The use of non-standard CT conversion ramps for Monte Carlo verification of 6 MV prostate IMRT plans

Monte Carlo (MC) dose calculation algorithms have been widely used to verify the accuracy of intensity-modulated radiotherapy (IMRT) dose distributions computed by conventional algorithms due to the ability to precisely account for the effects of tissue inhomogeneities and multileaf collimator characteristics. Both algorithms present, however, a particular difference in terms of dose calculation and report. Whereas dose from conventional methods is traditionally computed and reported as the water-equivalent dose (Dw), MC dose algorithms calculate and report dose to medium (Dm). In order to compare consistently both methods, the conversion of MC Dm into Dw is therefore necessary. This study aims to assess the effect of applying the conversion of MC-based Dm distributions to Dw for prostate IMRT plans generated for 6 MV photon beams. MC phantoms were created from the patient CT images using three different ramps to convert CT numbers into material and mass density: a conventional four material ramp (CTCREATE) and two simplified CT conversion ramps: (1) air and water with variable densities and (2) air and water with unit density. MC simulations were performed using the BEAMnrc code for the treatment head simulation and the DOSXYZnrc code for the patient dose calculation. The conversion of Dm to Dw by scaling with the stopping power ratios of water to medium was also performed in a post-MC calculation process. The comparison of MC dose distributions calculated in conventional and simplified (water with variable densities) phantoms showed that the effect of material composition on dose-volume histograms (DVH) was less than 1% for soft tissue and about 2.5% near and inside bone structures. The effect of material density on DVH was less than 1% for all tissues through the comparison of MC distributions performed in the two simplified phantoms considering water. Additionally, MC dose distributions were compared with the predictions from an Eclipse treatment planning system (TPS), which employed a pencil beam convolution (PBC) algorithm with Modified Batho Power Law heterogeneity correction. Eclipse PBC and MC calculations (conventional and simplified phantoms) agreed well (<1%) for soft tissues. For femoral heads, differences up to 3% were observed between the DVH for Eclipse PBC and MC calculated in conventional phantoms. The use of the CT conversion ramp of water with variable densities for MC simulations showed no dose discrepancies (0.5%) with the PBC algorithm. Moreover, converting Dm to Dw using mass stopping power ratios resulted in a significant shift (up to 6%) in the DVH for the femoral heads compared to the Eclipse PBC one. Our results show that, for prostate IMRT plans delivered with 6 MV photon beams, no conversion of MC dose from medium to water using stopping power ratio is needed. In contrast, MC dose calculations using water with variable density may be a simple way to solve the problem found using the dose conversion method based on the stopping power ratio.

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.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: A study case of the 1755 Lisbon tsunami in Algarve, Portugal

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.

Risk Aversion in a Mixed-Integer Nonlinear Approach to Support Decision-Making for a Hydro Power Producer

In this paper, a mixed-integer nonlinear approach is proposed to support decision-making for a hydro power producer, considering a head-dependent hydro chain. The aim is to maximize the profit of the hydro power producer from selling energy into the electric market. As a new contribution to earlier studies, a risk aversion criterion is taken into account, as well as head-dependency. The volatility of the expected profit is limited through the conditional value-at-risk (CVaR). The proposed approach has been applied successfully to solve a case study based on one of the main Portuguese cascaded hydro systems.

Scheduling of head-dependent cascaded reservoirs considering discharge ramping constraints and start/stop of units

This paper is on the problem of short-term hydro scheduling (STHS), particularly concerning head-dependent reservoirs under competitive environment. We propose a novel method, based on mixed-integer nonlinear programming (MINLP), for optimising power generation efficiency. This method considers hydroelectric power generation as a nonlinear function of water discharge and of the head. The main contribution of this paper is that discharge ramping constraints and start/stop of units are also considered, in order to obtain more realistic and feasible results. The proposed method has been applied successfully to solve two case studies based on Portuguese cascaded hydro systems, providing a higher profit at an acceptable computation time in comparison with classical optimisation methods based on mixed-integer linear programming (MILP).

Mixed-integer nonlinear approach for the optimal scheduling of a head-dependent hydro chain

This paper is on the problem of short-term hydro scheduling (STHS), particularly concerning a head-dependent hydro chain We propose a novel mixed-integer nonlinear programming (MINLP) approach, considering hydroelectric power generation as a nonlinear function of water discharge and of the head. As a new contribution to eat her studies, we model the on-off behavior of the hydro plants using integer variables, in order to avoid water discharges at forbidden areas Thus, an enhanced STHS is provided due to the more realistic modeling presented in this paper Our approach has been applied successfully to solve a test case based on one of the Portuguese cascaded hydro systems with a negligible computational time requirement.

Active and passive behaviors of soft tissues: Pelvic floor muscles

: A new active-contraction visco-elastic numerical model of the pelvic floor (skeletal) muscle is presented. Our model includes all elements that represent the muscle constitutive behavior, contraction and relaxation. In contrast with the previous models, the activation function can be null. The complete equations are shown and exactly linearized. Small verification and validation tests are performed and the pelvis is modeled using the data from the intra-abdominal pressure tests

Learning dependent sources using mixtures of Dirichlet: applications on hyperspectral unmixing

This paper is an elaboration of the DECA algorithm [1] to blindly unmix hyperspectral data. The underlying mixing model is linear, meaning that each pixel is a linear mixture of the endmembers signatures weighted by the correspondent abundance fractions. The proposed method, as DECA, is tailored to highly mixed mixtures in which the geometric based approaches fail to identify the simplex of minimum volume enclosing the observed spectral vectors. We resort then to a statitistical framework, where the abundance fractions are modeled as mixtures of Dirichlet densities, thus enforcing the constraints on abundance fractions imposed by the acquisition process, namely non-negativity and constant sum. With respect to DECA, we introduce two improvements: 1) the number of Dirichlet modes are inferred based on the minimum description length (MDL) principle; 2) The generalized expectation maximization (GEM) algorithm we adopt to infer the model parameters is improved by using alternating minimization and augmented Lagrangian methods to compute the mixing matrix. The effectiveness of the proposed algorithm is illustrated with simulated and read data.

Seasonal variation of total particulate matter and children respiratory diseases at Lisbon primary schools using passive methods

In this work, 14 primary schools of Lisbon city, Portugal, followed a questionnaire of the ISAAC - International Study of Asthma and Allergies in Childhood Program, in 2009/2010. The questionnaire contained questions to identify children with respiratory diseases (wheeze, asthma and rhinitis). Total particulate matter (TPM) was passively collected inside two classrooms of each of 14 primary schools. Two types of filter matrices were used to collect TPM: Millipore (IsoporeTM) polycarbonate and quartz. Three campaigns were selected for the measurement of TPM: Spring, Autumn and Winter. The highest difference between the two types of filters is that the mass of collected particles was higher in quartz filters than in polycarbonate filters, even if their correlation is excellent. The highest TPM depositions occurred between October 2009 and March 2010, when related with rhinitis proportion. Rhinitis was found to be related to TPM when the data were grouped seasonally and averaged for all the schools. For the data of 2006/2007, the seasonal variation was found to be related to outdoor particle deposition (below 10 μm).

Scheduling of head-dependent cascaded hydro systems: Mixed-integer quadratic programming approach

This paper is on the problem of short-term hydro, scheduling, particularly concerning head-dependent cascaded hydro systems. We propose a novel mixed-integer quadratic programming approach, considering not only head-dependency, but also discontinuous operating regions and discharge ramping constraints. Thus, an enhanced short-term hydro scheduling is provided due to the more realistic modeling presented in this paper. Numerical results from two case studies, based on Portuguese cascaded hydro systems, illustrate the proficiency of the proposed approach.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: A study case of the 1755 Lisbon tsunami in Algarve, Portugal

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.

Modalidades síncronas e assíncronas no ensino da radiologia do sistema nervoso: estilos e resultados de aprendizagem

Lidar com as problemáticas da saúde, implica um domínio dos processos cognitivos (raciocínio, resolução de problemas e tomada de decisão) e de desempenhos práticos, o que obriga a afectação de um conjunto de atitudes e comportamentos específicos. Este estudo, implementou e avaliou o impacto de experiências pedagógicas desenvolvidas com os estudantes da unidade curricular Radiologia do Sistema Nervoso (RSN) da Escola Superior de Tecnologia da Saúde de Lisboa (ESTeSL). Aplicaram-se metodologias de ensino mistas (presenciais e virtuais) utilizadas na leccionação teórica e prática no ano curricular 2008/2009. Para a avaliação do perfil de aprendizagem dos estudantes foi aplicado o método de Honey & Munford e para a avaliação e monitorização dos conhecimentos aplicaram-se check list baseadas nos conteúdos programáticos. A monitorização das ferramentas da plataforma moodle complementaram a restante informação. Verificou-se uma progressão de aprendizagem positiva para um grupo de estudantes maioritariamente do estilo reflexivo (média=10,6 estudantes). As conclusões apontaram para um impacto positivo quanto à aplicação das metodologias híbridas com maior índice de sucesso para a metodologia assíncrona. Verificou-se também mais flexibilidade no acesso aos conteúdos porém com algumas limitações tais como residência inicial por parte dos estudantes, maior carga de trabalho para os docentes, falta de terminais para acesso à plataforma e pouca experiência de todos os envolvidos no domínio e manipulação da plataforma. ABSTRACT - This study focused on the role of cognitive processes (reasoning, problem solving and decision making) and performance practice in the formation of attitudes and behaviours relating to health issues. It was conducted to evaluate the effects of pedagogical experiences on students who participated in the course in radiography in the Nervous System Imaging Unit (RSN) of the Lisbon Health School of Technology. Mixed (face-to-face and virtual) teaching methodologies were used in theory and practice sessions. Honey and Munford’s method was used to evaluate the learning profile of students. To monitor and evaluate students’ knowledge acquisition, check lists based on program topics were applied. Other information was supplied through the learning platform of Moodle. The student group with mostly a reflective learning style increased their knowledge. The asynchronous method was shown to produce a higher success rate and more flexibility in accessing content but also registered some limitations such as resistance by students, increased workload for teachers, lack of access to the platform and inexperience of all involved in handling the platform.

Structural and Microanalytical Studies of CrO2 Thin Films on c-Sapphire by High Resolution Electron Microscopy Methods

Chromium dioxide (CrO2) has been extensively used in the magnetic recording industry. However, it is its ferromagnetic half-metallic nature that has more recently attracted much attention, primarily for the development of spintronic devices. CrO2 is the only stoichiometric binary oxide theoretically predicted to be fully spin polarized at the Fermi level. It presents a Curie temperature of ∼ 396 K, i.e. well above room temperature, and a magnetic moment of 2 mB per formula unit. However an antiferromagnetic native insulating layer of Cr2O3 is always present on the CrO2 surface which enhances the CrO2 magnetoresistance and might be used as a barrier in magnetic tunnel junctions.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.