Automatic Small Bowel Tumor Diagnosis by Using Multi-Scale Wavelet-Based Analysis in Wireless Capsule Endoscopy Images

BACKGROUND: Wireless capsule endoscopy has been introduced as an innovative, non-invasive diagnostic technique for evaluation of the gastrointestinal tract, reaching places where conventional endoscopy is unable to. However, the output of this technique is an 8 hours video, whose analysis by the expert physician is very time consuming. Thus, a computer assisted diagnosis tool to help the physicians to evaluate CE exams faster and more accurately is an important technical challenge and an excellent economical opportunity. METHOD: The set of features proposed in this paper to code textural information is based on statistical modeling of second order textural measures extracted from co-occurrence matrices. To cope with both joint and marginal non-Gaussianity of second order textural measures, higher order moments are used. These statistical moments are taken from the two-dimensional color-scale feature space, where two different scales are considered. Second and higher order moments of textural measures are computed from the co-occurrence matrices computed from images synthesized by the inverse wavelet transform of the wavelet transform containing only the selected scales for the three color channels. The dimensionality of the data is reduced by using Principal Component Analysis. RESULTS: The proposed textural features are then used as the input of a classifier based on artificial neural networks. Classification performances of 93.1% specificity and 93.9% sensitivity are achieved on real data. These promising results open the path towards a deeper study regarding the applicability of this algorithm in computer aided diagnosis systems to assist physicians in their clinical practice.

Influence of abiotic stress factors on VOCs emission from Portuguese rice paddy fields: relation with increased climate change

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente Perfil de Gestão de Sistemas Ambientais

Ontology-based representation and generation of workflows for micro-task human-machine computation

Doctoral Program in Computer Science

In-line rheo-optical characterization during small-scale polymer processing and compounding

As increasingly more sophisticated materials and products are being developed and times-to-market need to be minimized, it is important to make available fast response characterization tools using small amounts of sample, capable of conveying data on the relationships between rheological response, process-induced material structure and product characteristics. For this purpose, a single / twin-screw mini-extrusion system of modular construction, with well-controlled outputs in the range 30-300 g/h, was coupled to a in- house developed rheo-optical slit die able to measure shear viscosity and normal-stress differences, as well as performing rheo-optical experiments, namely small angle light scattering (SALS) and polarized optical microscopy (POM). In addition, the mini-extruder is equipped with ports that allow sample collection, and the extrudate can be further processed into products to be tested later. Here, we present the concept and experimental set-up [1, 2]. As a typical application, we report on the characterization of the processing of a polymer blend and of the properties of extruded sheets. The morphological evolution of a PS/PMMA industrial blend along the extruder, the flow-induced structures developed and the corresponding rheological characteristics are presented, together with the mechanical and structural characteristics of produced sheets. The application of this experimental tool to other material systems will also be discussed.

Dispersion and re-agglomeration of graphite nanoplates in polypropylene melts under controlled flow conditions

The kinetics of GnP dispersion in polypropylene melt was studied using a prototype small scale modular extensional mixer. Its modular nature enabled the sequential application of a mixing step, melt relaxation, and a second mixing step. The latter could reproduce the flow conditions on the first mixing step, or generate milder flow conditions. The effect of these sequences of flow constraints upon GnP dispersion along the mixer length was studied for composites with 2 and 10 wt.% GnP. The samples collected along the first mixing zone showed a gradual decrease of number and size of GnP agglomerates, at a rate that was independent of the flow conditions imposed to the melt, but dependent on composition. The relaxation zone induced GnP re-agglomeration, and the application of a second mixing step caused variable dispersion results that were largely dependent on the hydrodynamic stresses generated.

Oxygen mass transfer impact on citric acid production by Yarrowia lipolytica from crude glycerol

Production of citric acid from crude glycerol from biodiesel industry, in batch cultures of Yarrowia lipolytica W29 was performed in a lab-scale stirred tank bioreactor in order to assess the effect of oxygen mass transfer rate in this bioprocess. An empirical correlation was proposed to describe oxygen volumetric mass transfer coefficient (kLa) as a function of operating conditions (stirring speed and specific air flow rate) and cellular density. kLa increased according with a power function with specific power input and superficial gas velocity, and slightly decreased with cellular density. The increase of initial kLa from 7 h-1 to 55 h-1 led to 7.8-fold increase of citric acid final concentration. Experiments were also performed at controlled dissolved oxygen (DO) and citric acid concentration increased with DO up to 60% of saturation. Thus, due to the simpler operation setting an optimal kLa than at controlled DO, it can be concluded that kLa is an adequate parameter for the optimization of citric acid production from crude glycerol by Y. lipolytica and to be considered in bioprocess scale-up. Our empirical correlation, considering the operating conditions and cellular density, will be a valid tool for this purpose.

Study of Coronary Flow Reserve with Intravenous Use of Microbubbles (Contrast Echocardiography) and Adenosine: Protocol for Clinical Application in Patients Suspected of Having Coronary Heart Disease

OBJECTIVE: To test the feasibility, safety and accuracy of the adenosine protocol in the study of myocardial perfusion with microbubbles contrast echocardiography. METHODS: 81 pts (64 male, 60+11 years) were submitted to contrast echocardiography with PESDA (sonicated solution of albumin 20%-1ml, dextrose 5%-12ml and deca-fluorobutane gas-8ml) to study the myocardial perfusion at rest and after bolus injection of adenosine (6 to 18mg) and to coronary angiography within 1 month each other. For each patient 3 left ventricle perfusion beds were considered (total of 243 territories). 208 territories were analyzed and 35 territories were excluded. PESDA was continuously infused (1-2ml/min), titrated for best myocardial contrast. Triggered (1:1) second harmonic imaging was used. RESULTS: Coronary angiography showed 70 flow limiting (> 75%) lesions and 138 no flow limiting lesions. At rest an obvious myocardium contrast enhancement was seen in at least 1 segment of a territory in all patients. After adenosine injection an unquestionable further increase in myocardial contrast was observed in 136 territories (99%) related to no flow limiting lesions, lasting < 10 s, and a myocardial perfusion defect was detected in 68 territories (97%) related to flow limiting lesions. It was observed only 4 false results. There were no serious complications. CONCLUSION: Myocardial perfusion study with PESDA and adenosine protocol is a practical, safe and accurate method to analyze the coronary flow reserve.

Flow and transport in electrochromatography

Analyte retention, analyte transport, axial dispersion, adsorption, charge-selectivity, concentration polarization, confocal laser scanning microscopy, donnan-exclusion, electrical double layer; electrochromatography; electrohydrodynamics, electrokinetic instability, electroosmosis; electroosmotic flow; electroosmotic mobility, electroosmotic perfusion, electrophoresis, hierarchical porous media, hydrodynamic flow, induced-charge electroosmosis, ion-permselectivity, ion-permselective transport, monolith, nonequilibrium electrical double layer, nonequilibrium electrokinetic effects, nonlinear electroosmosis, plate height, plate number, porous media, pore-scale dispersion, refractive index matching, space charge effects, sphere packing, quantitative imaging, wall effect, zeta-potential

Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MUSIASEM): an outline of rationale and theory

This paper presents an outline of rationale and theory of the MuSIASEM scheme (Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism). First, three points of the rationale behind our MuSIASEM scheme are discussed: (i) endosomatic and exosomatic metabolism in relation to Georgescu-Roegen’s flow-fund scheme; (2) the bioeconomic analogy of hypercycle and dissipative parts in ecosystems; (3) the dramatic reallocation of human time and land use patterns in various sectors of modern economy. Next, a flow-fund representation of the MUSIASEM scheme on three levels (the whole national level, the paid work sectors level, and the agricultural sector level) is illustrated to look at the structure of the human economy in relation to two primary factors: (i) human time - a fund; and (ii) exosomatic energy - a flow. The three levels representation uses extensive and intensive variables simultaneously. Key conceptual tools of the MuSIASEM scheme - mosaic effects and impredicative loop analysis - are explained using the three level flow-fund representation. Finally, we claim that the MuSIASEM scheme can be seen as a multi-purpose grammar useful to deal with sustainability issues.

Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium.

PURPOSE: The Cancer Vaccine Consortium of the Cancer Research Institute (CVC-CRI) conducted a multicenter HLA-peptide multimer proficiency panel (MPP) with a group of 27 laboratories to assess the performance of the assay. EXPERIMENTAL DESIGN: Participants used commercially available HLA-peptide multimers and a well characterized common source of peripheral blood mononuclear cells (PBMC). The frequency of CD8+ T cells specific for two HLA-A2-restricted model antigens was measured by flow cytometry. The panel design allowed for participants to use their preferred staining reagents and locally established protocols for both cell labeling, data acquisition and analysis. RESULTS: We observed significant differences in both the performance characteristics of the assay and the reported frequencies of specific T cells across laboratories. These results emphasize the need to identify the critical variables important for the observed variability to allow for harmonization of the technique across institutions. CONCLUSIONS: Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures.

Rapid high-performance liquid chromatographic determination with fluorescence detection of furosemide in human body fluids and its confirmation by gas chromatography-mass spectrometry.

Furosemide (FD: Lasix) is a loop diuretic which strongly increases both urine flow and electrolyte urinary excretion. Healthy volunteers were administered 40 mg orally (dissolved in water) and concentrations of FD were determined in serum and urine for up to 6 h for eight subjects, who absorbed water at a rate of 400 ml/h. Quantification was performed by HPLC with fluorescence detection (excitation at 233 nm, emission at 389 nm) with a limit of detection of 5 ng/ml for a 300-microliters sample. The elution of FD was completed within 4 min using a gradient of acetonitrile concentration rising from 30 to 50% in 0.08 M phosphoric acid. The delay to the peak serum concentration ranged from 60 to 120 min. FD was still easily measurable in the sera from all subjects 6 h after administration. In urine, the excretion rates reached their maximum between 1 and 3 h. The total amount of FD excreted in the urine averaged 11.2 mg (range 7.6-14.0 mg), with a mean urine volume of 3024 ml (range 2620-3596 ml). Moreover, the urine density was lower than 1.010 (recommended as an upper limit in doping analysis to screen diuretics) only for 2 h. An additional volunteer was administered 40 mg of FD and his urine was collected over a longer period. FD was still detectable 48 h after intake. Gas chromatography-mass spectrometry with different types of ionization was used to confirm the occurrence of FD after permethylation of the extract. Negative-ion chemical ionization, with ammonia as reactant gas, was found to be the most sensitive method of detection.

A first attempt of geographically-distributed Multi-scale integrated analysis of societal and ecosystem metabolism (MuSIASEM): mapping human time and energy throughput in metropolitan Barcelona

This study presents a first attempt to extend the “Multi-scale integrated analysis of societal and ecosystem metabolism (MuSIASEM)” approach to a spatial dimension using GIS techniques in the Metropolitan area of Barcelona. We use a combination of census and commercial databases along with a detailed land cover map to create a layer of Common Geographic Units that we populate with the local values of human time spent in different activities according to MuSIASEM hierarchical typology. In this way, we mapped the hours of available human time, in regards to the working hours spent in different locations, putting in evidence the gradients in spatial density between the residential location of workers (generating the work supply) and the places where the working hours are actually taking place. We found a strong three-modal pattern of clumps of areas with different combinations of values of time spent on household activities and on paid work. We also measured and mapped spatial segregation between these two activities and put forward the conjecture that this segregation increases with higher energy throughput, as the size of the functional units must be able to cope with the flow of exosomatic energy. Finally, we discuss the effectiveness of the approach by comparing our geographic representation of exosomatic throughput to the one issued from conventional methods.

Rockfall hazard and risk assessments along roads at a regional scale: Example in Swiss Alps

Unlike fragmental rockfall runout assessments, there are only few robust methods to quantify rock-mass-failure susceptibilities at regional scale. A detailed slope angle analysis of recent Digital Elevation Models (DEM) can be used to detect potential rockfall source areas, thanks to the Slope Angle Distribution procedure. However, this method does not provide any information on block-release frequencies inside identified areas. The present paper adds to the Slope Angle Distribution of cliffs unit its normalized cumulative distribution function. This improvement is assimilated to a quantitative weighting of slope angles, introducing rock-mass-failure susceptibilities inside rockfall source areas previously detected. Then rockfall runout assessment is performed using the GIS- and process-based software Flow-R, providing relative frequencies for runout. Thus, taking into consideration both susceptibility results, this approach can be used to establish, after calibration, hazard and risk maps at regional scale. As an example, a risk analysis of vehicle traffic exposed to rockfalls is performed along the main roads of the Swiss alpine valley of Bagnes.

High-resolution numerical modelling of flow-vegetation interactions

In this paper, we present and apply a new three-dimensional model for the prediction of canopy-flow and turbulence dynamics in open-channel flow. The approach uses a dynamic immersed boundary technique that is coupled in a sequentially staggered manner to a large eddy simulation. Two different biomechanical models are developed depending on whether the vegetation is dominated by bending or tensile forces. For bending plants, a model structured on the Euler-Bernoulli beam equation has been developed, whilst for tensile plants, an N-pendula model has been developed. Validation against flume data shows good agreement and demonstrates that for a given stem density, the models are able to simulate the extraction of energy from the mean flow at the stem-scale which leads to the drag discontinuity and associated mixing layer.

Prognostic accuracy of cerebral blood flow measurement by perfusion computed tomography, at the time of emergency room admission, in acute stroke patients.

The purpose of this study was to determine the prognostic accuracy of perfusion computed tomography (CT), performed at the time of emergency room admission, in acute stroke patients. Accuracy was determined by comparison of perfusion CT with delayed magnetic resonance (MR) and by monitoring the evolution of each patient's clinical condition. Twenty-two acute stroke patients underwent perfusion CT covering four contiguous 10mm slices on admission, as well as delayed MR, performed after a median interval of 3 days after emergency room admission. Eight were treated with thrombolytic agents. Infarct size on the admission perfusion CT was compared with that on the delayed diffusion-weighted (DWI)-MR, chosen as the gold standard. Delayed magnetic resonance angiography and perfusion-weighted MR were used to detect recanalization. A potential recuperation ratio, defined as PRR = penumbra size/(penumbra size + infarct size) on the admission perfusion CT, was compared with the evolution in each patient's clinical condition, defined by the National Institutes of Health Stroke Scale (NIHSS). In the 8 cases with arterial recanalization, the size of the cerebral infarct on the delayed DWI-MR was larger than or equal to that of the infarct on the admission perfusion CT, but smaller than or equal to that of the ischemic lesion on the admission perfusion CT; and the observed improvement in the NIHSS correlated with the PRR (correlation coefficient = 0.833). In the 14 cases with persistent arterial occlusion, infarct size on the delayed DWI-MR correlated with ischemic lesion size on the admission perfusion CT (r = 0.958). In all 22 patients, the admission NIHSS correlated with the size of the ischemic area on the admission perfusion CT (r = 0.627). Based on these findings, we conclude that perfusion CT allows the accurate prediction of the final infarct size and the evaluation of clinical prognosis for acute stroke patients at the time of emergency evaluation. It may also provide information about the extent of the penumbra. Perfusion CT could therefore be a valuable tool in the early management of acute stroke patients.