Genetic and Geo-Epidemiological Analysis of the Zika Virus Pandemic; Learning Lessons from the Recent Ebola Outbreak

“Outbreak” is a term referring to a virus or a parasite that is transmitted very aggressively and therefore could potentially cause fatalities, as the recent Ebola and Zika epidemics did. Nevertheless, looking back through history, quite a few outbreaks have been reported, which turned out so deadly that essentially changed, molded and literally re-shaped the society as it is today. In the present chapter, differences and similarities between the two most recent outbreaks have been studied, in order to pinpoint and design a trace model that will allow us to draw some conclusions for the connection of those two epidemics. Due to the high dimensionality of the problem, modern and state of the art geo-epidemiological methods have been used in an effort to provide the means necessary to establish the abovementioned model. It is only through geo-epidemiological analysis that it is possible to analyze concurrently a multitude of variables, such as genetic, environmental, behavioral, socioeconomic and a series of related infection risk factors

Real-Time Management of Multimodal Streaming Data for Monitoring of Epileptic Patients

This is the Accepted Manuscript version of the following article: I. Mporas, D. Triantafyllopoulos, V. Megalooikonomou, “Real-Time Management of Multimodal Streaming Data for Monitoring of Epileptic Patients”, Journal of Medical Systems, Vol. 40(45), December 2015. The final published versions is available at: https://link.springer.com/article/10.1007%2Fs10916-015-0403-3 © Springer Science+Business Media New York 2015.New generation of healthcare is represented by wearable health monitoring systems, which provide real-time monitoring of patient’s physiological parameters. It is expected that continuous ambulatory monitoring of vital signals will improve treatment of patients and enable proactive personal health management. In this paper, we present the implementation of a multimodal real-time system for epilepsy management. The proposed methodology is based on a data streaming architecture and efficient management of a big flow of physiological parameters. The performance of this architecture is examined for varying spatial resolution of the recorded data.Peer reviewe

Protein signatures using electrostatic molecular surfaces in harmonic space

We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the molecular electrostatic potential, whose three-dimensional coordinates have been either experimentally or theoretically determined. Thus we achieve a reduction of the initial three-dimensional information on the molecular surface to the one-dimensional information on pairs of points at a fixed scale apart. Consequently, the similarity search in our method is computationally less demanding and significantly faster than shape comparison methods. As proof of principle, we applied our method to a training set of viral proteins that are involved in major diseases such as Hepatitis C, Dengue fever, Yellow fever, Bovine viral diarrhea and West Nile fever. The training set contains proteins of four different protein families, as well as a mammalian representative enzyme. We found that the power spectrum successfully assigns a unique signature to each protein included in our training set, thus providing a direct probe of functional similarity among proteins. The results agree with established biological data from conventional structural biochemistry analyses.Comment: 9 pages, 10 figures Published in PeerJ (2013), https://peerj.com/articles/185

Introducing Thetis: a comprehensive suite for event detection in molecular dynamics

A suite of computer programs has been developed under the general name Thetis, for monitoring structural changes during molecular dynamics (MD) simulations on proteins. Conformational analysis includes estimation of structural similarities during the simulation and analysis of the secondary structure with emphasis on helices. In contrast to available freeware dealing with MD snapshots, Thetis can be used on a series of consecutive MD structures, thus allowing a detailed conformational analysis over the time course of the simulation

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence however is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D-convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The 2-layer architecture was investigated on a large dataset of 63,558 enzymes from the Protein Data Bank and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.Comment: 11 pages, 6 figure

Evaluation and Sociolinguistic Analysis of Text Features for Gender and Age Identification

The paper presents an interdisciplinary study in the field of automatic gender and age identification, under the scope of sociolinguistic knowledge on gendered and age linguistic choices that social media users make. The authors investigated and gathered standard and novel text features used in text mining approaches on the author's demographic information and profiling and they examined their efficacy in gender and age detection tasks on a corpus consisted of social media texts. An analysis of the most informative features is attempted according to the nature of each feature and the information derived after the characteristics' score of importance is discussed

3D structural analysis of proteins using electrostatic surfaces based on image segmentation

Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electrostatic surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.  

Tourism Demand in the Face of Geopolitical Risk: Insights From a Cross-Country Analysis

This paper develops a novel Bayesian heterogeneous panel vector autoregressive model (B-HP-VAR) that quantifies the impact of geopolitical risk shocks on the tourism industry of 14 emerging market and developing economies (EMDE). We find that increasing geopolitical tensions have a persistent negative effect on tourism demand in most of these countries, as shown by our impulse response estimates. Furthermore, evidence from forecast error variance decomposition reveals that geopolitical risk shocks in many EMDE economies constitute the main driver of tourism demand. Analysis from historical decompositions demonstrates that geopolitical tensions have been particularly influential in driving tourism demand in Ukraine, Russia, Turkey, China, Indonesia, Thailand, Colombia, and Mexico. Our main findings are robust to several perturbations to the benchmark specification. Our results have several important implications for policymakers in their efforts to strengthen the ability of the tourism industry to absorb shocks from geopolitical tensions