendoeira é uma árvore de altura média com ramos glabros os quais, com cerca de um ano de idade, apresentam uma cor verde-pálida a vermelho-acastanhada. Na maioria das cultivares mediterrânicas, incluindo as portuguesas, as folhas apresentam pecíolos e são lanceoladas a ovadas com um ápice agudo. Os ramos produzem botões foliares pontiagudos, e botões florais arredondados cujos primórdios florais surgem no início do Outono. De Novembro a Janeiro, dependendo da cultivar (cv.), ocorre a formação dos grãos de pólen (microsporogénese), e a maturação do ovário ocorre logo após a floração (Rugini, 1983). As flores são hermafroditas, sendo constituídas por 5 pétalas brancas ou rosa, 5 sépalas, l único pistilo contendo 2 óvulos, e 20-40 estames. A floração, a qual precede o rebentamento vegetativo, é extremamente precoce e ocorre de Janeiro a Março, dependendo da cultivar. A poção é geralmente entomófila (Rugini, 1983). O fruto consiste numa drupa em forma de ovo com um padrão de crescimento sigmóide. O pericarpo é geralmente fino (5-15mm) e sofre deiscência na maturidade. 0 endocarpo, o qual pode variar na forma, aparência superficial e consistência, é um importante factor na identificação de diferentes cultivares. O endocarpo envolve uma ou duas amêndoas as quais podem variar em tamanho, pesando 0,5-1,5g. Dois cotilédones bem desenvolvidos ocupam o volume total da amêndoa a qual é comestível, podendo ser doce ou amarga (Rugini, 1983). A amendoeira é uma espécie diplóide (2x = 16), tal como as espécies selvagens com ela relacionadas (Rugini, 1983). É altamente polimórfica, provavelmente por ser auto-incompatível e consequentemente necessitar de polinização cruzada, bem como devido à sua propagação, realizada exclusivamente por via seminal até finais do século XIX (Rugini, 1983; Socias i Company e Felipe, 1992 in Socias i Company, 1997). A sua variabilidade dificulta a distinção entre cultivares e linhagens híbridas genuínas, complexo designado por "ecotipos" (Grasselly e Crossa-Raynaud, 1980 in Rugini, 1983). A amendoeira exige clima quente e seco na Primavera, resistindo bem à secura desde que enxertada em porta-enxertos adequados. Por ser susceptível a asfixia radicular, exige solos com boa drenagem (IMAIAA, 1994). O porta-enxerto mais utilizado é o franco de amendoeira (amêndoa amarga). Contudo, os porta-enxertos híbridos de pessegueiro x amendoeira, apesar de serem mais caros, oferecem vantagens significativas em relação ao franco – a amendoeira apresenta maior vigor, produção e qualidade da amêndoa. O híbrido de pessegueiro x amendoeira que tem sido mais utilizado é o GF-677 (Cordeiro e Monteiro,1997).

Orientador: Carlile Campos Lavor
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática Estatística e Computação Científica
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Resumo: A geometria de distâncias é o estudo da geometria baseado no conceito de distância. Ela é útil em várias aplicações, onde os dados de entrada consistem de um conjunto incompleto de distâncias, e a saída é um conjunto de pontos no espaço euclidiano, que realiza as distâncias dadas. No Problema de Geometria de Distâncias (DGP), é dado um inteiro K > 0 e um grafo simples, não direcionado, G = (V,E,d), cujas arestas são ponderadas por uma função não negativa d. Queremos determinar se existe uma função (realização) que leva os vértices de V em coordenadas no espaço euclidiano K-dimensional, satisfazendo todas as restrições de distâncias dadas por d. Um DGPk (com K fixado) está fortemente relacionado a um outro tipo de problema, que trata dos possíveis completamentos de uma certa matriz de distâncias euclidianas. Este último pode ser visto, em um certo sentido, como o "dual do primeiro problema". Neste trabalho, exploramos essa dualidade com a finalidade de propor melhorias no método Branch-and-Prune aplicado a uma versão discreta do DGPk
Abstract: Distance Geometry is the study of geometry based on the concept of distance. It is useful in many applications where the input data consists of an incomplete set of distances, and the output is a set of points in some Euclidean space which realizes the given distances. In the Distance Geometry Problem (DGP), it is given an integer K > 0 and a simple undirected weighted graph G = (V,E,d), whose edges are weighted by a non-negative function d. We want to determine if there is a (realization) function that associates the vertices of V with coordinates of the K-dimensional Euclidean space satisfying all distance constraints given by d. A DGPk (with K fixed) is closely related to another type of problem, which treats the possible completions of a certain Euclidean distance matrix. In some sense, this is the "dual" of the first problem. We explore this duality in order to improve the Branch-and-Prune method applied to a discrete version of the DGPk
Doutorado
Matematica Aplicada
Doutor em Matemática Aplicada

Orientador: Carlile Campos Lavor
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática Estatística e Computação Científica
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Resumo: Motivado por estudos em estruturas 3D de proteínas, biomoléculas imprescindíveis no estudo da vida, surgiu um problema chamado Discretizable Molecular Distance Geometry Problem (DMDGP) que provou ser NP-Difícil. Para resolvê-lo, existe um algoritmo da literatura, Branch & Prune (BP), que utiliza uma estratégia combinatória de exploração de uma árvore binária de soluções associada ao problema. Além disso, foram descobertas relações de simetria que permitem obter uma solução, a partir de outra, através de reflexões nos chamados vértices de simetria. Alguns pesquisadores passaram a realizar este trabalho em paralelo (ParallelBP), dividindo uma instância em sub-instâncias, resolvendo localmente com o BP (o que pode ser feito em duas direções) e unindo as sub-soluções com movimentos rígidos, com o intuito de determinar as soluções em menor tempo. Nossa proposta é fornecer uma estratégia Dividir-e-Conquistar para resolver o DMDGP, de modo a melhorar a abordagem em paralelo. Ela possui três estágios. Inicialmente, dividimos uma instância em sub-instâncias duas-a-duas sobrepostas através dos vértices de simetria. Depois, utiliza-se os chamados gaps para decidir a direção em que o BP deve fornecer a solução local. Por fim, utilizamos rotações baseadas na Álgebra de Quatérnios para combinar as sub-soluções em soluções factíveis
Abstract: Motived by studies in 3D structures of proteins, essential biomolecules for Life, arised a problem called Discretizable Molecular Distance Geometry Problem (DMDGP) which proved to be NP-Hard. Aiming to solve it, there is an algorithm in the literature, Branch & Prune (BP), which uses a combinatorial strategy of exploring a binary tree of solutions that is associated to the problem. Moreover, some symmetry relations have been discovered which allows the obtainance of one solution from the other one by means of reflections in the so-called symmetry vertices. Some researchers started to do this work using parallel computing (ParallelBP), dividing one instance into sub-instances, solving the problem locally with the BP (what can be done in two directions) and joining the sub-solutions with rigid movements, with the objective of determining the solutions in a smaller time. Our purpose, thus, is to provide a Divide-and-Conquer strategy to solve the DMDGP in order to improve the parallel version. It has three stages. Initially, the instance is divided into sub-instances two-by-two overlapping by means of the symmetry vertices. After, the so-called gaps are used to decide the direction that the BP ought to provide the local solution. Finally, we propose to use Quaternion Rotations to combine sub-solutions into feasible solutions
Doutorado
Matematica Aplicada
Doutor em Matemática Aplicada

Relational database provide an efficient mechanism to store and retrieve structured data with ACID properties but it is not ideal for every scenario. Their scalability is limited because of huge data processing requirement of modern day systems. As an alternative NoSQL is different way of looking at a database, they generally have unstructured data and relax some of the ACID properties in order to achieve massive scalability. There are many flavors of NoSQL system, one of them is a key value store. Most of the key value stores currently available in the market offers reasonable performance but compromise on many important features such as lack of transactions, strong consistency and range queries. The stores that do offer these features lack good performance. The aim of this thesis is to design and implement VoloDB, a key value store that provides high throughput in terms of both reads and writes but without compromising on ACID properties. VoloDB is built over MySQL Cluster and instead of using high-level abstractions, it communicates with the cluster using the highly efficient native low level C++ asynchronous NDB API. VoloDB talks directly to the data nodes without the need to go through MySQL Server that further enhances the performance. It exploits many of MySQL Cluster’s features such as primary and partition key lookups and prune index scans to hit only one of the data nodes to achieve maximum performance. VoloDB offers a high level abstraction that hides the complexity of the underlying system without requiring the user to think about internal details. Our key value store also offers various additional features such as multi-query transactions and bulk operation support. C++ client libraries are also provided to allow developers to interface easily with our server. Extensive evaluation is performed which benchmarks various scenarios and also compares them with another high performance open source key value store.

Tumour microenvironment is a complex network of cells, including immune cells, with a role in tumorigenesis and metastatic spread. Among the immune cells, M2-polarized Tumour-Associated-Macrophages (M2-TAMs) show immunosuppressive activities by expressing inflammatory molecules, thus promoting tumorigenesis. Triple-Negative Breast Cancer (TNBC), lacking both hormone receptors (i.e. Progesterone Receptor [PgR] and Estrogen Receptor [ER]) and Human Epidermal growth factor Receptor 2 (HER2), is associated with poor prognosis and high probability of distant metastases. In TNBC, a large number of infiltrating M2-TAMs is positively correlated to higher risk of metastases and lower rates of Disease-Free Survival” (EFS) and Overall Survival (OS). Prune-1 belongs to DHH (Asp-His-His) phosphoesterase superfamily with an exopolyphosphatase activity. The overexpression of Prune-1 is correlated with metastases and poor prognosis in several tumours including Breast Cancer (BC). Prune-1 was also found to induce Epithelial-Mesenchimal-Transition (EMT) and metastatic dissemination throught the enhancement of canonical TGF-β signaling by counterbalancing its inhibition operated by NDPK-A. Further evidences suggested that lung cancer progression is driven by Prune-1 through the canonical WNT signaling pathway in both autocrine and paracrine manner via Wnt3a cytokine secretion, thus suggesting a potential role for Prune-1 also in extracellular environment. Here, we identified Prune-1 protein as overexpressed in TNBC patients and positively correlated to lynphnode metastases, inflammatory pathways and infiltrating M2-TAMs (CD68+/CD163+). Furthermore, we developed a Genetically Engineered Mouse Model (GEMM) of metastatic TNBC over-expressing both Prune-1 and Wnt-1 in mammary glands (MMTV-Prune1/Wnt1). We found Prune-1 to recruit TAMs and to enhance their polarization toward a pro-tumorigenic M2-phenotype in the tumour microenvironment, thus promoting lung metastases in this GEMM. We also show that Prune-1 takes part to the communication between TNBC cells and TAMs through intracellular pathways activation (i.e., TGF-b and NF-kB), but also in a paracrine manner by inducing the secretion of inflammatory cytokines (e.g., IL-17F and IL-28) and modulating the exosome protein contents. Finally, we found an anti-Prune-1 drug (AA7.1) with the ability to reduce the primary tumour growth by reducing the percentage of M2-TAMs in orthotopic xenograft immunocompetent models of TNBC. In conclusion, our GEMM of metastatic TNBC driven by Prune-1 will be a useful source for future immunotherapy pre-clinical trials targeting M2-polarized TAMs within the tumour microenvironment to inhibit distant metastases in TNBC with poor prognosis.

INTRODUÇÃO: A síndrome de prune belly (PBS) é caracterizada por uma tríade com flacidez da parede abdominal, criptorquidia bilateral e malformações do trato urinário que compreende bexiga de capacidade aumentada, com complacência elevada, hipossensibilidade, hipocontratilidade, com divertículo ou fístula uracal e resíduo pós-miccional elevado. Alguns autores recomendam tratamento clínico, porém outros propõe correção cirúrgica, com reconstrução da via urinária incluindo ureteroplastia e cistoplastia redutoras, orquidopexia e abdominoplastia. Mesmo após a cirurgia, alguns doentes necessitam de cateterismo limpo intermitente. A inervação vesical determina seu funcionamento, mediado por neuroreceptores na junção neuromuscular. Os adrenoreceptores a1 estão relacionados à contratilidade detrusora e o b3 ao seu relaxamento, e certas condições como obstrução infravesical levam à hiperexpressão de receptores a1. O objetivo da presente pesquisa é verificar se no detrusor de doentes com PBS há alteração na densidade de terminações nervosas, hiper ou hipoexpressão de receptores adrenérgicos a1a, a1b, a1d e b3 e proporção anormal dos tecidos muscular e conectivo. MÉTODO Trata-se de estudo retrospectivo de caso-controle que envolveu 14 espécimes de detrusor de doentes com PBS operados entre 1985 a 2005 no Hospital das Clínicas da FMUSP. Dois grupos foram constituídos como controle: 13 fragmentos de bexiga de doentes submetidos à prostatectomia radical no Departamento de Urologia da Universidade de Mainz, com urodinâmica pré-operatória normal (GC1), e cinco fragmentos de bexiga de crianças submetidas à necrópsia no SVOC-USP, sem anomalias neurológicas e de trato urinário. A coloração de van Gieson foi realizada para análise da proporção músculo/tecido conectivo, e a reação imunohistoquímica para os anticorpos policlonais anti-proteína S100 e antiadrenoreceptores a1a, a1b, a1d e b3. A coloração castanho foi considerada evidência da expressão do adrenoreceptor na célula. Cinco a dez imagens digitais foram tomadas por meio de câmara digital e microscopia óptica. Estas foram analisadas pelo programa Adobe Photoshop CS2Ò. A quantidade relativa de receptores foi calculada e a análise estatística realizada pelos testes Kruskal-Wallis e Mann-Whitney. RESULTADOS A média de idade foi de 1,28 ± 1,14 ano no grupo caso (PBS), e de 64 ± 5,22 anos e 1,41 ± 1,11 ano, nos grupos GC1 e GC2, respectivamente. A mediana da relação músculo/tecido conectivo foi de 1,08 para o grupo PBS, 1,59 para o GC1 e para o GC2 de 1,28 (p=0,173). A mediana da proporção S100/tecido muscular foi de 0,21 para o grupo caso (PBS), de 0,20 para o GC1 e para o grupo GC2 de 0,01 (p=0,003). A mediana da relação a1a/tecido muscular foi de 0,06 para o grupo PBS, de 0,16 para o GC1 e para o grupo GC2 de 0,14 (p=0,026). Para a1b, as medianas foram 0,06 no grupo PBS, 0,006 no GC1 e 0,007 no GC2 (p=0,781). No a1d, as medianas foram 0,04 (PBS), 0,04 (GC1) e 0,05 (GC2) (p=0,618). Com relação ao b3, as medianas foram 0,07 no grupo PBS, 0,14 no GC1 e 0,10 no GC2 (p=0,378). CONCLUSÕES Comparando-se fragmentos de detrusor de doentes com PBS e bexigas normais não se observou alteração na densidade de terminações nervosas. Observou-se hipoexpressão do adrenoreceptor a1a, e não houve alteração dos adrenoreceptores a1b, a1d e b3. Também não se observou alteração entre a proporção de tecido muscular e conectivo no detrusor destes doentes. Investigações adicionais, com diferentes métodos e incluindo outros receptores, são necessárias antes de se aplicar esses conhecimentos na prática clínica.
INTRODUCTION: Prune belly syndrome (PBS) is charactherized by a triad of abdominal wall flaccidity, bilateral criptorchidism and urinary tract malformation, that includes a large-capacity bladder, with high detrusor compliance, low sensibility and contractility, associated to urachal diverticulum or fistula and elevated post void residual volumes. Some autors recommend clinical treatment, but others propose surgery correction, with urinary tract reconstruction, including reductive ureteroplasty and cystoplasty, orchidopexy and abdominoplasty. Even after surgery, some patients need intermittent catheterism. The detrusor innervation determines its function, mediated by neuroceptors at the neuromuscular junction. The a1 adrenoceptors are related to detrusor contractility and b3 to relaxation, and some conditions, like infravesical obstruction, lead to a1 adrenoceptor up-regulation. The objective of this work is to verify whether, in the detrusor from patients with PBS, there is altered nerve density, up or down-regulation of a1a, a1b, a1d and b3 adrenergic receptors and if there is an abnormal proportion between muscle and connective tissue. MATERIALS AND METHODS A retrospective case-control study was performed involving 14 detrusor specimens from patients with PBS, who underwent surgical treatment between 1985 an 2005 at University of São Paulo, Medical School Hospital. Two groups were taken as control: 13 bladder fragments from patients who underwent radical prostatectomy at Department of Urology of Mainz University, with normal urodynamic study prior to the surgery (GC1) and 5 bladder fragments from children submitted to autopsy at SVOC-USP, with no neurological or urinary tract malformation (GC2). Staining was performed using the van Gieson dye to analyse the proportion between muscle and connective tissue, and immunohistochemical reaction was employed, with polyclonal antibodies against S100 protein, as well as a1a, a1b, a1d and b3 adrenoceptors. Brown colour was considered as evidence of adrenoceptor cell expression. Five to ten digital images were captured on an optic microscope with a digital camera. These images were analysed with Adobe Photoshop CS2Ò software. The relative quantity of receptors was calculated and the statistic analysis was done with the Kruskal-Wallis and Mann-Whitney tests. RESULTS Mean age was 1.28 ± 1.14 year in PBS patients, and 64 ± 5.22 yrs. and 1.41 ± 1.11 yrs. in GC1 and GC2, respectively. The median proportion between muscle and connective tissue was 1.08 in PBS, 1.59 in GC1 and in GC2 of 1.28 (p=0.173). The median proportion of S100/muscle area was 0.21 in PBS, 0.20 in GC1 and in GC2 of 0.01 (p=0.003). The median relative quantity of receptors of a1a was 0.06 in PBS, 0.16 in GC1 and 0.14 in GC2 (p=0.026). In a1b, the median values were 0.06 in PBS group, 0.006 in GC1 and 0.007 in GC2 (p=0.781). In a1d, the median values were 0.04 (PBS), 0.04 (GC1) and 0.05 (GC2) (p=0.618). Regarding b3, the median values were 0.07 in PBS, 0.14 in GC1 and 0.10 in GC2 (p=0.378). CONCLUSION Comparing detrusor fragments from patients with PBS and normal bladders, there was no alteration in the density of nerve endings. We observed downregulation of a1a adrenoceptors, but no alteration in the a1b, a1d and b3 receptors. Furthermore, there was no alteration of the proportion between muscle and connective tissue areas. Further investigations, with different methods and including other receptors, are necessary to transfer this knowledge to clinical use.

En bioinformatique structurale, une partie des méthodes computationnelles qui calculent les structures de protéines à l'aide de données expérimentales, effectuent une optimisation de la position des atomes sous les contraintes expérimentales mesurées sur le système étudié, ainsi que sous des contraintes provenant de la connaissance générique de la stéréochimie organique. Ces méthodes d'optimisation présentent l'inconvénient de ne pas garantir la détermination de la meilleure solution. De plus, la validation de l'optimisation se fait en comparant les résultats obtenus pour des calculs répétés, et le résultat d'un calcul est accepté dans la mesure où le même résultat est obtenu plusieurs fois. Par cette approche, on rend plus difficile la détection de conformations alternatives de protéines, qui sont pourtant le sujet d'un vif intérêt dans la littérature. En effet, le développement de la sensibilité des techniques de résonance magnétique nucléaire (RMN) a permis de mettre en évidence plusieurs cas d'échange conformationnel reliés à la fonction des protéines. Dans ce projet de thèse, nous avons étudié une nouvelle approche pour le calcul de structures des protéines et l'exploration de leurs espaces conformationnels, basée sur la résolution du problème de Géométrie de Distance associé aux contraintes de distances dans une protéine par l'algorithme "interval Branch and Prune". Le logiciel implémentant cette méthode est appelée iBPprot, il incarne l'une des premières tentatives d'échantillonnage exhaustive des espaces conformationnels des protéines. Dans un premier temps, on s'est intéressé à l'application de la méthode en utilisant exclusivement des constraintes de distances exactes. Les résultats ont démontré que iBPprot était capable de reconstruire des structures références en s'appuyant seulement sur quelques contraintes à courte portée. De plus, la reconstruction a été d'une précision telle que la conformation générée présentait un RMSD de 1 Angstrom maximum avec la structure référence. L'exploration exhaustive de l'espace conformationnel a été possible pour une bonne partie des protéines cibles. Les temps de calcul pour l'exploration des espaces conformationnels ont été très variables allant de quelques secondes pour quelques protéines jusqu'à des semaines pour d'autres. L'évaluation de la qualité des structures obtenues a démontré qu'au moins 68% des valeurs de phi et psi sont localisées dans la zone 'core' du diagramme de Ramachandran. Cependant, des clash stériques ont été détectées dans plusieurs conformations mettant en jeu jusqu'à 7% d'atomes dans quelques unes de ces conformations. Dans un deuxième temps, on s'est intéressé à l'application de la méthode en incluant des intervalles de distances comme contraintes dans les calculs. Dans ce cas de figure, la méthode a réussi a reconstruire des structures références avec un RMSD inférieur à 5 Angstrom pour plus de la moitié des protéines cibles. En contre partie, le parcours complet de l'espace conformationnel n'a été possible que pour la plus petite protéine de l'ensemble des protéines étudiées. Pour la moitié des autres protéines, plus de 70% des atomes ont vu leurs positions échantillonnées. La qualité des structures obtenues a regressé en comparaison avec les simulations faites avec des distances exactes. En effet, seulement 53% des valeurs de phi et psi étaient localisées dans la zone 'core' du diagramme de Ramachandran, et le pourcentage d'atomes impliqués dans un clash stérique s'élevait jusqu'à 22% pour quelques protéines. Concernant le temps de calcul, le taux de génération de conformations a été déterminé pour chaque protéine cible, et il s'est avéré que globalement sa valeur etait compétitive par rapport aux valeurs des taux observables dans la littérature
Structural biology has allowed us expand our knowledge of living organisms. It is defined as the investigation of the structure and function of biological systems at the molecular level. Studying a biomolecule's structure offers insight into its geometry, as angles and distances between the biomolecule's atoms are measured in order to determine the biomolecular structure. The values of these geometrical parameters may be obtained from biophysical techniques, such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. One of the most used methods to calculate protein structures from geometric restraints is simulated annealing. This method does not guarantee an exhaustive sampling of protein conformational space, which is a shortcoming as one protein may adopt multiple functional conformations, and it is important to determine them exhaustively. In this PhD project, the efficiency of a new method - derived from operations research and computational geometry - is studied in order to answer this question: How does this method explore the conformational spaces of small proteins? This method - implemented within the iBPprot software framework - treats protein structure determination as a distance geometry problem, which the interval branch-and-prune algorithm tries to solve by the full exploration of its solutions space. The results obtained by iBPprot on a set of test proteins, with sizes ranging from 24 to 120 residues and with known structures, are analyzed here. Using short-range exact distance restraints, it was possible to rebuild the structure of all protein targets, and for many of them it was possible to exhaustively explore their conformational spaces. In practice, it is not always possible to obtain exact distance restraints from experiments. Therefore, this method was then tested with interval data restraints. In these cases, iBPprot permitted the sampling of the positions of more than 70% of the atoms constituting the protein backbone for most of the targets. Furthermore, conformations whose r.m.s. deviations closer than 6 Angstrom to the target ones were obtained during the conformational space exploration. The quality of the generated structures was satisfactory with respect to Ramachandran plots, but needs improvement because of the presence of steric clashes in some conformers. The runtime for most performed calculations was competitive with existing structure determination method

Denna studie gick ut på att jämföra tre olika algoritmer som har använts för bred kollisionsdetektering, dessa algoritmer var Kd-tree, Octree och Sweep and prune. Kd-tree och Octree är spatiala datastrukturer, d.v.s. att de hanterar objekt inom specifika volymer. Sweep and prune använder istället listor för att ta reda på om objekt kolliderar. Fokus låg på att se hur stor skillnad algoritmernas exekveringstid hade jämfört med ’brute force’-implementationen och jämfört med varandra. Det utfördes ett antal olika experiment på algoritmerna med ett antal olika inställningar för att kunna utvärdera hur de presterar i olika situationer. Dessa inställningar var t.ex. antalet boids, deras hastighet och hur långt de kunde se. Resultatet visade att Sweep and prune presterade bäst med en liten mängd boids medans de andra algoritmerna kom ikapp och presterade bättre när antalet objekt ökade, då Kd-tree presterade bäst överlag. Studien kan vara till hjälp med att välja vilken bred kollisionsdetekteringsalgoritm som kan tänkas implementeras för en applikation.

Traditionally, burley tobacco has been harvested by hand because the green plant weight, volume, and leaf fragility make mechanical harvesting very challenging. This study examined possible ways to wilt a plant still standing in the field (termed ‘pre-wilting’) to reduce weight, volume, and leaf fragility. Several methods of pre-wilting burley tobacco plants in the field were explored including: root pruning, stalk girdling, freezing with liquid nitrogen, and burning. Experiments were conducted in three locations over three consecutive years during the tobacco harvest season. Leaf breaking angle, leaf moisture content and time-lapse photography were investigated as methods to quantify treatment effects on wilting. The time-lapse photography helped reveal that wilting was most prevalent during the late afternoon, and that wilted plants sometimes began to recover after more than five days, apparently due to root re-growth. Root pruning was the only mechanical means that caused witling reliably during the first two years of testing, and even then the results were somewhat inconsistent. During the third year, a high-clearance tobacco sprayer was modified with a hydraulically actuated coulter disc in order to root-prune a large number of subjects.

It has become well known that an evolutionary tree is inadequate to represent fully the history of life. Two possible ways of dealing with this are the rooted subtree prune and regraft distance between a pair of trees, which measures how different they are, and the slightly more biologically sound hybridisation number of a set of trees that attempts to determine the minimum number of hybrid events that must have occurred for a given set of evolutionary trees. When characterised via agreement forests both problems are, although NP hard, fixed parameter tractable---meaning the problem can be converted to a similar problem with a smaller input size. This thesis investigates ways of improving existing algorithms for calculating the minimum rooted subtree prune and regraft distance and hybridisation number for a pair or, in the latter case, set of trees. In both cases a technique is used that allows the problem to be rekernelised during the run of the program. Another, less effective method, is also looked at which finds the rooted subtree prune and regraft distance or hybridisation number solely on what cannot be contained within any agreement forest. Additionally the characterisation of the minimum rooted subtree prune and regraft distance via maximum agreement forests is extended to non-binary trees and the hybridisation number of a set of phylogenetic trees is extended to unrooted trees.

Despite being found in all presently sequenced genomes, the evolution of tandemly repeated sequences has only just begun to be understood. We can represent the duplication history of tandemly repeated sequences with duplication trees. Most phylogenetic techniques need to be modified to be used on duplication trees. Due to gene loss, it is not always possible to reconstruct the duplication history of a tandemly repeated sequence. This thesis addresses this problem by providing a polynomial-time locally optimal algorithm to reconstruct the duplication history of a tandemly repeated sequence in the presence of gene loss. Supertree methods cannot be directly applied to duplication trees. A polynomial-time algorithm that takes a forest of ordered phylogenies and looks for a super duplication tree is presented. If such a super duplication tree is found then the algorithm constructs the super duplication tree. However, the algorithm does not always find a super duplication tree when one exists. The SPR topological rearrangement in its current form cannot be used on duplication trees. The necessary modifications are made to an agreement forest so that the SPR operation can be used on duplication trees. This operation is called the duplication rooted subtree prune and regraft operation (DrSPR). The size of the DrSPR neighbourhood is calculated for simple duplication trees and the tree shapes that maximize and minimize this are given.

Dentre as técnicas de mineração existentes encontra-se a associação, responsável por identificar relações que ocorrem no conjunto de dados. Embora a associação seja uma das técnicas mais utilizadas, a quantidade de padrões extraídos pode vir a sobrecarregar o usuário de tal maneira que encontrar algo interessante dentre a imensidão de padrões obtidos passa a ser um novo desafio. Para solucionar esse problema, uma grande parte dos trabalhos relacionados à associação está voltada a etapa de pós-processamento. Esses trabalhos geralmente propõem abordagens de pós-processamento que visam, segundo determinada estratégia, facilitar a busca pelos padrões interessantes ao domínio. Nos últimos anos, essas abordagens têm incluído no processo o conhecimento e/ou interesse do usuário sobre o domínio. Contudo, nas abordagens atualmente existentes, o usuário deve, por meio de algum formalismo descrever explicitamente seu conhecimento e/ou interesse, requerendo do usuário um tempo considerável, podendo levar, inclusive, a especificações incompletas e/ou incorretas. Além disso, na maioria das vezes, o usuário não tem ideia do que é provavelmente interessante, nem a partir de quais relações iniciar a busca. Nota-se, portanto, que um dos desafios dessas abordagens é considerar o conhecimento e/ou interesse do usuário. Além disso, é necessário considerar também o número de regras que o usuário analisará. A análise de regras feita por um especialista é custosa e, na maioria dos casos, o usuário quer explorar as regras geradas sem limitar a exploração ao conhecimento que ele já possui. Portanto, é importante que o usuário avalie o menor número de regras possível e, com base nessa avaliação, abordagens de pós-processamento consigam o auxiliar na busca pelas regras que ele poderá considerar interessante. Para tanto, é proposto neste trabalho que o pós-processamento seja tratado como um problema de classificação semissupervisionada transdutiva, uma vez que permite que o usuário rotule, considerando classes pré-definidas (por exemplo, \"Interessante\" ou \"Não Interessante\"), apenas algumas regras do conjunto a ser explorado para que todas as outras regras sejam automaticamente rotuladas. Além disso, por meio da definição dos rótulos de algumas regras, é possível capturar implicitamente o conhecimento e/ou interesse do usuário sobre o domínio. Para tanto, é necessário que as regras sejam modeladas de maneira a permitir: (a) selecionar as regras a serem rotuladas pelo usuário a fim de capturar implicitamente seu conhecimento e/ou interesse; (b) propagar os rótulos das regras já classificadas pelo usuário a todas as outras regras não rotuladas. Desse modo, neste trabalho, as regras foram modeladas via redes, uma vez que: (i) uma vasta quantidade de medidas de exploração de redes pode ser utilizada, em conjunto com as informações fornecidas pelo usuário, a fim de viabilizar o item (a); (ii) algoritmos de propagação de rótulos podem ser utilizados a fim de viabilizar o item (b). Diante do apresentado, ressalta-se que as contribuições deste trabalho estão na capacidade de se extrair o conhecimento e/ou interesse do usuário de acordo com as características da base de dados e direcionar sua exploração sem a necessidade de se definir previamente o que será explorado. Além disso, os resultados obtidos demonstram a capacidade da PARLP em direcionar o usuário para o conhecimento considerado interessante, reduzindo, para tanto, a quantidade de regras a serem exploradas. Por fim, este trabalho contribui também para demonstrar que é possível tratar o pós-processamento de regras de associação como um problema de propagação de rótulos.
One of the existing data mining techniques is association rules, responsible for identifying relationships that occur in the data set. Although the association rule is one of the most widely used techniques, the amount of extracted patterns can overload the user in such a way that finding interesting patterns among the large amount of obtained patterns becomes a challenge. To solve this problem, a large part of the association-related work is focused on the post-processing step. These works generally propose a post-processing approaches that, according to a certain strategy, aims facilitating the search for interesting patterns. Nowadays, approaches have included the user knowledge in the domain and / or interests on the process. However, in the current existing approaches, the user knowledge and/or interest must be explicitly described by some formalism, requiring a considerable time and may even lead to incomplete and / or incorrect specifications. In addition, the user has no idea what probably is interesting or which patterns to begin the searching. Notice that one of the challenges of these approaches is to consider the knowledge and / or user interest. In addition, consider the number of rules the user will examine is necessary. The analysis of the rules by an expert is expensive and, in most cases, the user wants to explore the rules generated without limiting exploration to the knowledge he already has. Therefore, the user evaluate the fewest amount of rules possible is important and, based on this assessment, the post-processing approaches be able to assist in the search for the rules that he may consider interesting. So, in this work is proposed that the post-processing is treated as a transductive semi supervised classification problem, since it allows the user to label some rules based on two predefined classes (e.g. \"interesting\"or \"not interesting\"), in a way that just a small amount of the rule set needs to be explored and all other association rules are automatically labeled. Furthermore, you can implicitly capture the knowledge and / or user interest in the domain by labeling some rules. Thus, the rules need to be modeled to allow: (a) select the rules to be labeled by the user to implicitly capture their knowledge and / or interest; (b) propagate the rules\' labels classified by the user to all not labeled rules. To do so, the rules were modeled via networks in this work, due to: (i) a large amount of network measures can be used in conjunction with the information provided by the user, to make item (a) possible; (ii) label propagation algorithms can be used in order to make item (b) possible. Therefore, we highlight that the contributions of this work are the ability to extract knowledge and / or user interest according to database characteristics and direct the user exploration without previously defining what will be explored. In addition, the results demonstrate that the proposed approach is able to direct the user to the knowledge considered interesting, reducing the amount of rules to be explored. Finally, this work also contributes to demonstrate that treat the post-processing of association rules as a problem of propagation of labels is possible.

Dois experimentos foram conduzidos em casa de vegetação com o objetivo de avaliar a influência do espaçamento entre plantas, do sistema de condução e da altura de poda de mini melancia conduzidas na vertical. O híbrido utilizado foi o Smile. O delineamento experimental foi em blocos casualizados, com quatro repetições. O primeiro experimento foi conduzido no período de 12 de agosto a 25 de novembro de 2008, cujos tratamentos foram três alturas de poda da haste principal (1,7; 2,2 e 2,7 m) e dois espaçamentos entre plantas (30 e 45 cm). O segundo experimento foi conduzido no período de 20 de outubro de 2008 a 16 de janeiro de 2009 e os tratamentos foram compostos por três sistemas de condução (S1 = uma haste e um fruto por planta conduzido na haste principal; S2 = uma haste e um fruto por planta conduzido na haste secundária e S3 = duas hastes e um fruto por planta conduzido na haste principal) e dois espaçamentos entre plantas (30 e 60 cm). No primeiro experimento o índice de área foliar, o teor de sólidos solúveis (SS), de ácido ascórbico, a acidez titulável (AT) e a produtividade comercial foram maiores no espaçamento de 30 cm entre plantas. A produtividade total sofreu influência tanto da altura de poda como do espaçamento entre plantas, cujo maior valor foi obtido pela combinação da altura de poda de 2,7m e espaçamento de 30 cm. Por outro lado, foi na altura de poda de 2,2 m e espaçamento de 45 cm que ocorreu o maior valor para a relação SS/AT. A altura de poda de 1,7 m proporcionou maior porcentagem de frutos colhidos na última colheita. No segundo experimento, o sistema de condução S2 no espaçamento de 30 cm entre plantas proporcionou maior índice de área foliar e firmeza da polpa. A produtividade total foi maior no sistema de condução S3 em relação somente ao sistema de condução S1. Os sistemas de condução S1 e S3 promoveram maior porcentagem de frutos colhidos na primeira colheita, enquanto que no sistema S2 a maior parte dos frutos foi colhida na última colheita. Dessa forma, levando-se em consideração as características avaliadas, de modo geral, no primeiro experimento, a melhor opção para o produtor é a realização da poda da haste principal a 2,2 m de altura e espaçamento de 30 cm entre plantas. No segundo experimento, a condução com duas hastes e um fruto (S3) com espaçamento de 30 cm entre plantas, além de constituir um sistema de condução simples, proporciona elevada produtividade e qualidade dos frutos.
Two experiments were conducted in greenhouse in order to evaluate the influence of plants spacing, the training systems and the height of pruning of main stem of mini watermelon through vertical conduction. The hybrid used was \'Smile\'. The experimental design was randomized blocks with four replications. The first experiment was carried out from August 12 to November 25, 2008. The treatments were three heights of pruning of main stem (1.7, 2.2 and 2.7 m) and two plants spacing (30 and 45 cm). The second experiment was carried out from October 20, 2008 to January 16, 2009 and the treatments consist of three training systems (S1 = one stem and one fruit per plant fixed in the main stem, S2 = one stem and one fruit plant fixed in the lateral branch and S3 = two stems and one fruit per plant fixed in the main stem) and two plants spacing (30 and 60 cm). In the first experiment the leaf area index, the content of soluble solids content (SS), ascorbic acid, acidity titratable (AT) and marketable yield were higher in 30 cm plants spacing. The total yield was influenced both the height of pruning and the plants spacing, whose greatest value was obtained by the combination of height of pruning of 2.7 m and spacing of 30 cm. However, the highest value for the ratio SS/AT was observed in the pruning of 2.2 m, and spacing of 45 cm. The height of pruning of 1.7 m provided the greatest percentage of fruit harvested in the last harvest. In the second experiment, the training system S2 with spacing of 30 cm between plants provided higher leaf area index and firmness of flesh. The total yield was higher in the training system S3 only than the training system S1. The training systems S1 and S3 promoted higher percentage of fruit harvested in the first harvest, while the system S2 the majority of fruits were harvested at last. Thus, taking into account the characteristics evaluated, in general, in the first experiment, the better option for the producer is the performance of pruning to 2.2 m in height and 30 cm plants spacing. In the second experiment, the conduction with two stems and one fruit (S3) with spacing of 30 cm between plants, and as a simple training system, provide high productivity and quality of fruit.

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The objective of the present work was to determine the technical parameters for the compaction and the quality of the pellets produced from different types of forest biomass and residual agricultural biomass. The choice of the types of biomass was based on the production volume of the main agricultural and forestry crops of the State of Santa Catarina, and the economic, social and environmental importsnce of the same for the segments that produce them. In this way, the physical, chemical and energetic properties of four types of agricultural and forest residual biomass (Pinus chip, apple pruning branches, pinyon faults and araucaria grimpa) were used to produce the pellets. Thirteen treatments in the study were analyzed, consisting of pellets produced with: 100% pinus (P100), considered as a control treatment; 75% pinus and 25% of one of the analyzed residues (F25P75, when the residue was pinion failure, G25P75, for the treatment containing grimpa, and Pm25P75, when the treatment had apple pruning); 50% of pine and 50% of other analyzed components, being F50P50 (for pinion failure), G50P50 (grimpa) and Pm50P50 (apple pruning); (F100P25), G75P25 (Grimpa) and Pm75P25 (apple pruning) and the homogeneous treatments with 100% of failure (F100); 100% grimpa (G100) and 100% apple pruning (Pm100). For each treatment was established for the ideal parameters of temperature, pressure and compaction of the pellets produced in laboratory pelletizer. These data were established based on the physical and chemical properties of biomasses in nature and also on the quality of the non-process obtained pellet by means of successive compaction tests. After production of the pellets a quality of this biofuel was determined by its physical, mechanical, chemical and energetic properties. From the results obtained in the laboratory, pellets were classified based on the quality criteria of ISO 17225-2 for biomass pellets for energy generation. It was concluded that the treatments F75P25, G75P25 G50P50 and G25P75 were the only ones that reached quality for residential and commercial use. The treatment with better quality for residential and commercial use was treatment G25P75. The treatments Pm100, Pm75P25, Pm50P50, Pm25P75 and G100 did not achieve average ratings in relation to ISO 17225-2 for any quality category described in the standard
O objetivo do presente trabalho foi determinar os parâmetros técnicos para a compactação e a qualidade dos pellets produzidos a partir de diferentes tipos de biomassa florestal e agrícola residual. A escolha dos tipos de biomassa foi baseada no volume de produção dos resíduos das principais culturas agrícolas e florestais do Estado de Santa Catarina, e da importância econômica, social e ambiental dos mesmos para os segmentos que os produzem. Desta forma, foram caracterizadas as propriedades físicas, químicas e energéticas de quatro tipos de biomassas residuais agrícolas e florestais (maravalha de pinus, galhos de poda de macieira; falhas de pinhão; grimpa de araucária) que foram utilizadas para a produção dos pellets. Foram analisados 13 tratamentos no estudo, que consistiram de pellets produzidos com: 100% de pinus (P100), considerado como tratamento testemunha; 75% de pinus e 25% de um dos resíduos analisados (F25P75, quando o resíduo era a falha de pinhão, G25P75, para o tratamento contendo grimpa, e Pm25P75, quando o tratamento possuía poda de maça); 50% de pinus e 50% de outro componente analisado, sendo F50P50 (para falha de pinhão), G50P50 (grimpa) e Pm50P50 (poda de maça); misturas contendo 25% de pinus e 75% do outro resíduo analisado, sendo F75P25 (falha de pinhão), G75P25 (grimpa) e Pm75P25 (poda de maça) e os tratamentos homogêneos com 100% de falha (F100); 100% de grimpa (G100) e 100% de poda de maça (Pm100). Para cada tratamento foram estabelecidos os parâmetros ideais de temperatura, pressão e velocidade de compactação dos pellets produzidos em peletizadora piloto de laboratório. Estes parâmetros foram estabelecidos com base nas propriedades físicas e químicas das biomassas in natura, e também em função da qualidade do pellet obtido no processo, por meio de testes de compactação sucessivos. Após a produção dos pellets foi determinada a qualidade deste biocombustível por meio de suas propriedades físicas, mecânicas, químicas e energéticas. A partir dos resultados obtidos em laboratório, os pellets foram classificados com base nos critérios de qualidade da norma ISO 17225-2 para pellets de biomassa para geração de energia. Concluiu-se que os tratamentos F75P25, G75P25 G50P50 e G25P75 foram os únicos que atingiram qualidade para uso residencial e comercial. O tratamento com melhor qualidade para uso residencial e comercial foi o tratamento G25P75. Os tratamentos Pm100, Pm75P25, Pm50P50, Pm25P75 e G100 não conseguiram classificações médias em relação a ISO 17225-2 para nenhuma categoria de qualidade descrita na norma

En bioinformatique structurale, une partie des méthodes computationnelles qui calculent les structures de protéines à l'aide de données expérimentales, effectuent une optimisation de la position des atomes sous les contraintes expérimentales mesurées sur le système étudié, ainsi que sous des contraintes provenant de la connaissance générique de la stéréochimie organique. Ces méthodes d'optimisation présentent l'inconvénient de ne pas garantir la détermination de la meilleure solution. De plus, la validation de l'optimisation se fait en comparant les résultats obtenus pour des calculs répétés, et le résultat d'un calcul est accepté dans la mesure où le même résultat est obtenu plusieurs fois. Par cette approche, on rend plus difficile la détection de conformations alternatives de protéines, qui sont pourtant le sujet d'un vif intérêt dans la littérature. En effet, le développement de la sensibilité des techniques de résonance magnétique nucléaire (RMN) a permis de mettre en évidence plusieurs cas d'échange conformationnel reliés à la fonction des protéines. Dans ce projet de thèse, nous avons étudié une nouvelle approche pour le calcul de structures des protéines et l'exploration de leurs espaces conformationnels, basée sur la résolution du problème de Géométrie de Distance associé aux contraintes de distances dans une protéine par l'algorithme "interval Branch and Prune". Le logiciel implémentant cette méthode est appelée iBPprot, il incarne l'une des premières tentatives d'échantillonnage exhaustive des espaces conformationnels des protéines. Dans un premier temps, on s'est intéressé à l'application de la méthode en utilisant exclusivement des constraintes de distances exactes. Les résultats ont démontré que iBPprot était capable de reconstruire des structures références en s'appuyant seulement sur quelques contraintes à courte portée. De plus, la reconstruction a été d'une précision telle que la conformation générée présentait un RMSD de 1 Angstrom maximum avec la structure référence. L'exploration exhaustive de l'espace conformationnel a été possible pour une bonne partie des protéines cibles. Les temps de calcul pour l'exploration des espaces conformationnels ont été très variables allant de quelques secondes pour quelques protéines jusqu'à des semaines pour d'autres. L'évaluation de la qualité des structures obtenues a démontré qu'au moins 68% des valeurs de phi et psi sont localisées dans la zone 'core' du diagramme de Ramachandran. Cependant, des clash stériques ont été détectées dans plusieurs conformations mettant en jeu jusqu'à 7% d'atomes dans quelques unes de ces conformations. Dans un deuxième temps, on s'est intéressé à l'application de la méthode en incluant des intervalles de distances comme contraintes dans les calculs. Dans ce cas de figure, la méthode a réussi a reconstruire des structures références avec un RMSD inférieur à 5 Angstrom pour plus de la moitié des protéines cibles. En contre partie, le parcours complet de l'espace conformationnel n'a été possible que pour la plus petite protéine de l'ensemble des protéines étudiées. Pour la moitié des autres protéines, plus de 70% des atomes ont vu leurs positions échantillonnées. La qualité des structures obtenues a regressé en comparaison avec les simulations faites avec des distances exactes. En effet, seulement 53% des valeurs de phi et psi étaient localisées dans la zone 'core' du diagramme de Ramachandran, et le pourcentage d'atomes impliqués dans un clash stérique s'élevait jusqu'à 22% pour quelques protéines. Concernant le temps de calcul, le taux de génération de conformations a été déterminé pour chaque protéine cible, et il s'est avéré que globalement sa valeur etait compétitive par rapport aux valeurs des taux observables dans la littérature
Structural biology has allowed us expand our knowledge of living organisms. It is defined as the investigation of the structure and function of biological systems at the molecular level. Studying a biomolecule's structure offers insight into its geometry, as angles and distances between the biomolecule's atoms are measured in order to determine the biomolecular structure. The values of these geometrical parameters may be obtained from biophysical techniques, such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. One of the most used methods to calculate protein structures from geometric restraints is simulated annealing. This method does not guarantee an exhaustive sampling of protein conformational space, which is a shortcoming as one protein may adopt multiple functional conformations, and it is important to determine them exhaustively. In this PhD project, the efficiency of a new method - derived from operations research and computational geometry - is studied in order to answer this question: How does this method explore the conformational spaces of small proteins? This method - implemented within the iBPprot software framework - treats protein structure determination as a distance geometry problem, which the interval branch-and-prune algorithm tries to solve by the full exploration of its solutions space. The results obtained by iBPprot on a set of test proteins, with sizes ranging from 24 to 120 residues and with known structures, are analyzed here. Using short-range exact distance restraints, it was possible to rebuild the structure of all protein targets, and for many of them it was possible to exhaustively explore their conformational spaces. In practice, it is not always possible to obtain exact distance restraints from experiments. Therefore, this method was then tested with interval data restraints. In these cases, iBPprot permitted the sampling of the positions of more than 70% of the atoms constituting the protein backbone for most of the targets. Furthermore, conformations whose r.m.s. deviations closer than 6 Angstrom to the target ones were obtained during the conformational space exploration. The quality of the generated structures was satisfactory with respect to Ramachandran plots, but needs improvement because of the presence of steric clashes in some conformers. The runtime for most performed calculations was competitive with existing structure determination method

Thesis (M.A. in National Security Affairs) Naval Postgraduate School, December 1998.
"December 1998." Thesis advisor(s): Thomas C. Bruneau, Scott D. Tollefson. Includes bibliographical references (p. 93-96). Also available online.

Software is the heartbeat of modern technology. To keep up with the new demands and expansion of requirements, changes are constantly introduced to the software, i.e., changes can also be made to fix an existing fault/defect. However, these changes might also cause further faults/defects in the software. This study aims to investigate the possible correlation between change-proneness and fault-proneness in object- oriented systems. Forty releases of five different open-source systems are analysed to quantify change- and fault-proneness; Beam, Camel, Ignite, Jenkins, and JMe- ter, then statistic evidence is presented as to answer the following: (1) Is there is a relationship between change-proneness and fault-proneness for classes in object- oriented systems? (2) Is there a relationship between size and fault-proneness for classes in object-oriented systems? and (3) Is there a relationship between size and change-proneness for classes in object-oriented systems? Using the Wilcoxon rank- sum test, the results show that: (1) there is a correlation between change- and fault- proneness at a statistically significant level and (2) a correlation also exists betweenclass size and its change- and fault-proneness at a statistically significant level.

Multi environment trials conducted over mapping population are often used to test genotypes in a set of environments that represent the target environmental range. The first part of this work is the evaluation of the ‘Nure’ x ‘Tremois’ double-­‐haploid mapping population, together with an association panel comprising 185 barley varieties representative of the barley germplasm cultivated in the Mediterranean basin. Plant material was tested across eighteen site by year field trials combination, in six countries across the Mediterranean basin. Trials were growth at sites contrasting for natural rainfall (high vs low on the base of past meteorological data) or at the same site with one being rainfed and the other with supplementary irrigation. Trials conducted for two years in each one of the sites and this allowed tocollect a huge data series comprising agronomical traits defining grain yield and yield components, phenological and environmental data, subsequently used to identify genomic regions involved in barley adaptation. The 118 doubled haploid lines of the mapping population were genotyped with Diversity Array Technology® (DaRT) marker assay and subsequently a total of 15 CAPS and SSCP marker for candidate genes involved in phenology regulation and abiotic stress response were added to the linkage map based on DaRT markers. Data collected were firstly used to perform QTLs analysis with composite interval mapping for any environment/ trait combination, results showed eight QTLs for grain yield, days to heading and grain yield components. . The two mostly frequents QTLs for grain yield and days to heading were located on barley chromosome 1H (3 trials), 2H (8 trials) and 5H (5 trials) overlapping respectively HvFT3 gene, the earliness per se locus (eam6/Eps-­‐2) and the vernalization gene Vrn_H1. A further QTL multi-­‐environment analysis was performed and revealed that across the 18 field trials QTL for eam6/Eps-­‐2 (2H) and Vrn-­‐H1 (5H) were commons for days to heading and grain yield. We use all the environmental information collected to check QTLs sensitivities to co-­‐environmental co-­‐variables. Most of significant associations collected were related to temperature and temperature-­‐based variables troughtout the growing cycle. Eam6/Eps-­‐2 showed non-­‐crossover QTL.E interaction, while for Vrn-­‐H1 crossover interactions were revealed. The 185 barley accession were genotyped with 1536 SNPs and data collected for this population for cold resistance in two field trials in Spain an Italy, the first trial was characterized by an exceptional winter, while the second was previously know has frost-­‐prone environment. Results from genome wide association analysis showed 13 positive associations with specific genomic regions. Interestingly several of these QTL were coincident with the position of previously mapped loci for cold tolerance, on chromosomes 2HL, 4HL and 5HL.
Els assajos en localitats múltiplas de poblacions de mapeo s'utilitzen freqüentment per a testar genotips en un conjunt d'ambients representatius de la condicions climàtiques on es volen introduir aquests genotips. La primera part d'això treball ha estat l'avaluació de la població de mapeo ‘Nure x Tremois’ constituïda de 118 de doble haploides d'ordi, juntament amb panell d'associació que comprèn 185 varietats d'ordi representatives del germoplasma conreat en la conca Mediterrània. El material vegetal ha estat assajat en una combinació de divuit camps per any desllorigats en sis països de la conca mediterrània. Els assajos s'han portat a terme en camps amb diferent disponibilitat d'aigua, classificats sobre la base de les dades relatives a les freqüència i quantitat de les precipitacions o en el mateix lloc amb un camp en secà i altre regat. Els assajos es van portar a terme per dos anys en cada localitat i això va permetre la recollida d'un gran volum de dades que comprenen caràcters agronómicos relacionats amb rendiment i components del rendiment, dades fenológicos i ambientals. Aquestes dades es van utilitzar després per a la identificació de regions genomicas involucrades en l'adaptació de l'ordi a l'ambient. Els 118 dobles haploides de la població ‘Nure x Tremois’ es genotiparon amb marcadors DaRT (Diversity Array Technology), després un set de 15 marcadors CAPS I SCCP per a gens candidats involucrats en la regulació de les fases fenológicas van ser afegits al mapa de lligament construït amb els marcadors DaRT. Les dades van ser utilitzats per a fer una anàlisi de QTL amb procediment ‘Composite Interval Mapping’ para cada combinació ambienti/ caràcter. Es van trobar diversos QTLs per rendiment i data d'espigolat i components del rendiment. Els QTL mes freqüents trobats per rendiment i data de floració i components del rendiment estan localitzats en els cromosomes 1H (3 camps), 2H (8 camps) i 5H (5 camps) coincidents respectivament amb HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus i amb el locus de vernalización Vrn-­‐H1. Una ulterior anàlisi de QTL feta amb el mètode “Multi Environment Trial” ha revelat que els QTL localitzats en el locus eam6/Eps-­‐2 (cromosoma 2H) i Vrn-­‐H1 (cromosoma 5H) són comunes per rendiment i data de floració en els 18 camps d'assaig. Per això utilitzem tots el dades ambientals col·leccionades durant tot el cicle del cultiu per a investigar la sensibilitat de dites QTL a les co-­‐variables ambientals. La majoria de les associacions oposades estan relacionades amb temperatures i variables relacionades amb aquestes. Eam6/Eps-­‐2 mostra una interacció de tipus quantitatiu amb aquestes variables mentre Vrn-­‐H1 mostra una interacció de tipus qualitatiu amb aquestes variables. Les 185 varietats assajades van ser genotipadas amb 185 SNPs i fenotipadas per resistència a fred en dos assajos uneixo a Espanya i altre a Itàlia. El primer assaig va ser caracteritzat per un hivern excepcionalment fred, mentre el d'Itàlia ha estat utilitzat en passat per testar resistència a fred a causa de els hiverns rígids que solen registrar-­‐se en aquesta localitat. Les dades van ser utilitzats per a portar a terme la analisis GWAS “Genome Wide Association Analysis” . Els resultats van permetre identificar 13 regions genomicas involucrades en la resistència a frio. Entre elles tres regions coincideixen amb loci ja mapeados i coneguts per ser involucrats en la resposta a frio en los cromosomes 2HL, 4HL i 5HL.
Los ensayos en localidades múltiplas de poblaciones de mapeo se utilizan frecuentemente para testar genotipos en un conjunto de ambientes representativos de la condiciones climáticas donde se quieren introducir dichos genotipos. La primera parte de esto trabajo ha sido la evaluación de la población de mapeo ‘Nure x Tremois’ constituida de 118 de doble haploides de cebada, junto con panel de asociación que comprende 185 variedades de cebada representativas del germoplasma cultivado en la cuenca Mediterránea. El material vegetal ha sido ensayado en una combinación de dieciocho campos por año dislocados en seis países de la cuenca mediterránea. Los ensayos se han llevado a cabo en campos con diferente disponibilidad de agua, clasificados en base a los datos relativos a las frecuencia y cantidad de las precipitaciones o en el mismo sitio con un campo en secano y otro regado. Los ensayos se llevaron a cabo por dos años en cada localidad y esto permitió la recogida de un gran volumen de datos que comprenden caracteres agronómicos relacionados con rendimiento y componentes del rendimiento, datos fenológicos y ambientales. Dichos datos se utilizaron después para la identificación de regiones genomicas involucradas en la adaptación de la cebada al ambiente. Los 118 dobles haploides de la población ‘Nure x Tremois’ se genotiparon con marcadores DaRT (Diversity Array Technology), después un set de 15 marcadores CAPS Y SCCP para genes candidatos involucrados en la regulación de las fases fenológicas fueron añadidos al mapa de ligamento construido con los marcadores DaRT. Los datos fueron utilizados para hacer una análisis de QTL con procedimiento ‘Composite Interval Mapping’ para cada combinación ambiente/ carácter. Se encontraron varios QTLs por rendimiento y fecha de espigado y componentes del rendimiento. Los QTL mas frecuentes encontrados por rendimiento y fecha de floración y componentes del rendimiento están localizados en los cromosomas 1H (3 campos), 2H (8 campos) y 5H(5 campos) coincidentes respectivamente con HvFT3 locus, eam6/Eps-­‐2 (earliness per se) locus y con el locus de vernalización Vrn-­‐H1. Una ulterior análisis de QTL hecha con el método “Multi Environment Trial” ha revelado que los QTL localizados en el locus eam6/Eps-­‐2 (cromosoma 2H) y Vrn-­‐H1 (cromosoma 5H) son comunes por rendimiento y fecha de floración en los 18 campos de ensayo. Por esto utilizamos todos lo datos ambientales coleccionadas durante todo el ciclo del cultivo para investigar la sensibilidad de dichos QTL a las co-­‐variables ambientales. La mayoría de las asociaciones encontradas están relacionadas con temperaturas y variables relacionadas con estas. Eam6/Eps-­‐2 muestra una interacción de tipo cuantitativo con dichas variables mientras Vrn-­‐H1 muestra una interacción de tipo cualitativo con dichas variables. Las 185 variedades ensayadas fueron genotipadas con 185 SNPs y fenotipadas por resistencia a frío en dos ensayos uno en España y otro en Italia. El primer ensayo fue caracterizado por un invierno excepcionalmente frío, mientras el de Italia ha sido utilizado en pasado por testar resistencia a frío debido a los inviernos rígidos que suelen registrarse en dicha localidad. Los datos fueron utilizados para llevar a cabo la analisis GWAS “Genome Wide Association Analysis”. Los resultados permitieron identificar 13 regiones genomicas involucradas en la resistencia a frio. Entre ellas tres regiones coinciden con loci ya mapeados y conocidos por ser involucrados en la respuesta a frio en los cromosomas 2HL, 4HL y 5HL.

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Exploratory testing is a software testing approach that emphasizes the tester’s experience in the attempt to maximize the chances to find bugs and minimize the time effort applied on satisfying such a goal. It is naturally a GUI-oriented testing activity for GUI-based systems. However, inmost cases,exploratory testing strategies may not be accurate enough to reach changed code regions. To reduce this gap, in this work, we propose a way of aiding exploratory testing by providing a GUI model of the regions impacted by internal code changes (for example, as result of change requests to fix previous bugs as well as for software improvement). We create such a delimited GUI model by pruning an original GUI model, quickly built by static analysis, using a reachability relation between GUI elements (i.e., windows, buttons, text fields, etc.) and internal source code changes (classes and methods). To illustrate the idea we provide promising data from two experiments, one from the literature and another from our industrial partner.
Teste exploratório é uma abordagem de teste de software que enfatiza a experiência do testador na tentativa de maximizar as chances de encontrarbugs e minimizar o esforço de tempo aplicado na satisfação desse objetivo. É naturalmente uma atividade de testes orientada à GUI aplicada em sistemas que dispõem de GUI. No entanto, na maioria dos casos, as estratégias de testes exploratórios podem não ser suficientemente precisas para alcançar as regiões de código alteradas. Para reduzir esta lacuna, neste trabalho nós propomos uma forma de auxiliar os testes exploratórios, fornecendo um modelo de GUI das regiões impactadas pelas mudanças internas de código (por exemplo, como resultado de solicitações de mudanças para corrigirbugs anteriores, bem como, para realização de melhorias do software). Criamos um modelo de GUI delimitado, podando um modelo de GUI original, construído rapidamente através de análise estática, usando uma relação de alcançabilidade entre elementos de GUI (janelas, botões, campos de textos) e alterações de código interno (classes e métodos). Para ilustrar a ideia, nós fornecemos dados promissores de dois experimentos, um da literatura e outro de nosso parceiro industrial.

Since the introduction of the American Academy of Pediatrics Back to Sleep Campaign infants have not met the recommendation to “incorporate supervised, awake “prone play” in their infant’s daily routine to support motor development and minimize the risk of plagiocephaly”. Interventions are needed to increase infants’ tolerance for prone position and prone playtime to reduce the risk of plagiocephaly and motor delays. Associative learning is the ability to understand causal relationship between events. Operant conditioning is a form of associative learning that occurs by associating a behavior with positive or negative consequences. Operant conditions has been utilized to encourage behaviors such as kicking, reaching and sucking in infants by associating these behaviors with positive reinforcement. This dissertation is a compilation of three papers that each represent a study used to investigate a potential play based interventions to encourage prone motor skills in infants. The first paper describes a series of experiment used to develop the Prone Play Activity Center (PPAC) and experimental protocols used in the other studies. The purpose of the second study was to determine the feasibility of a clinical trial comparing usual care (low tech) to a high-tech intervention based on the principles of operant conditioning to increase tolerance for prone and improve prone motor skills. Ten infants participated in the study where parents of infants in the high tech intervention group (n=5) used the PPAC for 3 weeks to practice prone play. Findings from this study suggested the proposed intervention is feasible with some modifications for a future large-scale clinical trial. The purpose of the third study evaluated the ability of 3-6 months old infants to demonstrate AL in prone and remember the association learned a day later. Findings from this study suggested that a majority of infants demonstrated AL in prone with poor retention of the association, 24 hours later. Taken together these 3 papers provide preliminary evidence that a clinical trial of an intervention is feasible and that associative learning could be used to reinforce specific prone motor behaviors in the majority of infants.

The literature examining the offence supportive cognition of sexual offences against adult women appears to be divided into two different approaches. The social psychological approach utilises community samples of nonconvicted men such as men who demonstrate some level of Rape Proclivity, also known as rape prone men. In contrast, the forensic clinical literature utilises samples of convicted rapists. While the social psychology approach uses implicit methods in order to assess the non conscious aspect of cognition, forensic clinical researchers tend to rely on self report measures such as questionnaires and interviews. The purpose of this thesis was to amalgamate these two disparate approaches, in order to systematically investigate the rape supportive cognition of rape prone men. Four studies were conducted in order to examine the four stages of a social cognition framework; structures, operations, products, and behaviour. Studies One to Three utilised implicit measures alongside traditional self report measures in order to examine the relative utility of each methodology. Study Four employed a unique design in which participants interacted with a female confederate, in order to examine their social perception abilities and further to study the links between rape supportive cognition and behaviour itself. Contrary to expectations, the self report measure of rape supportive cognition appeared to be the most robust measure of cognition in rape prone men. The implicit measures used in Study One and Two, designed to measure rape supportive cognitive structure, however, faded to identify any such cognition in rape prone men. In Study Three, the implicit measure found evidence for just one of five rape supportive schema hypothesised to be held by rapists (Ward & Polaschek, 2002) in rape prone men. Finally, Study Four found some evidence for a social perception deficit in rape prone men, but this did not appear to have an impact on behaviour. The results of all four studies are discussed in terms of existing theory of rape supportive cognition, and the methodology used to assess such cognition.

Organisms utilise cytosine-5 DNA methylation to expand their repertoire of genetic transactions. Structural studies of DNA cytosine-5 methyltransferase have revealed that DNA methyltransferases incorporate nucleotide flipping into their catalytic cycle in order to access the otherwise buried pyrimidine ring from within duplex DNA. Interestingly, substituting the catalytic nucleophile Cys with Gly can produce cytotoxic forms of the bacterial methyltransferases and cause rearrangements in the DNA. In this study the generality of the cytotoxic effect has been studied on both mono and multi-specific methyltransferases. The effect of dimerisation of methyltransferases on the rearrangement event and the specificity of DNA damage have been defined. The involvement of two DNA repair proteins RecA and UmuDC has been studied. The wild type and mutant multispecific methyltransferase (M.SPRI) has been transcribed and translated in vitro and the proteins studied using surface plasmon resonance technique. The experiments described here demonstrate for the first time how a high affinity, catalytically deficient DNA methyltransferase induces error-prone deletions in E.coli.

Cette thèse étudie les reproches adressés par le philosophe et sophiste Dion de Pruse aux cités dans l'ensemble de ses discours. Nous montrons comment Dion, jugeant nécessaire de s'engager en politique, recourt à une habile stratégie pour blâmer des cités immorales. Nous définissons la conception dionéenne de la cité (un idéaltype de la polis). La première partie (" Dion et la tradition du blâme de cité ") examine les modèles du passé utilisés pour blâmer. La deuxième partie expose " les principes du blâme " : le pouvoir de blâmer de l'Empereur et des notables ; ensuite nous présentons les amis et les ennemis de Dion, les cercles et les clans. Nous étudions la richesse du vocabulaire dionéen du blâme, enfin, les valeurs qui inspirent le blâme les cités. Dans la troisième partie (" les reproches et leur efficacité "), nous dressons l'inventaire des différents topoi du blâme de cité. Puis sont étudiés les reproches politiques, économiques, sociaux et moraux. Enfin, nous évaluons l'efficacité réelle du blâme dionéen
Our thesis studies the blames directed by the philosopher and sophist Dio of Prusa at the cities in the whole of his discourses. We show how Dio, thinking his duty to commit himself in politics, uses a skilful way to blame the immoral cities. We define the dionean idea of the city (an idealtype of the polis). The first part of our works (" Dio and the tradition of the blame to the city ") surveys the models of the past Dio uses in order to blame. The second part defines " the principles of the blame " : the power to rebuke of the Emperor and of the notables ; then we show Dio's friends and enemies, the circles and the clans. We see how many are the terms Dio uses to signify reproach ; at last, the values for which the philosopher blames the cities. In the third part (" the rebukes and their efficacy "), we list the different topoi for the blame to the city. Then are investigated the rebukes in several fields : in politics, in economy, in social life and in ethics. Finally, we assess the real efficacy of the dionean blame

In this thesis, we study the journey planning problem in the context of transit networks. Given the timetable of a schedule-based transportation system (consisting, e.g., of trains, buses, etc), the problem seeks journeys optimizing some criteria, that is it asks to answer to natural queries such as, e.g., “find a journey that starts from a given source stop and arrives at a given target stop as early as possible”. The solution to this problem exhibiting the smallest query times is the algorithmic framework named Public Transit Labeling (ptl), proposed for the first time in [Delling et al., SEA 2015]. Said method consists of three main ingredients: i) a graph-based representation of the schedule of the transit network; ii) a labeling of such graph encoding its transitive closure (computed via a time-consuming preprocessing); iii) an efficient query algorithm exploiting both i) and ii) to answer quickly to queries of interest at runtime. Unfortunately, while transit networks’ timetables are inherently dynamic (they are often subject to delays or disruptions), ptl is not natively designed to handle updates in the schedule: even after a single change, precomputed data may become outdated and queries can return incorrect results. This is a major limitation, especially when dealing with massively sized inputs (e.g. metropolitan or continental sized networks), as recomputing the labeling from scratch, after each change, yields unsustainable time overheads that are not compatible with interactive applications. Contrary to this, there are solutions to handle dynamic timetables, however, their query times are very high as compared to that of ptl. In this work, we introduce a new framework that extends ptl to function in delay-prone transit networks. In particular, we provide a new set of algorithms able to update both the graph and the precomputed labeling whenever a delay affects the network, without performing any recomputation from scratch. We demonstrate the effectiveness of our solution through an extensive experimental evaluation conducted on real-world networks. Our experiments show that: i) the update time required by the new algorithms is, on average, orders of magnitude smaller than that required by the recomputation from scratch via ptl; ii) the updated graph and labeling induce both query time performance and space overhead that are equivalent to those that are obtained by the recomputation from scratch via ptl. This suggests that our new solution is an effective approach to handle the journey planning problem in delay-prone transit networks.

Projeto de Graduação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Licenciado em Fisioterapia
Objetivo: O presente estudo tem como objetivo avaliar a atividade muscular dos músculos reto abdominal e eretores da coluna durante o exercício de prancha com diferentes variações de estabilidade. Metodologia: A atividade eletromiográfica dos músculos de 15 participantes, 11 do sexo masculino e 4 do feminino (Mediana de idades: 22.00 (±2.00 anos); IMC: 23.41 (±3.83kg/m2)) foi analisada durante seis posições de prancha. Resultados: Foram verificadas diferenças estatisticamente significativas tanto na atividade muscular dos diferentes músculos em cada exercício, assim como diferentes atividades musculares entre cada exercício. Tendo em conta a ativação muscular de cada músculo, é possível observar que o músculo que foi mais ativado, foi o Reto Abdominal (94.01%CMV), não havendo diferenças significativas entre lado direito e lado esquerdo. Conclusão: A atividade electromiográfica dos músculos estudados foi dependente do tipo de variação do exercício de prancha, havendo maior ativação quanto mais instável fosse a superfície de apoio.
Objective: This study aims to evaluate the muscle activity of the rectus abdominis and spinal erector muscles during the exercise of plank, with different variations of stability. Methods: The muscle electromyographic activity of 15 participants, 11 males and 4 females (mean age: 22.00 (± 2.00 years); BMI: 23.41 (± 3.83 kg / m2)) was analyzed during six plank positions. Results: It is possible to observe that the muscle that was most activated was the Rectus Abdominis (94.01% CMV), and there were no significant differences between the right side and the left side. Conclusion: The electromyographic activity of the muscles studied was dependent on the type of variation of plank requested.
N/A

We investigate the difference between surface matching and target matching for pelvic radiation image guidance. The uniqueness of our study is that all patients have multiple CT-on-rails (CTOR) scans to compare to corresponding AlignRT images. Ten patients receiving pelvic radiation were enrolled in this study. Two simulation CT scans were performed in supine and prone positions for each patient. Body surface contours were generated in treatment planning system and exported to AlignRT to serve as reference images. During treatment day, the patient was aligned to treatment isocenter with room lasers, and then scanned with both CTOR and AlignRT. Image-guidance shifts were calculated for both modalities by comparison to the simulation CT and the differences between them were analyzed for both supine and prone positions, respectively. These procedures were performed for each patient once per week for five weeks. The difference of patient displacement between AlignRT and CTOR was analyzed. For supine position, five patients had an average difference of displacement between AlignRT and CTOR along any direction (vertical, longitudinal, and lateral) greater than 0.5 cm, and one patient greater than 1 cm. Four patients had a maximum difference greater than 1 cm. For prone position, seven patients had an average difference greater than 0.5 cm, and three patients greater than 1 cm. Nine patients had a maximum difference greater than 1 cm. The difference of displacement between AlignRT and CTOR was greater for the prone position than for the supine position. For the patients studied here, surface matching does not appear to be an advisable image-guidance approach for pelvic radiation therapy for patients with either supine or prone position. There appears to be a potential for large alignment discrepancies (up to 2.25 cm) between surface matching and target matching.

Med utviklingen som har funnet sted innenfor den norske oljebransjen de siste årene har både teknologien og utfordringene blitt mer komplekse. Subsea-operasjoner har blitt mer vanlig og gir utslag i at det på havbunnen i mange felt er sammenkoblede systemer av konstruksjoner. I relasjon til seismisk aktivitet reises da spørsmålet om disse systemene med brønner, rør og andre konstruksjoner kan tåle å bli utsatt for et jordskjelv av en viss størrelse. For å ta et steg i retningen av å besvare dette spørsmålet, dreier denne hovedoppgaven seg om studien av en beskyttelseskonstruksjon som utsettes for grunnakselerasjoner funnet ved probabilistisk evaluering av valgte jordskjelvdata tilgjengelig for den norske kontinentalsokkelen.Den valgte konstruksjonen er lokalisert i Åsgårdfeltet på Haltenbanken vest for midt-Norge. Det er en ganske liten og slank konstruksjon hvis funksjon er å beskytte oljeinstallasjoner fra eventuelle skader forårsaket fra trål og fallende objekter i forbindelse med fiskeriindustrien. I modelleringen av konstruksjonen vurderes den som et produkt av tre forskjellige systemer. Det første systemet er konstruksjonen alene, det andre systemet er jordsystemet og det tredje er fluidsystemet. Dermed ble tre modeller laget der de forskjellige systemegenskapene (fjærer/dempere, hydrodynamiske krefter) ble introdusert stegvis.For å undersøke konstruksjonens respons i forhold til påsatte grunnakselerasjoner, måtte representative tidsrekker for jordskjelv brukes. Disse tidsrekkene ble funnet ved hjelp av probabilistisk vurdering av en syntetisk jorskjelvkatalog. Denne jordskjelvkatalogen ble generert ved å bruke Gutenberg-Richter relasjonen, og de tilhørende parametrene og områdene de gjelder for ble funnet i en rapport angående seismisk inndeling av Norge \cite{zonation}. Jordskjelvparameteren som ble valgt var maksimum grunnakselerasjon (PGA) i både horisontal og vertikal retning estimert ved en relasjon funnet av Ambraseys, med flere \cite{ambhor}\cite{ambver}. Videre ble ordningsstatistikk brukt på de genererte PGA-verdiene ved å bruke Gumbels fordeling for maksima. De resulterende PGA-verdiene i horisontal og vertikal retning ble så brukt for å finne en passende tidsrekke for akselerasjon i en database over jordskjelv for Europa og Midtøsten \cite{esmd}. Deretter ble disse akselerasjonene påsatt de tre modellene og responsen ble evaluert ved ikkelineær direkte implisitt integrasjon. Videre ble en modal analysis av responene utført på den fullt neddykkede modellen for sammenlikningens skyld. Enda en tidsserie ble også påsatt den fullt neddykkede modellen som ble generert basert på det området med høyest seismisk aktivitet, funnet i rapporten nevnt ovenfor for å vurdere det verst tenkelige tilfellet.Resultatene av disse analysene viste at med introduksjon av jord-konstruksjon-interaksjon modellert ved fjærer og dempere, så økte forskyvningene sammenliknet med den fast innspente modellen (konstruksjonen alene). Videre så økte forskyvningene ytterligere ved å introdusere hydrodynamiske krefter. På grunn av små forskyvninger dominerte treghetskreftene responsen for den neddykkede modellen. Med tanke på konstruksjonens oppførsel så ble konstruksjonen nesten ikke affisert av de påsatte grunnakselerasjonene - som er et godt tegn. Imidlertid er det vanskelig å konkludere hvordan andre typer konstruksjoner som rør og platformer ville ha respondert hvis de ble utsatt for de samme grunnakselerasjonene ettersom disse har mye større dimensjoner og annerledes geometri.

The redundancy-associated deficit often found in schizophrenic simple reaction time was studied utilizing hypothetically schizophrenia-prone college students. The embedded-set procedure established by Bellissimo and Steffy (1972) with two methodological modifications was employed. As predicted normal and psychiatric controls did not show the redundancy-associated deficit. The hypothetically schizophrenia-prone college students did not show the cross-over effect typically produced by process schizophrenics. Several explanations were offered for these results.

Le projet de ce travail est de montrer de quelle facon la reflexion sur le patrimoine culturel de la grece, et l'utilisation qui en est faite dans le discours, ont pu determiner le comportement de dion ecrivain, et le conduire a elaborer des strategies litteraires complexes. L'attitude de dion face au probleme de l'education et de la culture dans le monde grec d'epoque imperiale est analysee ; il entend evaluer et reformer si necessaire, un ensemble de phenomenes contemporains selon une visee de moraliste et en reference aux donnees livresque traditionnelles. On a tente de determiner dans la deuxieme partie de quelle facon dion se servait des cadres que la paideia lui proposait en matiere de communication orale. Sa libre utilisation d'un discours tres proche de la lalia des sophistes lui permet de se demarquer d'un type de conferenciers dont il ne partage pas les ambitions, et l'amene a choisir des tactiques lui permettant de conduire son auditoire a l'evocation des questions qui lui sont cheres. La definition d'une eloquence philosophique visant a produire un bouleversement des ames justifie et recommande l'emploi de procedes stylistiques tres proche de ceux de l'agrement oratoire. Ils sont souvent utilises par dion de facon abondante et detaillee : il s'agit du tableau, du recit et du dialogue. Ils permettent tous les trois la representation des comportements et des passions. Cependant c'est la narration, conte ou anecdote, que dion semble preferer. Elle peut aussi devenir un moyen d'expression privilegie, et recourir a la contamination des influences litteraires pour rendre compte d'experiences ou la recherche d'une verite culturelle et autobiographique laisse leur place a certains procedes de la fiction romanesque
The aim of this work is to show how dio's attitude as a writer has been influenced by his point of view on the greek culture and the way the latter has to be used in ancient oratory. It led him to look for elaborate stategies in literature. Dio's thoughts about the problem of education and culture in the greek world, during the 1rst century a. D. , are being analysed here : he sets himself to assess and change if necessary contemporary facts, from the point of view of a moralist. His references are the classical literature. The purpose of the second part is to explain how dio used the elements offered by the greek paideia in oral communication. The uses with great liberty a type of speech very near to the sophistic lalia, and therefore, sets himself apart from the other speakers. For his main purpose in the oratory activity is the moral edification. According to his definition of philosophical eloquence wich seeks a upheaval of the soul, literary devices must be very close to that commonly used in the attractive speeches of the sophists. Meticulous pictures, narratives and dialogues are profusely used by dio. They allow a clear representation of mankind's moral attitudes and upper feelings. However, dio seems to prefer the narration, myth, tale or anecdote. With the narration, he can also express his ideas and feelings in a better way. Then literary memories and genres are mixed, and they contribute to relating some experiences in which the search of cultural and personal truth integrate the novelist's te

Background: Injury remains a leading cause of childhood morbidity and mortality in the developing world. Probability of injury occurrence is influenced by agent, host and environmental factors. Studies of repeat injuries in childhood thus provide insight into factors in the epidemiological triad predisposing children to injury. Objectives: The study objectives were to determine the proportion of children and the factors associated with repeat presentations to Red Cross War Memorial Children’s Hospital Trauma Unit (RCWMCH TU) for all non-transport related injuries in childhood. Methods: This was a retrospective cohort study using data from RCWMCH TU. We included children aged 0-10 years with first presentation from January 1997 to June 2013, and followed up until the earliest of age 13 years or June 2016. We assessed individual and population-level factors associated with repeat injury using multilevel Poisson regression. Child Dependency Ratios were derived from the 2011 national census. Results: Between 1997 and 2013, 72 490 children under 10 years of age (59% male) presented to RCWMCH TU for the first time with injuries. After the initial injury, 9 417 (13%) presented with a repeat injury by 2016 and before age 13 years. After adjusting for health Sub-District, distance from RCWMCH TU and age at first presentation, factors associated with reduced repeat presentation were: injury identified as due to abuse (adjusted incidence rate ratio [aIRR] 0.6; 95% confidence interval [CI]: 0.4 - 0.7), fluid burn (aIRR 0.6; 95% CI: 0.6 - 0.7), foreign body ingestion (aIRR 0.7; 95% CI: 0.7 - 0.9), moderate and severe (vs minor) initial injury (aIRR 0.9; 95% CI: 0.8 - 0.9) and (aIRR 0.7; 95% CI: 0.6 - 0.8 respectively), whilst boys were more likely to have repeat injury presentations (aIRR 1.4; 95% CI: 1.4 - 1.5). Conclusion: Repeat presentations constituted a substantial proportion of disease burden. Factors associated with repeat presentations were identified, strengthening the argument that injuries arise due to sustained exposure to host, agent and environmental risk factors. While it is reassuring that children with initial injuries due to abuse and severe initial injuries are less likely to present again, injury prevention education should not neglect patients with minor and unintentional injuries. The findings of this study suggest that post-injury health promotion activities should not exclude patients who present with minor injuries, and that targeted education and further research is indicated for specific injuries, including those due to non-height falls and injuries sustained whilst playing sport.

Achieving sustained economic growth and development has been an area of concern for policy-makers in the Anglophone Caribbean since the transition from colonial rule to self-governance. To date, the researcher did not find any research that has explicitly examined the role of policy-making effectiveness as a strategy for achieving the goals of sustainable development. This qualitative multiple case study of Barbados and Grenada was conceptualized from the perspective of critical theory from the World Commission on Environment and Development to explore and understand why sustainability has not been sufficiently realized and how sustainable development may be pursued in territories that are small and prone to hazards. Purposive sampling was used to identify 30 candidates for the study. Eighteen key policy-makers participated in semi-structured interviews. Secondary data from publicly available government documents in Barbados and Grenada were acquired. All data were inductively coded and data analysis was carried out at three levels using thematic, content, and cross-case analyses. Key findings suggest a need exists to increase understanding of the concept of sustainable development and the unique characteristics of the territories to enable policy-makers to better define the safe operating space for human development. Recommendations for positive social change include advice to strengthen institutional capacity across the full spectrum of policy-making practice for sustainable development including mechanisms to promote a learning culture and accountability in policy-making practice in the Anglophone Caribbean, particularly among those territories that are small and prone to hazards.

There are many types of membrane lipids throughout Nature. Still little is known about synthesizing pathways and how different lipids affect the embedded membrane proteins. The most common lipids are glycolipids since they dominate plant green tissue. Glycolipids also exist in mammal cells as well as in most Gram-positive bacteria. Glycosyltransferases (GTs) catalyze the final enzymatic steps for these glycolipids. In the bacteria Acholeplasma laidlawii and Streptococcus pneumonie and in the plant Arabidopsis thaliana, GTs for mono-/di-glycosyl-diacylglycerol (-DAG) are suggested to be regulated to keep a certain membrane curvature close to a bilayer/nonbilayer phase transition. The monoglycosylDAGs are nonbilayer-prone with small headgroups, hence by themselves they will not form bilayer structures.

Here we have determined the genes encoding the main glycolipids of A. laidlawii and S. pneumonie. We have also shown that these GTs belong to a large enzyme group widely spread in Nature, and that all four enzymes are differently regulated by membrane lipids. The importance of different lipid properties were traced in a lipid mutant of Escherichia coli lacking the major (75 %), nonbilayer-prone/zwitterionic, lipid phosphatidylethanolamine. Introducing the genes for the GTs of A. laidlawii and two analogous genes from A. thaliana yielded new strains containing 50 percent of glyco-DAG lipids. The monoglyco-DAG strains contain significant amounts of nonbilayer-prone lipids while the diglyco-DAG strains contain no such lipids. Comparing these new strains for viability and the state of membrane-associated functions made it possible to connect different functions to certain lipid properties. In summary, a low surface charge density of anionic lipids is important in E.coli membranes, but this fails to be supportive if the diluting species have a too large headgroup. This indicates that a certain magnitude of the curvature stress is crucial for the membrane bilayer in vivo.

I due temi trattati nella mia tesi di dottorato sono strettamente correlati alle mie esperienze professionali. Infatti, ho trascorso il primo periodo presso l'Università degli Studi di Milano-Bicocca nel laboratorio di terapia intensiva preclinica diretto dal Prof. Giacomo Bellani, dove il mio lavoro si è concentrato nello studio della disfunzione diaframmatica a seguito di ventilazione meccanica (VIDD); in particolare, nello studio di efficacia di un trattamento terapeutico con Angiotensina-(1-7) in un modello VIDD di ratto. Nella seconda parte del mio corso di dottorato, ho avuto la possibilità di svolgere un’esperienza presso l'Università della Pennsylvania per condurre una ricerca simile ma riguardante la progressione del danno polmonare. Nel laboratorio di anestesia del Prof. Maurizio Cereda, lo scopo principale è stato quello di indagare e valutare gli effetti della pronazione in un modello ARDS di grande animale. La disfunzione diaframmatica e lo stress polmonare durante la ventilazione meccanica sono condizioni gravi che riducono gli outcomes positivi e il successo nell’estubazione dei pazienti in terapia intensiva. La disfunzione diaframmatica indotta dal ventilatore (VIDD) è un evento comune durante la ventilazione meccanica (MV) che porta a una rapida atrofia muscolare e disfunzione contrattile. Il primo studio nella mia tesi è stato progettato per valutare gli effetti del trattamento con Ang-(1-7) in un modello di ratto di VIDD. La VM ha determinato una significativa riduzione della contrattilità diaframmatica in tutti i gruppi trattati. I ratti trattati con Ang-(1-7) hanno mostrato un'area della sezione trasversale delle fibre muscolari più alta e livelli inferiori di mRNA di Atrogin-1 e Myogenin, rispetto al trattamento con Veicolo. Il trattamento con gli antagonisti di Mas e AT2R ha causato una significativa riduzione della contrattilità muscolare e un aumento dei livelli di mRNA di Atrogin-1 e MuRF-1, senza influenzare l'area delle fibre della sezione trasversale e i livelli di mRNA di Myogenin. Possiamo quindi concludere che la somministrazione sistemica di Ang- (1-7) durante la VM esercita un ruolo protettivo sulle fibre muscolari del diaframma preservando l'anatomia delle fibre muscolari riducendo l'atrofia. Il coinvolgimento di Mas e AT2R nel meccanismo d'azione di Ang- (1-7) rimane ancora controverso. Non è noto come la progressione del danno polmonare durante la ventilazione meccanica modifichi le risposte polmonari al posizionamento prono. Lo scopo del secondo lavoro della mia tesi è stato confrontare l'efficacia della pronazione sull'aerazione polmonare regionale nelle fasi tardive e iniziali del danno polmonare utilizzando un modello di maiale di ARDS. I risultati principali hanno riportato che lo scambio di gas e la meccanica respiratoria sono peggiorati nell'arco delle 24 ore, indicando la progressione del danno indotto dal ventilatore. Il giorno 1, il posizionamento prono ha rigonfiato il 18,9 ± 5,2% della massa polmonare nelle regioni polmonari posteriori-caudali. Al giorno 2, la re-inflazione dorsale associata alla posizione è stata ridotta a 7,3 ± 1,5% (P <0,05). La pronazione ha diminuito l'aerazione nei polmoni anteriori in entrambi i giorni. Nei primi pazienti con ARDS, la ventilazione in posizione prona ha migliorato la compliance polmonare posteriore, ma non ha avuto effetti nei soggetti con ARDS in ritardo. Nel complesso, gli effetti della pronazione sull'aerazione polmonare possono dipendere dallo stadio del danno polmonare e dalla durata della ventilazione; ciò può limitare l'efficacia clinica di questo trattamento se applicato in ritardo.
The two topics covered in this work are strictly correlated to the professional experiences. Particularly, I spent the first period at the University of Milan-Bicocca in the preclinical ICU laboratory directed by Prof. Giacomo Bellani, where my work has been focused on the diaphragm dysfunction during a mechanical ventilation (VIDD); in particular, in the effectiveness study of a therapeutical treatment with Angiotensin-(1-7) in a rat model of VIDD. In the second part of my PhD course, I had a chance to rotate at the University of Pennsylvania to conduct a similar research but in the progression of lung injury. In the anesthesia laboratory of Prof. Maurizio Cereda, the main purpose has been investigating and evaluating the effects of pronation in a large model of ARDS. Diaphragmatic dysfunction and pulmonary stress during mechanical ventilation are serious conditions that reducing positive outcomes and weaning successful in ICU patients. Ventilator-induced diaphragmatic dysfunction (VIDD) is a common event during mechanical ventilation (MV) leading to rapid muscular atrophy and contractile dysfunction. The first study in my thesis was designed to evaluate the effects of the treatment with Ang-(1-7) in a rat model of VIDD. MV resulted in a significant reduction of diaphragmatic contractility in all groups of treatment. Ang-(1-7)-treated rats showed higher muscular fibers cross sectional area and lower Atrogin-1 and Myogenin mRNA levels, compared to Vehicle treatment. Treatment with the antagonists of Mas and AT2R caused a significant reduction of muscular contractility and an increase of Atrogin-1 and MuRF-1 mRNA levels, not affecting the cross sectional fiber area and Myogenin mRNA levels. Systemic Ang-(1-7) administration during MV exerts a protective role on the muscular fibers of the diaphragm preserving muscular fibers anatomy and reducing atrophy. The involvement of Mas and AT2R in the mechanism of action of Ang-(1-7) still remains controversial. It is not known how lung injury progression during mechanical ventilation modifies pulmonary responses to prone positioning. The aim of the second work of my thesis was compared the efficacy of prone positioning on regional lung aeration in late vs. early stages of lung injury using a pig model of ARDS. The main findings reported that gas exchange and respiratory mechanics worsened over 24 hours, indicating ventilator-induced injury progression. On Day 1, prone positioning reinflated 18.9 ± 5.2% of lung mass in the posterior-caudal lung regions. On Day 2, position-associated dorsal reinflation was reduced to 7.3 ± 1.5% (P<0.05). Prone positioning decreased aeration in the anterior lungs on both days. In the early ARDS patients, prone positioning improved posterior lung compliance, but it had no effect in late ARDS subjects. Overall, the effects of prone positioning on lung aeration may depend on the stage of lung injury and duration of ventilation; this may limit the clinical efficacy of this treatment if applied late.