Monte Carlo modeling and simulations of the High Definition (HD120) micro MLC and validation against measurements for a 6 MV beam

Purpose: The most recent Varian® micro multileaf collimator(MLC), the High Definition (HD120) MLC, was modeled using the BEAMNRCMonte Carlo code. This model was incorporated into a Varian medical linear accelerator, for a 6 MV beam, in static and dynamic mode. The model was validated by comparing simulated profiles with measurements. Methods: The Varian® Trilogy® (2300C/D) accelerator model was accurately implemented using the state-of-the-art Monte Carlo simulation program BEAMNRC and validated against off-axis and depth dose profiles measured using ionization chambers, by adjusting the energy and the full width at half maximum (FWHM) of the initial electron beam. The HD120 MLC was modeled by developing a new BEAMNRC component module (CM), designated HDMLC, adapting the available DYNVMLC CM and incorporating the specific characteristics of this new micro MLC. The leaf dimensions were provided by the manufacturer. The geometry was visualized by tracing particles through the CM and recording their position when a leaf boundary is crossed. The leaf material density and abutting air gap between leaves were adjusted in order to obtain a good agreement between the simulated leakage profiles and EBT2 film measurements performed in a solid water phantom. To validate the HDMLC implementation, additional MLC static patterns were also simulated and compared to additional measurements. Furthermore, the ability to simulate dynamic MLC fields was implemented in the HDMLC CM. The simulation results of these fields were compared with EBT2 film measurements performed in a solid water phantom. Results: Overall, the discrepancies, with and without MLC, between the opened field simulations and the measurements using ionization chambers in a water phantom, for the off-axis profiles are below 2% and in depth-dose profiles are below 2% after the maximum dose depth and below 4% in the build-up region. On the conditions of these simulations, this tungsten-based MLC has a density of 18.7 g cm− 3 and an overall leakage of about 1.1 ± 0.03%. The discrepancies between the film measured and simulated closed and blocked fields are below 2% and 8%, respectively. Other measurements were performed for alternated leaf patterns and the agreement is satisfactory (to within 4%). The dynamic mode for this MLC was implemented and the discrepancies between film measurements and simulations are within 4%. Conclusions: The Varian® Trilogy® (2300 C/D) linear accelerator including the HD120 MLC was successfully modeled and simulated using the Monte CarloBEAMNRC code by developing an independent CM, the HDMLC CM, either in static and dynamic modes.

An ultrasound based computer-aided diagnosis tool for steatosis detection

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. In this paper, a new computer-aided diagnosis (CAD) system for steatosis classification, in a local and global basis, is presented. Bayes factor is computed from objective ultrasound textural features extracted from the liver parenchyma. The goal is to develop a CAD screening tool, to help in the steatosis detection. Results showed an accuracy of 93.33%, with a sensitivity of 94.59% and specificity of 92.11%, using the Bayes classifier. The proposed CAD system is a suitable graphical display for steatosis classification.

Global and local detection of liver steatosis from ultrasound

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. Steatosis is usually a diffuse liver disease, since it is globally affected. However, steatosis can also be focal affecting only some foci difficult to discriminate. In both cases, steatosis is detected by laboratorial analysis and visual inspection of ultrasound images of the hepatic parenchyma. Liver biopsy is the most accurate diagnostic method but its invasive nature suggest the use of other non-invasive methods, while visual inspection of the ultrasound images is subjective and prone to error. In this paper a new Computer Aided Diagnosis (CAD) system for steatosis classification and analysis is presented, where the Bayes Factor, obatined from objective intensity and textural features extracted from US images of the liver, is computed in a local or global basis. The main goal is to provide the physician with an application to make it faster and accurate the diagnosis and quantification of steatosis, namely in a screening approach. The results showed an overall accuracy of 93.54% with a sensibility of 95.83% and 85.71% for normal and steatosis class, respectively. The proposed CAD system seemed suitable as a graphical display for steatosis classification and comparison with some of the most recent works in the literature is also presented.

Data mining framework for fatty liver disease classification in ultrasound: a hybrid feature extraction paradigm

PURPOSE: Fatty liver disease (FLD) is an increasing prevalent disease that can be reversed if detected early. Ultrasound is the safest and ubiquitous method for identifying FLD. Since expert sonographers are required to accurately interpret the liver ultrasound images, lack of the same will result in interobserver variability. For more objective interpretation, high accuracy, and quick second opinions, computer aided diagnostic (CAD) techniques may be exploited. The purpose of this work is to develop one such CAD technique for accurate classification of normal livers and abnormal livers affected by FLD. METHODS: In this paper, the authors present a CAD technique (called Symtosis) that uses a novel combination of significant features based on the texture, wavelet transform, and higher order spectra of the liver ultrasound images in various supervised learning-based classifiers in order to determine parameters that classify normal and FLD-affected abnormal livers. RESULTS: On evaluating the proposed technique on a database of 58 abnormal and 42 normal liver ultrasound images, the authors were able to achieve a high classification accuracy of 93.3% using the decision tree classifier. CONCLUSIONS: This high accuracy added to the completely automated classification procedure makes the authors' proposed technique highly suitable for clinical deployment and usage.

Mould and yeast identification in archival settings: preliminary results on the use of traditional methods and molecular biology options in Portuguese archives

This project was developed to fully assess the indoor air quality in archives and libraries from a fungal flora point of view. It uses classical methodologies such as traditional culture media – for the viable fungi – and modern molecular biology protocols, especially relevant to assess the non-viable fraction of the biological contaminants. Denaturing high-performance liquid chromatography (DHPLC) has emerged as an alternative to denaturing gradient gel electrophoresis (DGGE) and has already been applied to the study of a few bacterial communities. We propose the application of DHPLC to the study of fungal colonization on paper-based archive materials. This technology allows for the identification of each component of a mixture of fungi based on their genetic variation. In a highly complex mixture of microbial DNA this method can be used simply to study the population dynamics, and it also allows for sample fraction collection, which can, in many cases, be immediately sequenced, circumventing the need for cloning. Some examples of the methodological application are shown. Also applied is fragment length analysis for the study of mixed Candida samples. Both of these methods can later be applied in various fields, such as clinical and sand sample analysis. So far, the environmental analyses have been extremely useful to determine potentially pathogenic/toxinogenic fungi such as Stachybotrys sp., Aspergillus niger, Aspergillus fumigatus, and Fusarium sp. This work will hopefully lead to more accurate evaluation of environmental conditions for both human health and the preservation of documents.

Determination of the radiochemical purity of 99mTc-Tetrofosmin: comparision between five methods

GOAL: The manufacturing and distribution of strips of instant thin - layer chromatography with silica gel (ITLC - SG) (reference method) is currently discontinued so there is a need for an alternative method f or the determination of radiochemical purity (RCP) of 99m Tc - tetrofosmin. This study aims to compare five alternative methods proposed by the producer to determine the RCP of 99m Tc - tetrofosmin. METHODS: Nineteen vials of tetrofosmin were radiolabelled with 99m Tc and the percentages of the RCP were determined. Five different methods were compared with the standard RCP testing method (ITLC - SG, 2x20 cm): Whatman 3MM (1x10 cm) with acetone and dichloro - methane (method 1); Whatman 3MM (1x1 0 cm) with ethyl acetate (method 2); aluminum oxide - coated plastic thin - layer chromatography (TLC) plate (1x10 cm) and ethanol (method 3); Whatman 3MM (2x20 cm) with acetone and dichloro - methane (method 4); solid - phase extraction method C18 cartridge (meth od 5). RESULTS: The average values of RCP were 95,30% ± 1,28% (method 1), 93,95 ± 0,61% (method 2), 96,85% ± 0,93% (method 3), 92,94% ± 0,99% (method 4) and 96,25% ± 2,57% (method 5) (n=12 each), and 93,15% ± 1,13% for the standard method (n=19). There we re statistical significant differences in the values obtained for methods 1 (P=0,001), 3 (P=0,000) and 5 (P=0,004), and there were no statistical significant differences in the values obtained for methods 2 (P=0,113) and 4 (P=0,327). CONCLUSION: From the results obtained, methods 2 and 4 showed a higher correlation with the standard method. Unlike method 4, method 2 is less time - consuming than the reference method and can overcome the problems associated with the solvent toxicity. The remaining methods (1, 3 and 5) tended to overestimate RCP value compared to the standard method.

Practical Quality Control: Comparision of Methods on the Quantification of Stationary Phases in Paper and Thin-Layer Chromatographic Systems

Introduction: Paper and thin layer chromatography methods are frequently used in Classic Nuclear Medicine for the determination of radiochemical purity (RCP) on radiopharmaceutical preparations. An aliquot of the radiopharmaceutical to be tested is spotted at the origin of a chromatographic strip (stationary phase), which in turn is placed in a chromatographic chamber in order to separate and quantify radiochemical species present in the radiopharmaceutical preparation. There are several methods for the RCP measurement, based on the use of equipment as dose calibrators, well scintillation counters, radiochromatografic scanners and gamma cameras. The purpose of this study was to compare these quantification methods for the determination of RCP. Material and Methods: 99mTc-Tetrofosmin and 99mTc-HDP are the radiopharmaceuticals chosen to serve as the basis for this study. For the determination of RCP of 99mTc-Tetrofosmin we used ITLC-SG (2.5 x 10 cm) and 2-butanone (99mTc-tetrofosmin Rf = 0.55, 99mTcO4- Rf = 1.0, other labeled impurities 99mTc-RH RF = 0.0). For the determination of RCP of 99mTc-HDP, Whatman 31ET and acetone was used (99mTc-HDP Rf = 0.0, 99mTcO4- Rf = 1.0, other labeled impurities RF = 0.0). After the development of the solvent front, the strips were allowed to dry and then imaged on the gamma camera (256x256 matrix; zoom 2; LEHR parallel-hole collimator; 5-minute image) and on the radiochromatogram scanner. Then, strips were cut in Rf 0.8 in the case of 99mTc-tetrofosmin and Rf 0.5 in the case of 99mTc-HDP. The resultant pieces were smashed in an assay tube (to minimize the effect of counting geometry) and counted in the dose calibrator and in the well scintillation counter (during 1 minute). The RCP was calculated using the formula: % 99mTc-Complex = [(99mTc-Complex) / (Total amount of 99mTc-labeled species)] x 100. Statistical analysis was done using the test of hypotheses for the difference between means in independent samples. Results:The gamma camera based method demonstrated higher operator-dependency (especially concerning the drawing of the ROIs) and the measures obtained using the dose calibrator are very sensitive to the amount of activity spotted in the chromatographic strip, so the use of a minimum of 3.7 MBq activity is essential to minimize quantification errors. Radiochromatographic scanner and well scintillation counter showed concordant results and demonstrated the higher level of precision. Conclusions: Radiochromatographic scanners and well scintillation counters based methods demonstrate to be the most accurate and less operator-dependant methods.

Comparative study between two distinct methods for attenuation correction and the use of no-attenuation correction for the assessment of relative uptake of 99mTc-DMSA on pediatric patients

Introduction: Although relative uptake values aren’t the most important objective of a 99mTc-DMSA scan, they are important quantitative information. In most of the dynamic renal scintigraphies attenuation correction is essential if one wants to obtain a reliable result of the quantification process. Although in DMSA scans the absent of significant background and the lesser attenuation in pediatric patients, makes that this attenuation correction techniques are actually not applied. The geometric mean is the most common method, but that includes the acquisition of an anterior (extra) projection, which it is not acquired by a large number of NM departments. This method and the attenuation factors proposed by Tonnesen will be correlated with the absence of attenuation correction procedures. Material and Methods: Images from 20 individuals (aged 3 years +/- 2) were used and the two attenuation correction methods applied. The mean time of acquisition (time post DMSA administration) was 3.5 hours +/- 0.8h. Results: The absence of attenuation correction showed a good correlation with both attenuation methods (r=0.73 +/- 0.11) and the mean difference verified on the uptake values between the different methods were 4 +/- 3. The correlation was higher when the age was lower. The attenuation correction methods correlation was higher between them two than with the “no attenuation correction” method (r=0.82 +/- 0.8), and the mean differences of the uptake values were 2 +/- 2. Conclusion: The decision of not doing any kind of attenuation correction method can be justified by the minor differences verified on the relative kidney uptake values. Nevertheless, if it is recognized that there is a need for an accurate value of the relative kidney uptake, then an attenuation correction method should be used. Attenuation correction factors proposed by Tonnesen can be easily implemented and so become a practical and easy to implement alternative, namely when the anterior projection - needed for the geometric mean methodology – is not acquired.

Efficiency of sampling methods and effort to assess arthropod diversity in Azorean native forests

The BALA project (Biodiversity of Arthropods of Laurisilva of the Azores) is a research initiative to quantify the spatial distribution of arthropod biodiversity in native forests of the Azores archipelago. Arthropods were collected using a combination of two techniques, targeting epigean (ground dwelling) and canopy (arboreal) arthropods: pitfall traps (with Turquin and Ethylene solutions) and beating samples (using the three most dominant plant species). A total of 109 transects distributed amongst 18 forest fragments in seven of the nine Azorean islands were used in this study. The performance of alternative sampling methods and effort were tested. No significant differences were found in the accumulated number of species captured whether an alternative method was used or whether another transect with similar effort was established in another location within the same fragment. A combination of Ethylene and Turquin traps captured more species per individual, Turquin and beating captured more species per sample, and Turquin captured more species per unit time. An optimization exercise was performed and we found that the protocol applied during recent years is very close to optimal, allowing its future replication with confidence. The minimum combinations of sampling effort and methods, in order to monitor or to inventory diversity, taking into account different proportions of sample completeness are discussed.

Long-term monitoring across elevational gradients to assess ecological hypothesis : a description of standardized sampling methods in oceanic islands and first results

We are launching a long-term study to characterize the biodiversity at different elevations in several Azorean Islands. Our aim is to use the Azores as a model archipelago to answer the fundamental question of what generates and maintains the global spatial heterogeneity of diversity in islands and to be able to understand the dynamics of change across time. An extensive, standardized sampling protocol was applied in most of the remnant forest fragments of five Azorean Islands. Fieldwork followed BRYOLAT methodology for the collection of bryophytes, ferns and other vascular plant species. A modified version of the BALA protocol was used for arthropods. A total of 70 plots (10 m x 10 m) are already established in five islands (Flores, Pico, São Jorge, Terceira and São Miguel), all respecting an elevation step of 200 m, resulting in 24 stations examined in Pico, 12 in Terceira, 10 in Flores, 12 in São Miguel and 12 in São Jorge. The first results regarding the vascular plants inventory include 138 vascular species including taxa from Lycopodiophyta (N=2), Pteridophyta (N=27), Pinophyta (N=2) and Magnoliophyta (N=107). In this contribution we also present the main research question for the next six years within the 2020 Horizon.

Gestão do risco em mercados de energia eléctrica recorrendo ao VaR por simulação de Monte Carlo

Mestrado em Engenharia Electrotécnica – Sistemas Eléctricos de Energia.

Biblioteca de navegação autónoma baseada em campos de potencial

Trabalho de Final de Mestrado para obtenção do grau de Mestre em Engenharia Informática e de Computadores

Complementarity of conventional and molecular methods in the assessment of fungal contamination caused by Aspergillus fumigatus complex in one Portuguese composting plant

The handling of waste and compost that occurs frequently in composting plants (compost turning, shredding, and screening) has been shown to be responsible for the release of dust and air borne microorganisms and their compounds in the air. Thermophilic fungi, such as A. fumigatus, have been reported and this kind of contamination in composting facilities has been associated with increased respiratory symptoms among compost workers. This study intended to characterize fungal contamination in a totally indoor composting plant located in Portugal. Besides conventional methods, molecular biology was also applied to overcome eventual limitations.

Testes de ajuste a distribuições estatísticas e métodos para estimação dos parâmetros em análises de fiabilidade

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica