Artículos de publicaciones periódicas

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Herramienta web para post-análisis de simulaciones de dinámica molecular
(2013) Borgna, Karina Giselle; Fernández, María Laura; Risk, Marcelo
"En este trabajo se busca desarrollar una aplicación web interactiva y personalizada que permita analizar resultados generados mediante simulaciones de dinámica molecular. Con esta herramienta se pretende analizar las propiedades cada átomo o molécula de manera individual o conjunta a partir de una trayectoria, permitiendo segmentaciones tridimensionales que el usuario puede personalizar, así como análisis estadísticos no disponibles en las aplicaciones de post análisis que brindan los paquetes de dinámica molecular. Una herramienta de estas características es de gran ayuda en el estudio de los datos obtenidos permitiendo al usuario proponer el análisis o representación de los mismos que considere necesarios. Para este trabajo, como ejemplo, se tomaron datos generados por el programa Gromacs y fueron incorporados a una base de datos desarrollada en un entorno web. Se seleccionaron simulaciones de una bicapa lipídica expuesta a un campo eléctrico por el gran costo computacional que presenta de modo de generar una aplicación que pueda ser capaz de analizar datos independientemente de la demanda que éstos requieran. El sitio web se desarrolló con el framework Django, el cual permite utilizar Python, mientras que la base de datos se implementó en PostgreSQL. Se obtuvo una aplicación web que permite cargar datos de una trayectoria y generar un análisis estadístico, así como gráficos y representaciones espaciales. Se propone generar modelos 3D que permitan estimar superficie o volumen de la selección de átomos que el usuario considere necesarios."
Nanobioingeniería: historia y futuro
(2015) Risk, Marcelo
"Las aplicaciones de la nanotecnología desde la ingeniería a los ámbitos de la biología y la medicina constituyen la nanobioingeniería. Entonces la nanobioingeniería se puede describir como un área de trabajo multidisciplinaria, donde convergen las ciencias básicas como biología, matemática, química y física, con la medicina, la electrónica, la mecánica, informática y los aspectos éticos y legales."
Enhanced retention of bacteria by TiO2 nanoparticles in saturated porous media
(2016) Gentile, Guillermina J.; Fidalgo de Cortalezzi, María M.
The simultaneous transport of TiO2 nanoparticles and bacteria Pseudomonas aeruginosa in saturated porous media was investigated. Nanoparticle and bacterium size and surface charge were measured as a function of electrolyte concentration. Sand column breakthrough curves were obtained for single and combined suspensions, at four different ionic strengths. DLVO and classical filtration theories were employed to model the interactions between particles and between particles and sand grains. Attachment of TiO2 to the sand was explained by electrostatic forces and these nanoparticles acted as bonds between the bacteria and the sand, leading to retention. Presence of TiO2 significantly increased the retention of bacteria in the sand bed, but microorganisms were released when nanomaterial influx ceased. The inclusion of nanomaterials in saturated porous media may have implications for the design and operation of sand filters in water treatment.
User-centered design improves the usability of drug-drug interaction alerts: experimental comparison of interfaces
(2017) Luna, Daniel; Rizzato Lede, Daniel; Otero, Carlos; Risk, Marcelo; González Bernaldo de Quirós, Fernán
"Clinical Decision Support Systems can alert health professionals about drug interactions when they prescribe medications. The Hospital Italiano de Buenos Aires in Argentina developed an electronic health record with drug-drug interaction alerts, using traditional software engineering techniques and requirements. Despite enhancing the drug-drug interaction knowledge database, the alert override rate of this system was very high. We redesigned the alert system using user-centered design (UCD) and participatory design techniques to enhance the drug-drug interaction alert interface. This paper describes the methodology of our UCD. We used crossover method with realistic, clinical vignettes to compare usability of the standard and new software versions in terms of efficiency, effectiveness, and user satisfaction. Our study showed that, compared to the traditional alert system, the UCD alert system was more efficient (alerts faster resolution), more effective (tasks completed with fewer errors), and more satisfying. These results indicate that UCD techniques that follow ISO 9241-210 can generate more usable alerts than traditional design."
Classification of normal and pre-ictal EEG signals using permutation entropies and a generalized linear model as a classifier
(2017-02) Redelico, Francisco; Traversaro Varela, Francisco; García, María del Carmen; Silva, Walter; Rosso, Osvaldo A.; Risk, Marcelo
"In this contribution, a comparison between different permutation entropies as classifiers of electroencephalogram (EEG) records corresponding to normal and pre-ictal states is made. A discrete probability distribution function derived from symbolization techniques applied to the EEG signal is used to calculate the Tsallis entropy, Shannon Entropy, Renyi Entropy, and Min Entropy, and they are used separately as the only independent variable in a logistic regression model in order to evaluate its capacity as a classification variable in a inferential manner. The area under the Receiver Operating Characteristic (ROC) curve, along with the accuracy, sensitivity, and specificity are used to compare the models. All the permutation entropies are excellent classifiers, with an accuracy greater than 94.5% in every case, and a sensitivity greater than 97%. Accounting for the amplitude in the symbolization technique retains more information of the signal than its counterparts, and it could be a good candidate for automatic classification of EEG signals."
Real-time detection of imminent ventricular fibrillation using mean and standard deviation of beat-to-beat HRV
(2018) Mosquera, Candelaria; Racca, Dora María; Quintero-Rincón, Antonio
"It is estimated that 50% of all cardiovascular deaths are caused by a sudden cardiac arrest (SCA), which represents 15% of global mortality, and its main cause is ventricular fibrillation (VF). Therefore, it is of interest to design new methods capable to detect changes in heart rate (HR or RR interval) that could announce the beginning of an imminent fibrillation. In this work, an effective novel indicator, based on mean and standard deviation of Heart Rate Variability (HRV), was studied and used to develop an algorithm that predicts imminent VF with 100% sensitivity and 100% specificity. The study was based on 65 RR intervals signals. The algorithm’s simplicity provides a quick-to-use implementation in a micro controller unit (MCU) for real-time VF detection, allowing its application in a variety of medical devices with electrocardiogram (ECG) modules."
Predicción de crisis epilépticas utilizando el coeficiente de correlación producto-momento de Pearson a partir de un clasificador lineal de la distribución Gaussiana generalizada
(2018) Quintero-Rincón, Antonio; D'Giano, Carlos; Risk, Marcelo
"Predecir una crisis epiléptica significa la capacidad de determinar de antemano el momento de una crisis con la mayor precisión posible. Un pronóstico correcto de un evento epiléptico en aplicaciones clínicas es un problema típico en procesamiento de senales biomédicas, lo cual ayuda a un diagnóstico y tratamiento apropiado de esta enfermedad. En este trabajo, utilizamos el coeficiente de correlación producto-momento de Pearson a partir de las clases estimadas con un clasificador lineal, usando los parámetros de la distribución Gaussiana generalizada. Esto con el fin de poder pronosticar eventos con crisis y eventos con no-crisis en senales epilépticas. El desempeño en 36 eventos epilépticos de 9 pacientes muestra un buen rendimiento, con un 100% de efectividad para sensibilidad y especificidad superior al 83% para eventos con crisis en todos los ritmos cerebrales. El test de Pearson indica que todos los ritmos cerebrales están altamente correlacionados en los eventos con no-crisis, más no durante los eventos con crisis. Esto indica que nuestro modelo puede escalarse con el coeficiente de correlación producto-momento de Pearson para la detección de crisis en senales epilépticas."
Spike-and-wave detection in epileptic signals using cross-correlation and decision trees
(2018) Quintero-Rincón, Antonio; Alanis, Manuela; Muro, Valeria; D'Giano, Carlos
"Identify spike-and-waves patterns in epileptic signals is a typical problem in electroencephalographic (EEG) signal processing. In this paper we propose cross-correlation coupled with decision tree model as new method in order to assess and detect spike-and-wave discharges (SWD) in long-term epileptic signals. The proposed approach is demonstrated in terms of accuracy, sensitivity and specificity classification on real EEG signals using a database developed with medical annotations."
Asymmetric patterns of small molecule transport after nanosecond and microsecond electropermeabilization
(2018) Sözer, Esin B.; Pocetti, Florencia; Vernier, P. Thomas
"Imaging of fluorescent small molecule transport into electropermeabilized cells reveals polarized patterns of entry, which must reflect in some way the mechanisms of the migration of these molecules across the compromised membrane barrier. In some reports, transport occurs primarily across the areas of the membrane nearest the positive electrode (anode), but in others cathode-facing entry dominates. Here we compare YO-PRO-1, propidium, and calcein uptake into U-937 cells after nanosecond (6 ns) and microsecond (220 ls) electric pulse exposures. Each of the three dyes exhibits a different pattern. Calcein shows no preference for anode- or cathode-facing entry that is detectable with our measurement system. Immediately after a microsecond pulse, YO-PRO-1 and propidium enter the cell roughly equally from the positive and negative poles, but transport through the cathode-facing side dominates in less than 1 s. After nanosecond pulse permeabilization, YO-PRO-1 and propidium enter primarily on the anode-facing side of the cell."
Fast statistical model-based classification of epileptic EEG signals
(2018-01) Quintero-Rincón, Antonio; Pereyra, Marcelo; D'Giano, Carlos; Risk, Marcelo; Batatia, Hadj
"This paper presents a supervised classification method to accurately detect epileptic brain activity in real-time from electroencephalography (EEG) data. The proposed method has three main strengths: it has low computational cost, making it suitable for real-time implementation in EEG devices; it performs detection separately for each brain rhythm or EEG spectral band, following the current medical practices; and it can be trained with small datasets, which is key in clinical problems where there is limited annotated data available. This is in sharp contrast with modern approaches based on machine learning techniques, which achieve very high sensitivity and specificity but require large training sets with expert annotations that may not be available. The proposed method proceeds by first separating EEG signals into their five brain rhythms by using awavelet filter bank. Each brain rhythm signal is then mapped to a low-dimensional manifold by using a generalized Gaussian statistical model; this dimensionality reduction step is computationally straightforward and greatly improves supervised classification performance in problems with little training data available. Finally, this is followed by parallel linear classifications on the statistical manifold to detect if the signals exhibit healthy or abnormal brain activity in each spectral band. The good performance of the proposed method is demonstrated with an application to paediatric neurology using 39 EEG recordings from the Children's Hospital Boston database, where it achieves an average sensitivity of 98%, specificity of 88%, and detection latency of 4 s, performing similarly to the best approaches from the literature."
Transport of charged small molecules after electropermeabilization — drift and diffusion
(2018-03) Sözer, Esin B.; Pocetti, Florencia; Vernier, P. Thomas
"We provide a direct quantitative comparison of molecular transport of three similarly sized but chemically different fluorescent indicators of membrane permeabilization — two cationic molecules (YO-PRO-1 and propidium), and one anionic molecule (calcein). Our results show that the influx of YO-PRO-1 and propidium (both cations) into electropermeabilized cells is an order of magnitude greater than that of calcein (an anion) after the same pulse exposure. Calcein efflux from cells loaded before permeabilization, however, is similar in magnitude to YO-PRO-1 and propidium influx."
Electropore formation in mechanically constrained phospholipid bilayers
(2018-04) Fernández, María Laura; Risk, Marcelo; Vernier, P. Thomas
"Molecular dynamics simulations of lipid bilayers in aqueous systems reveal how an applied electric field stabilizes the reorganization of the water–membrane interface into water-filled, membrane-spanning, conductive pores with a symmetric, toroidal geometry. The pore formation process and the resulting symmetric structures are consistent with other mathematical approaches such as continuum models formulated to describe the electroporation process. Some experimental data suggest, however, that the shape of lipid electropores in living cell membranes may be asymmetric. We describe here the axially asym-metric pores that form when mechanical constraints are applied to selected phospholipid atoms. Electropore formation pro-ceeds even with severe constraints in place, but pore shape and pore formation time are affected. Since lateral and transverse movement of phospholipids may be restricted in cell membranes by covalent attachments to or non-covalent associations with other components of the membrane or to membrane-proximate intracellular or extracellular biomolecular assemblies, these lipid-constrained molecular models point the way to more realistic representations of cell membranes in electric fields."
Confidence intervals and hypothesis testing for the Permutation Entropy with an application to epilepsy
(2018-04) Traversaro Varela, Francisco; Redelico, Francisco
"In nonlinear dynamics, and to a lesser extent in other fields, a widely used measure of complexity is the Permutation Entropy. But there is still no known method to determine the accuracy of this measure. There has been little research on the statistical properties of this quantity that characterize time series. The literature describes some resampling methods of quantities used in nonlinear dynamics - as the largest Lyapunov exponent - but these seems to fail. In this contribution, we propose a parametric bootstrap methodology using a symbolic representation of the time series to obtain the distribution of the Permutation Entropy estimator. We perform several time series simulations given by well-known stochastic processes: the 1/f α noise family, and show in each case that the proposed accuracy measure is as efficient as the one obtained by the frequentist approach of repeating the experiment. The complexity of brain electrical activity, measured by the Permutation Entropy, has been extensively used in epilepsy research for detection in dynamical changes in electroencephalogram (EEG) signal with no consideration of the variability of this complexity measure. An application of the parametric bootstrap methodology is used to compare normal and pre-ictal EEG signals."
Sizing the lung in dogs: the inspiratory capacity defines the tidal volume
(2018-06) Donati, Pablo Alejandro; Gogniat, Emiliano; Madorno, Matías; Guevara, Juan Manuel; Guillemi, Eliana Carolina; Lavalle, María del Carmen; Scorza, Francisco Patricio; Mayer, Germán Federico; Rodríguez, Pablo Oscar
"To evaluate a novel physiological approach for setting the tidal volume in mechanical ventilation according to inspiratory capacity, and to determine if it results in an appropriate mechanical and gas exchange measurements in healthy and critically ill dogs."
Dead space analysis at different levels of positive end-expiratory pressure in acute respiratory distress syndrome patients
(2018-06) Gogniat, Emiliano; Ducrey, Marcela; Dianti, José; Madorno, Matías; Roux, Nicolás; Midley, Alejandro; Raffo, Julio; Giannasi, Sergio; San Román, Eduardo; Suárez-Sipmann, Fernando; Tusman, Gerardo
"To analyze the effects of positive end-expiratory pressure (PEEP) on Bohr's dead space (VDBohr/VT) in patients with acute respiratory distress syndrome (ARDS)."
Bandt-Pompe symbolization dynamics for time series with tied values: a data-driven approach
(2018-07) Traversaro Varela, Francisco; Redelico, Francisco; Risk, Marcelo; Frery, Alejandro C.; Rosso, Osvaldo A.
"In 2002, Bandt and Pompe [Phys. Rev. Lett. 88, 174102 (2002)] introduced a successfully symbolic encoding scheme based on the ordinal relation between the amplitude of neighboring values of a given data sequence, from which the permutation entropy can be evaluated. Equalities in the analyzed sequence, for example, repeated equal values, deserve special attention and treatment as was shown recently by Zunino and co-workers [Phys. Lett. A 381, 1883 (2017)]. A significant number of equal values can give rise to false conclusions regarding the underlying temporal structures in practical contexts. In the present contribution, we review the different existing methodologies for treating time series with tied values by classifying them according to their different strategies. In addition, a novel data-driven imputation is presented that proves to outperform the existing methodologies and avoid the false conclusions pointed by Zunino and co-workers."
Analysis of ischaemic crisis using the informational causal entropy-complexity plane
(2018-07) Legnani, Walter; Traversaro Varela, Francisco; Redelico, Francisco; Cymberknop, Leandro J.; Armentano, Ricardo L.; Rosso, Osvaldo A.
"In the present work, an ischaemic process, mainly focused on the reperfusion stage, is studied using the informational causal entropy-complexity plane. Ischaemic wall behavior under this condition was analyzed through wall thickness and ventricular pressure variations, acquired during an obstructive flow maneuver performed on left coronary arteries of surgically instrumented animals. Basically, the induction of ischaemia depends on the temporary occlusion of left circumflex coronary artery (which supplies blood to the posterior left ventricular wall) that lasts for a few seconds. Normal perfusion of the wall was then reestablished while the anterior ventricular wall remained adequately perfused during the entire maneuver. The obtained results showed that system dynamics could be effectively described by entropy-complexity loops, in both abnormally and well perfused walls. These results could contribute to making an objective indicator of the recovery heart tissues after an ischaemic process, in a way to quantify the restoration of myocardial behavior after the supply of oxygen to the ventricular wall was suppressed for a brief period."
Study on epileptic seizure detection in EEG signals using largest Lyapunov exponents and logistic regression
(2019) Quintero-Rincón, Antonio; Flugelman, Máximo; Prendes, Jorge; D'Giano, Carlos
"Seizure detection plays a central role in most aspects of epilepsy care. Understanding the complex epileptic signals system is a typical problem in electroencephalographic (EEG) signal processing. This problem requires different analysis to reveal the underlying behavior of EEG signals. An example of this is the non-linear dynamic: mathematical tools applied to biomedical problems with the purpose of extracting features or quantifying EEG data. In this work, we studied epileptic seizure detection independently in each brain rhythms from a multilevel 1D wavelet decomposition followed by the independent component analysis (ICA) representation of multivariate EEG signals. Next, the largest Lyapunov exponents (LLE) and their scaling given by its standard deviation are estimated in order to obtain the vectors to be used during the training and classification stage. With this information, a logistic regression classification is proposed with the aim of discriminating between seizure and non-seizure. Preliminary experiments with 99 epileptic events suggest that the proposed methodology is a powerful tool for detecting seizures in epileptic signals in terms of classification accuracy, sensitivity and specificity."
Multimodal non‑invasive monitoring to apply an open lung approach strategy in morbidly obese patients during bariatric surgery
(2019) Tusman, Gerardo; Acosta, Cecilia M.; Ochoa, Marcos; Böhm, Stephan H.; Gogniat, Emiliano; Martínez Arca, Jorge; Scandurra, Adriana; Madorno, Matías; Ferrando, Carlos; Suárez-Sipmann, Fernando
"To evaluate the use of non-invasive variables for monitoring an open-lung approach (OLA) strategy in bariatric surgery. Twelve morbidly obese patients undergoing bariatric surgery received a baseline protective ventilation with 8 cmH2O of positive-end expiratory pressure (PEEP). Then, the OLA strategy was applied consisting in lung recruitment followed by a decremental PEEP trial, from 20 to 8 cmH2O, in steps of 2 cmH2O to find the lung’s closing pressure. Baseline ventila-tion was then resumed setting open lung PEEP (OL-PEEP) at 2 cmH2O above this pressure. The multimodal non-invasive variables used for monitoring OLA consisted in pulse oximetry (SpO2), respiratory compliance (Crs), end-expiratory lung volume measured by a capnodynamic method (EELVCO2), and esophageal manometry. OLPEEP was detected at 15.9 ± 1.7 cmH2O corresponding to a positive end-expiratory transpulmonary pressure (PL,ee) of 0.9 ± 1.1 cmH2O. ROC analysis showed that SpO2 was more accurate (AUC 0.92, IC95% 0.87–0.97) than Crs (AUC 0.76, IC95% 0.87–0.97) and EELVCO2 (AUC 0.73, IC95% 0.64–0.82) to detect the lung’s closing pressure according to the change of PL,ee from positive to negative values. Compared to baseline ventilation with 8 cmH2O of PEEP, OLA increased EELVCO2 (1309 ± 517 vs. 2177 ± 679 mL) and decreased driving pressure (18.3 ± 2.2 vs. 10.1 ± 1.7 cmH2O), estimated shunt (17.7 ± 3.4 vs. 4.2 ± 1.4%), lung strain (0.39 ± 0.07 vs. 0.22 ± 0.06) and lung elastance (28.4 ± 5.8 vs. 15.3 ± 4.3 cmH2O/L), respectively; all p < 0.0001. The OLA strategy can be monitored using noninvasive variables during bariatric surgery. This strategy decreased lung strain, elastance and driving pressure compared with standard protective ventilatory settings."
Photoplethysmographic characterization of vascular tone mediated changes in arterial pressure: an observational study
(2019-10) Tusman, Gerardo; Acosta, Cecilia M.; Pulletz, Sven; Böhm, Stephan H.; Scandurra, Adriana; Martínez Arca, Jorge; Madorno, Matías; Suárez-Sipmann, Fernando
"To determine whether a classification based on the contour of the photoplethysmography signal (PPGc) can detect changes in systolic arterial blood pressure (SAP) and vascular tone. Episodes of normotension (SAP 90–140 mmHg), hypertension (SAP > 140 mmHg) and hypotension (SAP < 90 mmHg) were analyzed in 15 cardiac surgery patients. SAP and two surrogates of the vascular tone, systemic vascular resistance (SVR) and vascular compliance (Cvasc = stroke volume/pulse pressure) were compared with PPGc. Changes in PPG amplitude (foot-to-peak distance) and dicrotic notch position were used to define 6 classes taking class III as a normal vascular tone with a notch placed between 20 and 50% of the PPG amplitude. Class I-to-II represented vasoconstriction with notch placed > 50% in a small PPG, while class IV-to-VI described vasodilation with a notch placed < 20% in a tall PPG wave. 190 datasets were analyzed including 61 episodes of hypertension [SAP = 159 (151–170) mmHg (median 1st–3rd quartiles)], 84 of normotension, SAP = 124 (113–131) mmHg and 45 of hypotension SAP = 85(80–87) mmHg. SAP were well correlated with SVR (r = 0.78, p < 0.0001) and Cvasc (r = 0.84, p < 0.0001). The PPG-based classification correlated well with SAP (r = − 0.90, p < 0.0001), SVR (r = − 0.72, p < 0.0001) and Cvasc (r = 0.82, p < 0.0001). The PPGc misclassified 7 out of the 190 episodes, presenting good accuracy (98.4% and 97.8%), sensitivity (100% and 94.9%) and specificity (97.9% and 99.2%) for detecting episodes of hypotension and hypertension, respectively. Changes in arterial pressure and vascular tone were closely related to the proposed classification based on PPG waveform."

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