3,802 research outputs found
Variable density sampling based on physically plausible gradient waveform. Application to 3D MRI angiography
Performing k-space variable density sampling is a popular way of reducing
scanning time in Magnetic Resonance Imaging (MRI). Unfortunately, given a
sampling trajectory, it is not clear how to traverse it using gradient
waveforms. In this paper, we actually show that existing methods [1, 2] can
yield large traversal time if the trajectory contains high curvature areas.
Therefore, we consider here a new method for gradient waveform design which is
based on the projection of unrealistic initial trajectory onto the set of
hardware constraints. Next, we show on realistic simulations that this
algorithm allows implementing variable density trajectories resulting from the
piecewise linear solution of the Travelling Salesman Problem in a reasonable
time. Finally, we demonstrate the application of this approach to 2D MRI
reconstruction and 3D angiography in the mouse brain.Comment: IEEE International Symposium on Biomedical Imaging (ISBI), Apr 2015,
New-York, United State
Computational Geometry Column 38
Recent results on curve reconstruction are described.Comment: 3 pages, 1 figure, 18 ref
A projection algorithm for gradient waveforms design in Magnetic Resonance Imaging
International audienceCollecting the maximal amount of information in a given scanning time is a major concern in Magnetic Resonance Imaging (MRI) to speed up image acquisition. The hardware constraints (gradient magnitude, slew rate, ...), physical distortions (e.g., off-resonance effects) and sampling theorems (Shannon, compressed sensing) must be taken into account simultaneously, which makes this problem extremely challenging. To date, the main approach to design gradient waveform has consisted of selecting an initial shape (e.g. spiral, radial lines, ...) and then traversing it as fast as possible using optimal control. In this paper, we propose an alternative solution which first consists of defining a desired parameterization of the trajectory and then of optimizing for minimal deviation of the sampling points within gradient constraints. This method has various advantages. First, it better preserves the density of the input curve which is critical in sampling theory. Second, it allows to smooth high curvature areas making the acquisition time shorter in some cases. Third, it can be used both in the Shannon and CS sampling theories. Last, the optimized trajectory is computed as the solution of an efficient iterative algorithm based on convex programming. For piecewise linear trajectories, as compared to optimal control reparameterization, our approach generates a gain in scanning time of 10% in echo planar imaging while improving image quality in terms of signal-to-noise ratio (SNR) by more than 6 dB. We also investigate original trajectories relying on traveling salesman problem solutions. In this context, the sampling patterns obtained using the proposed projection algorithm are shown to provide significantly better reconstructions (more than 6 dB) while lasting the same scanning time
Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism
Tese de mestrado. Biologia (Bioinformática e Biologia Computacional). Universidade de Lisboa, Faculdade de Ciências, 2012The model organisms Caenorhabditis elegans and E. coli form one of the simplest gut microbe host interaction models. Interventions in the microbe that increase the host longevity including inhibition of folate synthesis have been reported previously. To find novel single gene knockouts with an effect on lifespan, a screen of the Keio collection of E. coli was undertaken, and some of the genes found are directly involved in metabolism. The next step in those specific cases is to understand how these mutations perturb metabolism systematically, so that hypotheses can be generated. For that, I employed dynamic Flux Balance Analysis (dFBA), a constraint-based modeling technique capable of simulating the dynamics of metabolism in a batch culture and making predictions about changes in intracellular flux distribution. Since the specificities of the C. elegans lifespan experiments demand us to culture microbes in conditions differing from most of the published literature on E. coli physiology, novel data must be acquired to characterize and make dFBA simulations as realistic as possible. To do this exchange fluxes were measured using quantitative H NMR Time-Resolved Metabolic Footprinting. Furthermore, I also investigate the combination of TReF and dFBA as a tool in microbial metabolism studies. These approaches were tested by comparing wild type E. coli with one of the knockout strains found, ΔmetL, a knockout of the metL gene which encodes a byfunctional enzyme involved in aspartate and threonine metabolism. I found that the strain exhibits a slower growth rate than the wild type. Model simulation results revealed that reduced homoserine and methionine synthesis, as well as impaired sulfur and folate metabolism are the main effects of this knockout and the reasons for the growth deficiency. These results indicate that there are common mechanisms of the lifespan extension between ΔmetL and inhibition of folate biosynthesis and that the flux balance analysis/metabolic footprinting approach can help us understand the nature of these mechanisms.Os organismos modelo Caenorhabditis elegans e E. coli formam um dos modelos mais simples de interacções entre micróbio do tracto digestivo e hospedeiro. Intervenções no micróbio capazes de aumentar a longevidade do hospedeiro, incluindo inibição de síntese de folatos, foram reportadas previamente. Para encontrar novas delecções génicas do micróbio capazes de aumentar a longevidade do hospedeiro, a colecção Keio de deleções génicas de E. coli foi rastreada. Alguns dos genes encontrados participam em processos metabólicos, e nesses casos, o próximpo passo é perceber como as deleções perturbam o metabolismo sistémicamente, para gerar hipóteses. Para isso, utilizo dynamic Flux Balance Analysis (dFBA), uma técnica de modelação metabólica capaz de fazer previsões sobre alterações na distribuição intracelular de fluxos. As especificidades das experiências de tempo de vida em C.elegans obrigam-nos a trabalhar em condições diferentes das usadas na maioria da literatura publicada em fisiologia de E. coli, e para dar o máximo realismo às simulações de dFBA novos dados foram adquiridos, utilizando H NMR Time-Resolved Metabolic Footprinting para medir fluxos de troca de metabolitos entre microorganismo e meio de cultura. A combinação de TReF e dFBA como ferramenta de estudo do metabolism microbiano é também investigada. Estas abordagens foram testadas ao comparar E. coli wild-type com uma das estirpes encontradas no rastreio, ΔmetL, knockout do gene metL, que codifica um enzima bifunctional participante no metabolismo de aspartato e treonina, e que exibe uma taxa de crescimento reduzida comparativamente ao wild-type. Os resultados das simulações revelaram que os principais efeitos da deleção deste gene, e as razões para a menor taxa de crescimento observada, são a produção reduzida de homoserina e metionina e os efeitos que provoca no metabolismo de folatos e enxofre. Estes resultados indicam que há mecanismos comuns na extensão da longevidade causada por esta deleção e inibição de síntese de folatos, e que a combinação metabolic footprinting/flux balance analysis pode ajudar-nos a compreender a natureza desses mecanismos
Economic structure, development policy and environmental quality : an empirical analysis of environmental Kuznets curves with Chinese municipal data
In many cases, the relationship between environmental pollution and economic development can be generally depicted by an inverted U-shaped curve, or an environmental Kuznets curve, where pollution increases with income at the beginning and decreases after a certain level of income. However, what determine the shape of an enviornmental Kuznets curve, such as the height and the turning point of the curve, have not been thoroughly studied. A good understanding of the determinants is vitally important to the development community, especially for the developing world, where income growth is a high priority and yet environmental pollution also needs to be carefully controlled. This study analyzes the impacts of economic structure, development strategy and environmental regulation on the shape of the environmental Kuznets curve with a city-level panel dataset obtained from China. The results show that economic structure, development strategy and environmental regulation can all have important implications on the relationship between environmental environmental quality and economic development but the impacts can be different at different development stages.Environmental Economics&Policies,Economic Theory&Research,Emerging Markets,Population Policies,Green Issues
Tuning phase-stability and short-range order through Al-doping in (CoCrFeMn)100-xAlx high entropy alloys
For (CoCrFeMn)Al high-entropy alloys, we investigate the
phase evolution with increasing Al-content (0 x 20 at.%). From
first-principles theory, the Al-doping drives the alloy structurally from FCC
to BCC separated by a narrow two-phase region (FCC+BCC), which is well
supported by our experiments. We highlight the effect of Al-doping on the
formation enthalpy and electronic structure of (CoCrFeMn)Al
alloys. As chemical short-range order (SRO) in multicomponent alloys indicates
the nascent local order (and entropy changes), as well as expected
low-temperature ordering behavior, we use thermodynamic linear-response within
density-functional theory to predict SRO and ordering transformation and
temperatures inherent in (CoCrFeMn)Al. The predictions agree
with our present experimental findings, and other reported ones.Comment: 27 pages, 9 figures, 1 tabl
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