Optimization and Data Analysis in Biomedical Informatics

Abstract Intravascular ultrasound (IVUS) is a catheter-based medical imaging modality that is capable of providing cross-sectional images of the interior of blood vessels. A comprehensive analysis of the IVUS data allows collecting information about the morphology and structure of the vessel and the atherosclerotic plaque, if present. Atherosclerotic plaque formation is considered to be a part of an inflammatory process. Recent evidence has suggested that the presence and proliferation of vasa vasorum (VV) in the plaque is correlated with the increase of plaque inflammation and the processes which lead to its destabilization. Hence, the detection and measurement of VV in plaque has the potential to enable the development of an index of plaque vulnerability. In this paper, we review the research at the Computational Biomedicine Lab towards the development of a complete pipeline for the detection and quantification of extra-luminal blood detection from IVUS data which may be an indication of the existence of VV

Effect of fish and oil nature on frying process and nutritional product quality

The modifications on a lean fish (cod-Gadus morhua) and a fatty fish (farmed salmon-Salmo salar) after the application of pan-frying using 2 types of oil with different lipid profile (extra virgin olive oil and sunflower oil) was the aim of this study. Fat content and total energetic value increased significantly after the frying process only in the lean fish, without relevant changes in the fatty fish. Extra virgin olive oil led to a higher fat absorption rate than sunflower oil in both fish. Frying hardly affected the lipid profile of farmed salmon regardless the oil used, however it drastically changed in fried cod compared to raw cod. Omega-6/omega-3 ratio increased from 0.08 in raw cod to 1.01 and 6.63 in fried cod with olive oil and sunflower oil, respectively. In farmed salmon, the omega-6/omega-3 ratio was 0.38 (raw), and 0.39 to 0.58 in fried salmon. The amount of EPA + DHA slightly decreased with frying in salmon, and increased in cod. The type of oil has more influence in the nutritional fish quality for the lean fish compared to that of the fatty fish. The use of extra virgin olive oil was efficient to avoid a significant increase of the lipid oxidation intensity during frying in cod but not in salmon. PRACTICAL APPLICATION: Food modifies its composition and nutritional value with the application of cooking technologies. As most food table composition tables are based on raw food products, this article contributes with interesting data on pan-fried fish composition, which may improve the approach to achieve a real intake of healthy nutrients as omega 3 fatty acids

Public supply well fields as a valuable groundwater quality monitoring network

Stuijfzand, P.J. [Promotor

SDRS: a new lossless dimensionality reduction for text corpora

In recent years, most content-based spam filters have been implemented using Machine Learning (ML) approaches by means of token-based representations of textual contents. After introducing multiple performance enhancements, the impact has been virtually irrelevant. Recent studies have introduced synset-based content representations as a reliable way to improve classification, as well as different forms to take advantage of semantic information to address problems, such as dimensionality reduction. These preliminary solutions present some limitations and enforce simplifications that must be gradually redefined in order to obtain significant improvements in spam content filtering. This study addresses the problem of feature reduction by introducing a new semantic-based proposal (SDRS) that avoids losing knowledge (lossless). Synset-features can be semantically grouped by taking advantage of taxonomic relations (mainly hypernyms) provided by BabelNet ontological dictionary (e.g. “Viagra” and “Cialis” can be summarized into the single features “anti-impotence drug”, “drug” or “chemical substance” depending on the generalization of 1, 2 or 3 levels). In order to decide how many levels should be used to generalize each synset of a dataset, our proposal takes advantage of Multi-Objective Evolutionary Algorithms (MOEA) and particularly, of the Non-dominated Sorting Genetic Algorithm (NSGA-II). We have compared the performance achieved by a Naïve Bayes classifier, using both token-based and synset-based dataset representations, with and without executing dimensional reductions. As a result, our lossless semantic reduction strategy was able to find optimal semantic-based feature grouping strategies for the input texts, leading to a better performance of Naïve Bayes classifiers.info:eu-repo/semantics/acceptedVersio

Nitric oxide synthase-independent release of nitric oxide induced by KCl in the perfused mesenteric bed of the rat

The aim of the present study was to test whether the contractile responses elicited by KCl in the rat mesenteric bed are coupled to the release of nitric oxide (NO). Contractions induced by 70 mM KCl were coincident with the release of NO to the perfusate. The in vitro exposure to the nitric oxide synthase (NOS) inhibitor L-N(ω)-nitro-L-arginine methyl ester, L-NAME (1-100 μM) potentiated the vascular responses to 70 mM KCl and, unexpectedly, increased the KCl-stimulated release of NO. Moreover, even after the chronic treatment with L-NAME (70 mg/kg/day during 4 weeks), the KCl-induced release of NO was not reduced, whereas the potentiation of contractile responses was indeed achieved. The possibility that NOS had not been completely inhibited under our experimental conditions can be precluded because NOS activity was significantly inhibited after both L-NAME treatments. After the in vitro treatment with 1 to 100 μM L-NAME, the inhibition of NOS was concentration-dependent (from 50% to 90%). With regard to the basal release of NO, the inhibition caused by L-NAME was not concentration-dependent and reached a maximum of 40%, suggesting that basal NO outflow is only partially dependent on NOS activity. An eventual enhancement of NOS activity caused by KCl was disregarded because the activity of this enzyme measured in homogenates from mesenteric beds perfused with 70 mM KCl was significantly reduced. On the other hand, endothelium removal, employed as a negative control, almost abolished NOS activity, whereas the incubation with the Ca2+ ionophore A23187, employed as a positive control, induced an increase in NOS activity. It is concluded that in the mesenteric arterial bed of the rat, the contractile responses elicited by depolarization through KCl are coincident with a NOS-independent release of NO. This observation, which differs from the results obtained with noradrenaline, do not support the use of KCl as an alternative contractile agent whenever the participation of NO is under study. (C) 2000 Elsevier Science B.V.Fil: Mendizabal, Victoria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; ArgentinaFil: Poblete, I.. Pontificia Universidad Católica de Chile; ChileFil: Lomniczi, A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Besuhli, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Huidobro Toro, J. P.. Pontificia Universidad Católica de Chile; ChileFil: Adler, Edda. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; Argentin

Conocimiento acerca del proceso de consentimiento informado en investigación en salud en estudiantes de medicina

La importancia del proceso de consentimiento informado en bioética es asegurar el respeto de los derechos y seguridad de los participantes en una investigación en salud. Se generó un cuestionario con el objetivo de determinar el conocimiento acerca del proceso de consentimiento informado en investigación en salud, en 461 estudiantes de segundo a sexto año de la Carrera de Médico y Cirujano de la Facultad de Ciencias Médicas, USAC, durante octubre a noviembre de 2016. Se evaluaron los conocimientos sobre conceptos y aplicación de los principios bioéticos, la importancia y elementos que forman el proceso de consentimiento informado en investigación en salud a través de un cuestionario electrónico vía internet (un tema por serie, cuatro series, preguntas de selección múltiple por tema; 18 preguntas); se evaluó como suficiente (? 61% de respuestas correctas) o insuficiente (< 61% de respuestas correctas). El mayor acierto de los estudiantes a las preguntas fue sobre práctica en ética, aplicaciónde principios bioéticos, 89%; e importancia del proceso de consentimiento informado, 94%, y el menor acierto en preguntas sobre teoría de ética, concepto de los principios bioéticos, 70%

Multi-objective evolutionary optimization for dimensionality reduction of texts represented by synsets

Despite new developments in machine learning classification techniques, improving the accuracy of spam filtering is a difficult task due to linguistic phenomena that limit its effectiveness. In particular, we highlight polysemy, synonymy, the usage of hypernyms/hyponyms, and the presence of irrelevant/confusing words. These problems should be solved at the pre-processing stage to avoid using inconsistent information in the building of classification models. Previous studies have suggested that the use of synset-based representation strategies could be successfully used to solve synonymy and polysemy problems. Complementarily, it is possible to take advantage of hyponymy/hypernymy-based to implement dimensionality reduction strategies. These strategies could unify textual terms to model the intentions of the document without losing any information (e.g., bringing together the synsets “viagra”, “ciallis”, “levitra” and other representing similar drugs by using “virility drug” which is a hyponym for all of them). These feature reduction schemes are known as lossless strategies as the information is not removed but only generalised. However, in some types of text classification problems (such as spam filtering) it may not be worthwhile to keep all the information and let dimensionality reduction algorithms discard information that may be irrelevant or confusing. In this work, we are introducing the feature reduction as a multi-objective optimisation problem to be solved using a Multi-Objective Evolutionary Algorithm (MOEA). Our algorithm allows, with minor modifications, to implement lossless (using only semantic-based synset grouping), low-loss (discarding irrelevant information and using semantic-based synset grouping) or lossy (discarding only irrelevant information) strategies. The contribution of this study is two-fold: (i) to introduce different dimensionality reduction methods (lossless, low-loss and lossy) as an optimization problem that can be solved using MOEA and (ii) to provide an experimental comparison of lossless and low-loss schemes for text representation. The results obtained support the usefulness of the low-loss method to improve the efficiency of classifiers.info:eu-repo/semantics/publishedVersio

Prediction of brain clozapine and norclozapine concentrations in humans from a scaled pharmacokinetic model for rat brain and plasma pharmacokinetics

BACKGROUND: Clozapine is highly effective in treatment-resistant schizophrenia, although, there remains significant variability in the response to this drug. To better understand this variability, the objective of this study was to predict brain extracellular fluid (ECF) concentrations and receptor occupancy of clozapine and norclozapine in human central nervous system by translating plasma and brain ECF pharmacokinetic (PK) relationships in the rat and coupling these with known human disposition of clozapine in the plasma. METHODS: Unbound concentrations of clozapine and norclozapine were measured in rat brain ECF using quantitative microdialysis after subcutaneous administration of a 10 mg/kg single dose of clozapine or norclozapine. These data were linked with plasma concentrations obtained in the same rats to develop a plasma-brain ECF compartmental model. Parameters describing brain ECF disposition were then allometrically scaled and linked with published human plasma PK to predict human ECF concentrations. Subsequently, prediction of human receptor occupancy at several CNS receptors was based on an effect model that related the predicted ECF concentrations to published concentration-driven receptor occupancy parameters. RESULTS: A one compartment model with first order absorption and elimination best described clozapine and norclozapine plasma concentrations in rats. A delay in the transfer of clozapine and norclozapine from plasma to the brain ECF compartment was captured using a transit compartment model approach. Human clozapine and norclozapine concentrations in brain ECF were simulated, and from these the median percentage of receptor occupancy of dopamine-2, serotonin-2A, muscarinic-1, alpha-1 adrenergic, alpha-2 adrenergic and histamine-1 for clozapine, and dopamine-2 for norclozapine were consistent with values reported in the literature. CONCLUSIONS: A PK model that relates clozapine and norclozapine disposition in rat plasma and brain, including blood-brain barrier transport, was developed. Using allometry and published human plasma PK, the model was successfully translated to predict clozapine and norclozapine concentrations and accordant receptor occupancy of both agents in human brain. These predicted exposure and occupancy measures at several receptors that bind clozapine may be employed to extend our understanding of clozapine's complex behavioral effects in humans

Back-to-back azimuthal correlations in Z+jet events at high transverse momentum in the TMD parton branching method at next-to-leading order

Azimuthal correlations in Z+jet production at large transverse momenta are computed by matching Parton - Branching (PB) TMD parton distributions and showers with NLO calculations via MCatNLO. The predictions are compared with those for dijet production in the same kinematic range. The azimuthal correlations $\Delta\phi$ between the Z boson and the leading jet are steeper compared to those in dijet production at transverse momenta ${\cal O}(100)$ GeV , while they become similar for very high transverse momenta ${\cal O}(1000)$ GeV. The different patterns of Z+jet and dijet azimuthal correlations can be used to search for potential factorization - breaking effects in the back-to-back region, which depend on the different color and spin structure of the final states and their interferences with the initial states. In order to investigate these effects experimentally, we propose to measure the ratio of the distributions in $\Delta\phi$ for Z+jet - and multijet production at low and at high transverse momenta, and compare the results to predictions obtained assuming factorization. We examine the role of theoretical uncertainties by performing variations of the factorization scale, renormalization scale and matching scale. In particular, we present a comparative study of matching scale uncertainties in the cases of PB -TMD and collinear parton showers

Impact of metabolic comorbidity on the association between body mass index and heatlh-related quality of life: a Scotland-wide cross-sectional study of 5,608 participants

<p/>Background: The prevalence of obesity is rising in Scotland and globally. Overall, obesity is associated with increased morbidity, mortality and reduced health-related quality of life. Studies suggest that "healthy obesity" (obesity without metabolic comorbidity) may not be associated with morbidity or mortality. Its impact on health-related quality of life is unknown. <p/>Methods: We extracted data from the Scottish Health Survey on self-reported health-related quality of life, body mass index (BMI), demographic information and comorbidity. SF-12 responses were converted into an overall health utility score. Linear regression analyses were used to explore the association between BMI and health utility, stratified by the presence or absence of metabolic comorbidity (diabetes, hypertension, hypercholesterolemia or cardiovascular disease), and adjusted for potential confounders (age, sex and deprivation quintile). <p/>Results: Of the 5,608 individuals, 3,744 (66.8%) were either overweight or obese and 921 (16.4%) had metabolic comorbidity. There was an inverted U-shaped relationship whereby health utility was highest among overweight individuals and fell with increasing BMI. There was a significant interaction with metabolic comorbidity (p = 0.007). Individuals with metabolic comorbidty had lower utility scores and a steeper decline in utility with increasing BMI (morbidly obese, adjusted coefficient: -0.064, 95% CI -0.115, -0.012, p = 0.015 for metabolic comorbidity versus -0.042, 95% CI -0.067, -0.018, p = 0.001 for no metabolic comorbidity). <p/>Conclusions: The adverse impact of obesity on health-related quality of life is greater among individuals with metabolic comorbidity. However, increased BMI is associated with reduced health-related quality of life even in the absence of metabolic comorbidity, casting doubt on the notion of "healthy obesity"