Combined LRRK2 mutation, aging and chronic low dose oral rotenone as a model of Parkinson’s disease

published_or_final_versio

Herbs and Rehabilitation after Stroke Study: A Multi-center, Double-blinded, Randomized Trial in Hong Kong

published_or_final_versio

Merged consensus clustering to assess and improve class discovery with microarray data

<p>Abstract</p> <p>Background</p> <p>One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups. There are a large number of methods available to perform clustering, but it is often unclear which method is best suited to the data and how to quantify the quality of the classifications produced.</p> <p>Results</p> <p>Here we describe an R package containing methods to analyse the consistency of clustering results from any number of different clustering methods using resampling statistics. These methods allow the identification of the the best supported clusters and additionally rank cluster members by their fidelity within the cluster. These metrics allow us to compare the performance of different clustering algorithms under different experimental conditions and to select those that produce the most reliable clustering structures. We show the application of this method to simulated data, canonical gene expression experiments and our own novel analysis of genes involved in the specification of the peripheral nervous system in the fruitfly, <it>Drosophila melanogaster</it>.</p> <p>Conclusions</p> <p>Our package enables users to apply the merged consensus clustering methodology conveniently within the R programming environment, providing both analysis and graphical display functions for exploring clustering approaches. It extends the basic principle of consensus clustering by allowing the merging of results between different methods to provide an averaged clustering robustness. We show that this extension is useful in correcting for the tendency of clustering algorithms to treat outliers differently within datasets. The R package, <it>clusterCons</it>, is freely available at CRAN and sourceforge under the GNU public licence.</p

Derivation of V function for LR 115 SSNTD from its sensitivity to 220Rn in a diffusion chamber

The sensitivity of the LR 115 detector inside a diffusion chamber to 220Rn gas concentration is dependent on the removed active layer thickness during chemical etching. This dependence is related to the V function for the LR 115 detector (where V is the ratio between the track etch velocity V t and the bulk etch velocity V b) and the geometry of the diffusion chamber. The present paper presents the experimentally determined relationship between the sensitivity of the LR 115 detector inside a Karlsruhe diffusion chamber (determined from the number of etched tracks completely penetrating the active cellulose nitrate layer) and the removed active layer thickness. These data were used to derive the V function for the LR 115 detector, which took the functional form of the Durrani-Green's function, i.e., V = 1 + (a 1 e - a2 R + a 3 e - a4 R) (1 - e - a5 R), with the best-fitted constants as a 1 = 14.50, a 2 = 0.50, a 3 = 3.9 and a 4 = 0.066. © 2006 Elsevier Ltd. All rights reserved.link_to_subscribed_fulltex

A study of the polyethylene membrane used in diffusion chambers for radon gas concentration measurements

Solid-state nuclear track detectors (SSNTDs) in diffusion chambers have been routinely used for long-term measurements of radon gas concentrations. In usual practice, a filter is added across the top of the diffusion chamber to stop the progeny from entering. Thoron can also be deterred from entering the diffusion chamber by using a polyethylene (PE) membrane. However, the thickness of the PE membrane is rarely specified in the literature. In this paper, we will present our experimental results for a radon exposure that the number of alpha-particle tracks registered by the LR 115 SSNTD in a Karlsruhe diffusion chamber covered with one layer of PE membrane is actually enhanced. This is explained by enhanced deposition of radon progeny on the outside surface of the PE membrane and the insufficient thickness of the PE membrane to stop the alpha particles emitted from these deposited radon progeny to reach the SSNTD. We will present the PE thickness which can stop the alpha particles emitted from the deposited radon or thoron progeny. For the “twin diffusion chambers method”, one of the diffusion chambers is covered with PE membranes. The optimal number of thickness of PE membranes will be determined, which allows the largest amount of radon gas to diffuse into the diffusion chamber while at the same time screening out the largest amount of thoron gas.link_to_subscribed_fulltex

A study of the polyethylene membrane used in diffusion chambers for radon gas concentration measurements

Solid-state nuclear track detectors (SSNTDs) in diffusion chambers have been routinely used for long-term measurements of radon gas concentrations. In usual practice, a filter is added across the top of the diffusion chamber to stop the progeny from entering. Thoron can also be deterred from entering the diffusion chamber by using a polyethylene (PE) membrane. However, the thickness of the PE membrane is rarely specified in the literature. In this paper, we will present our experimental results for a radon exposure that the number of alpha-particle tracks registered by the LR 115 SSNTD in a Karlsruhe diffusion chamber covered with one layer of PE membrane is actually enhanced. This is explained by enhanced deposition of radon progeny on the outside surface of the PE membrane and the insufficient thickness of the PE membrane to stop the alpha particles emitted from these deposited radon progeny to reach the SSNTD. We will present the PE thickness which can stop the alpha particles emitted from the deposited radon or thoron progeny. For the "twin diffusion chambers method", one of the diffusion chambers is covered with PE membranes. The optimal number of thickness of PE membranes will be determined, which allows the largest amount of radon gas to diffuse into the diffusion chamber while at the same time screening out the largest amount of thoron gas. © 2007 Elsevier B.V. All rights reserved.link_to_subscribed_fulltex

Equilibrium factor determination using SSNTDs

The proxy equilibrium factor F p was recently proposed by Nikezic et al. [2004. Theoretical basis for long-term measurements of equilibrium factor using LR 115 detector. Appl. Radiat. Isot. 61, 1431-1435] and Yu et al. [2005. Long-term measurements of radon progeny concentrations with solid state nuclear track detectors. Radiat. Meas. 40, 560-568] for long-term passive monitoring of the equilibrium factor F for short-lived 222Rn progeny. In the present paper, we further look into the details for the F p method and study the potential factors affecting the measurements of F using this technique. These factors include (1) the removed active layer of the LR 115 detector, (2) the presence of 220Rn in the ambient environment, and (3) the deposition of dust particles on the LR 115 detector. The corresponding results are: (1) the removed active layer thickness of the LR 115 detector is a very critical parameter in determining F p and hence F; (2) the presence of thoron in the ambient environment will affect the track densities on the bare LR 115 detector but can be corrected for using the partial sensitivities to thoron; and (3) deposition of dust particles on the bare LR 115 detectors normally will not have significant effects. In addition, a mini-survey of radon and thoron gas concentration and the radon equilibrium factor in different indoor environments has been carried out in different seasons. The conclusion is that the use of an assumed constant F value can result in inaccurate determinations of the effective dose; therefore, actual (long-term) measurements of the F values should be made. © 2008 Elsevier Ltd. All rights reserved.link_to_subscribed_fulltex

Sensitivity of LR 115 SSNTD in a diffusion chamber

Solid-state nuclear track detectors (SSNTDs), such as LR 115, have been commonly used in diffusion chambers for long-term measurements of radon gas concentrations. For the LR 115 SSNTD, it has been found that the active layer removed during chemical etching is significantly affected by the presence and amount of stirring, and thus cannot be controlled easily. However, the sensitivity of the LR 115 detector inside a diffusion chamber to the radon and/or thoron gas concentration is dependent on the actual removed active layer thickness. This relationship is dependant on the geometry of the diffusion chamber and the deposition fraction of 218Po in the diffusion chamber, as well as the V function for the LR 115 detector (V is the ratio between the track etch velocity Vt to the bulk etch velocity Vb). This paper presents the experimentally determined relationships between the sensitivity of the LR 115 detector inside a Karlsruhe diffusion chamber and the removed active layer thickness, for both radon and thoron. A V function was adjusted to simulate the relationships. In particular, for the case of 222Rn, we have found f ∼ 0.5, where f is the fraction of 218Po which decays inside the diffusion chamber before deposition onto available inner surfaces of the chamber. In conclusion, we have found that the sensitivities critically depend on the actual removed active layer thickness, so this should be monitored and used in determining the sensitivities.link_to_subscribed_fulltex

A further study of the (CR-LR) difference technique for retrospective radon exposure assessment

The (CR-LR) difference technique, based on the CR-39 and LR 115 detectors, for the determination of implanted 210Po in glass after deposition of short-lived radon progeny, was analyzed in details in this paper. The sensitivities of both detectors were calculated using the Monte Carlo method with V functions particularly derived in our previous works for the detectors used in the present experiments. The dependency of the sensitivity ratio on the removed layer of both detectors was determined and verified experimentally. The simulated sensitivity ratios correlate well with the experimental ones. A major finding of the present work is that the sensitivity ratio between the CR-39 and LR 115 detectors depends only weakly on the ratio between the 238U and 232Th concentrations in the glass samples. This is crucial for the application of the (CR-LR) difference technique for retrospective radon exposure assessments, since measurements of the 238U and 232Th concentrations in the relatively small real-life glass samples will make the retrospective radon exposure assessments impractical. © 2006 Elsevier B.V. All rights reserved.link_to_subscribed_fulltex