AML is thought to be sustained by sub-populations of LSCs, which possess the capacity for self-renewal and differentiation and are believed to be responsible for disease initiation, relapse and chemo-resistance. Previous studies demonstrated that aberrant splicing is prevalent in AML patients, in particular within the LSC populations. Dysregulated AS pathway members may represent key therapeutic targets and diagnostic markers for facilitating AML treatments. Here, we demonstrated the splicing factor RBM17 is significantly higher expressed in LSCs and is associated with AML poor prognosis. Gene expression signature of AML patients with higher RBM17 expression is similar to LSC gene signature. Importantly, knockdown of RBM17 in primitive primary AML cells results in myeloid differentiation and the impairment of their stem and progenitor potential. By performing global analysis of the RBM17-RNA interactome and proteome changes downstream of RBM17 knockdown, we show that RBM17 knockdown leads to inclusion of poison exons and production of nonsense-mediated decay (NMD)-sensitive transcripts for pro-leukemic factors such as RBM39 and EZH2, along with the translation initiation factor EIF4A2. We further show that EIF4A2 expression is enriched in LSC populations and inhibition of EIF4A2 impairs colony-forming ability of primary AML. Proteome analysis of AML cells after EIF4A2 knockdown demonstrate that knockdown of EIF4A2 largely recapitulates the biological effect of RBM17 knockdown. These two proteins also share downstream proteins enriched in ribosome biogenesis pathways. By applying a modified dCas9/sgRNA assisted chromatin-protein complex purification method, we identify CDK12 and USP16 as two potential upstream regulators of RBM17 and demonstrate that RBM17 mRNA expression is repressed by CDK12 knockdown but promoted by USP16 knockdown. Altogether, these results provide a rationale to target RBM17 and/or its downstream NMD-sensitive splicing substrates and upstream regulators in primitive leukemic cells for AML treatment. / Thesis / Doctor of Philosophy (PhD) / Acute myeloid leukemia (AML) is a cancer of blood and bone marrow, accounts for 30% of all leukemia and is associated with low overall survival rate and high relapse frequency due to AML chemo-resistance. It is believed that relapse and resistance are in part due to the persistence of leukemic stem cells (LSCs). Aberrant alternative splicing (AS) is a common characteristic of AML and LSC, involved splicing factors may represent useful therapeutic targets. Through data-mining survey for 203 splicing factors, comparing their expressions in LSC-enriched and non-LSC subsets of AML patients and correlations with AML prognosis, we identified RNA-binding motif protein 17 (RBM17) as the only one of these splicing factors that is strongly linked to poor prognosis in AML and has higher expression in LSC-enriched AML samples. RBM17 has been observed in high levels in several solid tumors and was able to confer cancer cells to chemo-resistance, yet the mechanism and its role in AML LSC remain to be determined. By manipulating RBM17 in AML samples, we observed how RBM17 affect the disease progression. Further, through applying omics technologies, we identified RNA binding sites, splicing substrates, downstream protein targets, and upstream regulators of RBM17 in AML, establishing the critical role of RBM17 in regulating AS program in LSC to support disease maintenance. Overall, this work provides potential strategies to target RBM17-related core pathways for AML treatment.

No description available.

Made available in DSpace on 2011-03-23T21:19:44Z (GMT). No. of bitstreams: 0 / Item created via OAI harvest from source: http://www.bdtd.ufpa.br/tde_oai/oai2.php on 2011-03-23T21:19:44Z (GMT). Item's OAI Record identifier: oai:bdtd.ufpa.br:356 / CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico / Traditional modal parameter identification usually require measurements of both the input force and the resulting response in laboratory conditions. However, when modal properties are to be identified from large structures in operation, usually the possibilities to control and measure the loading on the structure is rather limited. In this case, the modal testing is usually performed using response data only. Operational Modal Analysis (OMA) or Operational Modal Testing is a method where no artificial excitation needs to be applied to the structure or force signals to be measured. In this case, the modal parameters estimation is based upon the response signals, thereby minimizing the work of preparation for the test. However, standard OMA techniques, such as NExT, are limited to the case when excitation to the system is a white stationary noise. The NexT assumes that the correlation functions are similar to the impulse response functions, and then, traditional time domain identification methods can be applied. However, if harmonic components are present in addition to the white noise, these components can be misunderstood as natural modes in the plot of response spectrum. In this work, it is shown that it is possible identify if a peak in the response spectrum correspond to a natural mode or an operational mode. It is achieved through the application of the probability density function. It is also presented a modification in the LSCE algorithm in such manner that it can support harmonics in the operational excitation. In order to validate the methods presented in this work, it is shown numerical and experimental cases. In the former, results for a mass-spring-damper of five degree of freedom are presented, and in the latter a beam supporting an unbalanced motor is analyzed. / A metodologia tradicional de identificação de parâmetros na análise modal de estruturas é realizada a partir de sinais medidos de força de entrada e de movimento de resposta da estrutura em condições laboratoriais controladas. Entretanto, quando é necessária a obtenção dos parâmetros modais de estruturas de máquinas em operação, as condições para controlar e medir a excitação nestas situações impossibilita a realização da análise modal tradicional. Neste caso, o teste modal é realizado utilizando somente dados de resposta do sistema. A Análise Modal Operacional (AMO) é um método de extração modal em que nenhuma excitação artificial necessita ser aplicada ao sistema, utilizando-se a própria excitação operacional como entrada para medição da resposta do sistema. A técnica clássica de Análise Modal Operacional NExT considera, para isso, que a excitação operacional do sistema seja um ruído branco. Esta técnica faz a consideração de que as funções de correlação obtidas de estruturas podem ser consideradas como funções de resposta ao impulso e então métodos tradicionais de identificação modal no domínio do tempo podem ser empregados. Entretanto, caso a excitação operacional contenha componentes harmônicos que se sobressaiam, estes podem ser confundidos como modos naturais do sistema. Neste trabalho é demonstrada que através da função densidade de probabilidade da banda estreita contendo o pico de um modo, é possível identifica-lo como natural ou operacional (proveniente da excitação operacional da estrutura). É apresentada também uma modificação no método de identificação modal Exponencial Complexa Mínimos Quadrados (LSCE), passando a considerar sinais harmônicos de freqüências conhecidas presentes na excitação operacional, em um ensaio utilizando a técnica NExT. Para validação desses métodos, utiliza-se um modelo teórico de parâmetros modais conhecidos analiticamente e como estudo de caso experimental, um sistema formado por uma viga bi-apoiada suportando um motor elétrico com desbalanceamento de massa.

<p>Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.</p>

The problem of relating inter-agent and intra-agent behavioral specifications is investigated. These two views are complimentary, in that the former is closer to scenario-based user requirements whereas the latter is design-oriented. We use a graphical, user-friendly and very simple language as inter-agent specification language: Live Sequence Charts (LSC). LSC is presented and its properties are investigated: it is highly succinct, but inexpressive. There are essentially two ways to relate inter-agent and intra-agent specifications: (i) by checking that an intra-agent specification is correct with respect to some LSC specification and (ii) by automatically building an intra-agent specification from an LSC specification. Several variants of these problems exist: closed/open systems and centralized/distributed systems. We give inefficient but optimal algorithms solving all problems, besides synthesis of open distributed systems, which we show is undecidable. All the problems considered are difficult, even for a very restricted subset of LSCs, without alternatives, interleaving, conditions nor loops. We investigate the cost of extending the language with control flow constructs, conditions, real-time and symbolic instances. An implementation of the algorithms is proposed. The applicability of the language is illustrated on a real-world case study.

Inorganic chlorine (Clinorg) is generally considered to be inert and has been used as a tracer for groundwater movements. This assumption is thereby fundamental for current knowledge about soil biogeochemistry. However, recent work showed that Clinorg can be retained, i.e. immobilised, in soil, which contradicts the previous assumptions. The aim of this laboratory study was to investigate if the processes that immobilise Clinorg in soil are affected by molecular oxygen (O2), and if the immobilisation occurs in the top soil layer only or also further down were the soil structure is different from the upper soil layer. Two experimental set-ups have been established. In the first experiment regarding the O2 regime (OXANIS), the immobilisation of Clinorg was studied in soil under oxic and anoxic conditions, respectively. In a second incubation study (SOLIS) the immobilisation was studied under oxic conditions in different layers of a coniferous forest soil. To investigate the immobilisation of Clinorg, a method using radiolabelled chloride 36 (36Clinorg) was applied. The use of radiolabelled chloride is an excellent and reliable method for studying transformation processes in soil systems. The results of the laboratory study showed that Clinorg retention rates under oxic conditions were much higher than retention rates under anoxic conditions, indicating an important role of O2. Furthermore, the immobilisation of Clinorg occurred in all soil layers were oxygen is provided, but rates were highest in the top soil layer (organic layer, O-horizon). Clearly, O2 influenced the net Clinorg retention, but additional studies are required to identify the processes behind this result. The calculated immobilisation rates for Clinorg in the three soil horizons correspond to the amount of organic material detected in the different soil horizons indicating a strong connection between the occurrence of organic matter in soil and the immobilisation of Clinorg.

Geodesy deals with the accurate analysis of spatial and temporal variations in the geometry and physics of the Earth at local and global scales. In geodesy, least-squares collocation (LSC) is a bridge between the physical and statistical understanding of different functionals of the gravitational field of the Earth. This thesis specifically focuses on the [incorrect] implicit LSC assumptions of isotropy and homogeneity that create limitations on the application of LSC in non-stationary gravity field modeling. In particular, the work seeks to derive expressions for local and global analytical covariance functions that account for the anisotropy and heterogeneity of the Earth's gravity field. / Standard LSC assumes 2D stationarity and 3D isotropy, and relies on a covariance function to account for spatial dependence in the observed data. However, the assumption that the spatial dependence is constant throughout the region of interest may sometimes be violated. Assuming a stationary covariance structure can result in over-smoothing, e.g., of the gravity field in mountains and under-smoothing in great plains. The kernel convolution method from spatial statistics is introduced for non-stationary covariance structures, and its advantage in dealing with non-stationarity in geodetic data is demonstrated. / Tests of the new non-stationary solutions were performed over the Darling Fault, Western Australia, where the anomalous gravity field is anisotropic and non-stationary. Stationary and non-stationary covariance functions are compared in 2D LSC to the empirical example of gravity anomaly interpolation. The results with non-stationary covariance functions are better than standard LSC in terms of formal errors and cross-validation. Both non-stationarity of mean and covariance are considered in planar geoid determination by LSC to test how differently non-stationarity of mean and covariance affects the LSC result compared with GPS-levelling points in this area. Non-stationarity of the mean was not very considerable in this case, but non-stationary covariances were very effective when optimising the gravimetric quasigeoid to agree with the geometric quasigeoid. / In addition, the importance of the choice of the parameters of the non-stationary covariance functions within a Bayesian framework and the improvement of the new method for different functionals on the globe are pointed out.

As cores have become better at exposing Instruction-Level Parallelism (ILP), they have become bigger, more complex, and consumes more power. These cores are approaching the Power- and Memory-wall quickly. A new microarchitecture proposed by Carlson et. al claims to solve these problems. They claim that the new microarchitecture, the Load Slice Core, is able to outperform both In-Order and Out-of-Order designs in an area and power restricted environment. Based on Carlson et. al.’s work, we have implemented and evaluated a prototype version of their Load Slice Core using the In-Order Core Ariane. We evaluated the Load Slice Core by comparing the LSC to an IOC when running a microbenchmark designed by us, and when running a set of Application Benchmarks. The results from the Microbenchmark are promising, the LSC outperformed the comparable IOC in each test but problems related to the configuration of the design were found. The results from the Application Benchmarks are inconclusive. Due to time constraints, only a partially functioning LSC were compared to a comparable IOC. From these results we found that the LSC performed comparably or slightly worse than its IOC counterpart. More research on the subject is required for any conclusive statement on the microarchitecture can be made, but it is the opinion of this paper’s authors that it does show promise.

No description available.

The diploma thesis deals with the study of Rayleigh-Bénard convection for Rayleigh numbers in the range 1E8-1E14. The evaluated data come from an experiment with cryogenic helium in a cylindrical cell in a configuration with cell diameter D = 30 cm, height L = 30 cm and a second configuration with cell diameter D = 30 cm, height L = 15 cm. Miniature sensors recorded temperature fluctuations over time under various physical conditions and properties of helium. Using MATLAB software, the output parameters of the system (Nusselt and Reynolds numbers) and their dependence on the control parameters (Rayleigh and Prandtl numbers) were determined from the measured data. A new approach to the distribution of measured signals according to the direction of large scale circulation was used in the work, which leads to improved analysis. Reynolds numbers were evaluated using the so-called elliptic method. Furthermore, the work deals with the study of the coherent structure of the large scale circulation inside the cell.