Sample Entropy Analysis of Noisy Atrial Electrograms during Atrial Fibrillation

[EN] Most cardiac arrhythmias can be classified as atrial flutter, focal atrial tachycardia, or atrial fibrillation. They have been usually treated using drugs, but catheter ablation has proven more effective. This is an invasive method devised to destroy the heart tissue that disturbs correct heart rhythm. In order to accurately localise the focus of this disturbance, the acquisition and processing of atrial electrograms form the usual mapping technique. They can be single potentials, double potentials, or complex fractionated atrial electrogram (CFAE) potentials, and last ones are the most effective targets for ablation. The electrophysiological substrate is then localised by a suitable signal processing method. Sample Entropy is a statistic scarcely applied to electrograms but can arguably become a powerful tool to analyse these time series, supported by its results in other similar biomedical applications. However, the lack of an analysis of its dependence on the perturbations usually found in electrogram data, such as missing samples or spikes, is even more marked. This paper applied SampEn to the segmentation between non-CFAE and CFAE records and assessed its class segmentation power loss at different levels of these perturbations. The results confirmed that SampEn was able to significantly distinguish between non-CFAE and CFAE records, even under very unfavourable conditions, such as 50% of missing data or 10% of spikes.This research was supported by Research Center for Informatics (no. CZ.02.1.01/0.0/0.0/16-019/0000765).Cirugeda Roldan, EM.; Molina Picó, A.; Novák, D.; Cuesta Frau, D.; Kremen, V. (2018). Sample Entropy Analysis of Noisy Atrial Electrograms during Atrial Fibrillation. Computational and Mathematical Methods in Medicine. https://doi.org/10.1155/2018/1874651SAhmed, S., Claughton, A., & Gould, P. A. (2015). Atrial Flutter — Diagnosis, Management and Treatment. Abnormal Heart Rhythms. doi:10.5772/60700Kirchhof, P., & Calkins, H. (2016). Catheter ablation in patients with persistent atrial fibrillation. European Heart Journal, 38(1), 20-26. doi:10.1093/eurheartj/ehw260Nademanee, K., Lockwood, E., Oketani, N., & Gidney, B. (2010). Catheter ablation of atrial fibrillation guided by complex fractionated atrial electrogram mapping of atrial fibrillation substrate. Journal of Cardiology, 55(1), 1-12. doi:10.1016/j.jjcc.2009.11.002NG, J., & GOLDBERGER, J. J. (2007). Understanding and Interpreting Dominant Frequency Analysis of AF Electrograms. Journal of Cardiovascular Electrophysiology, 18(6), 680-685. doi:10.1111/j.1540-8167.2007.00832.xKottkamp, H., & Hindricks, G. (2007). Complex fractionated atrial electrograms in atrial fibrillation: A promising target for ablation, but why, when, and how? Heart Rhythm, 4(8), 1021-1023. doi:10.1016/j.hrthm.2007.05.011Křemen, V., Lhotská, L., Macaš, M., Čihák, R., Vančura, V., Kautzner, J., & Wichterle, D. (2008). A new approach to automated assessment of fractionation of endocardial electrograms during atrial fibrillation. Physiological Measurement, 29(12), 1371-1381. doi:10.1088/0967-3334/29/12/002Nademanee, K., McKenzie, J., Kosar, E., Schwab, M., Sunsaneewitayakul, B., Vasavakul, T., … Ngarmukos, T. (2004). A new approach for catheter ablation of atrial fibrillation: mapping of the electrophysiologic substrate. Journal of the American College of Cardiology, 43(11), 2044-2053. doi:10.1016/j.jacc.2003.12.054Scherr, D., Dalal, D., Cheema, A., Cheng, A., Henrikson, C. A., Spragg, D., … Dong, J. (2007). Automated detection and characterization of complex fractionated atrial electrograms in human left atrium during atrial fibrillation. Heart Rhythm, 4(8), 1013-1020. doi:10.1016/j.hrthm.2007.04.021Almeida, T. P., Chu, G. S., Salinet, J. L., Vanheusden, F. J., Li, X., Tuan, J. H., … Schlindwein, F. S. (2016). Minimizing discordances in automated classification of fractionated electrograms in human persistent atrial fibrillation. Medical & Biological Engineering & Computing, 54(11), 1695-1706. doi:10.1007/s11517-016-1456-2Molina-Picó, A., Cuesta-Frau, D., Aboy, M., Crespo, C., Miró-Martínez, P., & Oltra-Crespo, S. (2011). Comparative study of approximate entropy and sample entropy robustness to spikes. Artificial Intelligence in Medicine, 53(2), 97-106. doi:10.1016/j.artmed.2011.06.007Cuesta–Frau, D., Miró–Martínez, P., Jordán Núñez, J., Oltra–Crespo, S., & Molina Picó, A. (2017). Noisy EEG signals classification based on entropy metrics. Performance assessment using first and second generation statistics. Computers in Biology and Medicine, 87, 141-151. doi:10.1016/j.compbiomed.2017.05.028Demont-Guignard, S., Benquet, P., Gerber, U., & Wendling, F. (2009). Analysis of Intracerebral EEG Recordings of Epileptic Spikes: Insights From a Neural Network Model. IEEE Transactions on Biomedical Engineering, 56(12), 2782-2795. doi:10.1109/tbme.2009.2028015Molina–Picó, A., Cuesta–Frau, D., Miró–Martínez, P., Oltra–Crespo, S., & Aboy, M. (2013). Influence of QRS complex detection errors on entropy algorithms. Application to heart rate variability discrimination. Computer Methods and Programs in Biomedicine, 110(1), 2-11. doi:10.1016/j.cmpb.2012.10.014Ganesan, P., Cherry, E. M., Pertsov, A. M., & Ghoraani, B. (2015). Characterization of Electrograms from Multipolar Diagnostic Catheters during Atrial Fibrillation. BioMed Research International, 2015, 1-9. doi:10.1155/2015/272954Lake, D. E., Richman, J. S., Griffin, M. P., & Moorman, J. R. (2002). Sample entropy analysis of neonatal heart rate variability. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology, 283(3), R789-R797. doi:10.1152/ajpregu.00069.2002Kim, K. K., Baek, H. J., Lim, Y. G., & Park, K. S. (2012). Effect of missing RR-interval data on nonlinear heart rate variability analysis. Computer Methods and Programs in Biomedicine, 106(3), 210-218. doi:10.1016/j.cmpb.2010.11.011Richman, J. S., & Moorman, J. R. (2000). Physiological time-series analysis using approximate entropy and sample entropy. American Journal of Physiology-Heart and Circulatory Physiology, 278(6), H2039-H2049. doi:10.1152/ajpheart.2000.278.6.h2039Cirugeda–Roldán, E., Novak, D., Kremen, V., Cuesta–Frau, D., Keller, M., Luik, A., & Srutova, M. (2015). Characterization of Complex Fractionated Atrial Electrograms by Sample Entropy: An International Multi-Center Study. Entropy, 17(12), 7493-7509. doi:10.3390/e17117493PORTER, M., SPEAR, W., AKAR, J. G., HELMS, R., BRYSIEWICZ, N., SANTUCCI, P., & WILBER, D. J. (2008). Prospective Study of Atrial Fibrillation Termination During Ablation Guided by Automated Detection of Fractionated Electrograms. Journal of Cardiovascular Electrophysiology, 19(6), 613-620. doi:10.1111/j.1540-8167.2008.01189.xKonings, K. T., Kirchhof, C. J., Smeets, J. R., Wellens, H. J., Penn, O. C., & Allessie, M. A. (1994). High-density mapping of electrically induced atrial fibrillation in humans. Circulation, 89(4), 1665-1680. doi:10.1161/01.cir.89.4.1665Fay, M. P., & Proschan, M. A. (2010). Wilcoxon-Mann-Whitney or t-test? On assumptions for hypothesis tests and multiple interpretations of decision rules. Statistics Surveys, 4(0), 1-39. doi:10.1214/09-ss051Richman, J. S. (2007). Sample Entropy Statistics and Testing for Order in Complex Physiological Signals. Communications in Statistics - Theory and Methods, 36(5), 1005-1019. doi:10.1080/03610920601036481Pincus, S. M., Gladstone, I. M., & Ehrenkranz, R. A. (1991). A regularity statistic for medical data analysis. Journal of Clinical Monitoring, 7(4), 335-345. doi:10.1007/bf01619355Alcaraz, R., & Rieta, J. J. (2009). Non-invasive organization variation assessment in the onset and termination of paroxysmal atrial fibrillation. Computer Methods and Programs in Biomedicine, 93(2), 148-154. doi:10.1016/j.cmpb.2008.09.001Alcaraz, R., Abásolo, D., Hornero, R., & Rieta, J. J. (2010). Optimal parameters study for sample entropy-based atrial fibrillation organization analysis. Computer Methods and Programs in Biomedicine, 99(1), 124-132. doi:10.1016/j.cmpb.2010.02.009Costa, M., Goldberger, A. L., & Peng, C.-K. (2002). Multiscale Entropy Analysis of Complex Physiologic Time Series. Physical Review Letters, 89(6). doi:10.1103/physrevlett.89.06810

Heterozygous deficiency of endoglin decreases insulin and hepatic triglyceride levels during high fat diet

Endoglin is a transmembrane auxiliary receptor for transforming growth factor-beta (TGF-beta) that is predominantly expressed on proliferating endothelial cells. It plays a wide range of physiological roles but its importance on energy balance or insulin sensitivity has been unexplored. Endoglin deficient mice die during midgestation due to cardiovascular defects. Here we report for first time that heterozygous endoglin deficiency in mice decreases high fat diet-induced hepatic triglyceride content and insulin levels. Importantly, these effects are independent of changes in body weight or adiposity. At molecular level, we failed to detect relevant changes in the insulin signalling pathway at basal levels in liver, muscle or adipose tissues that could explain the insulin-dependent effect. However, we found decreased triglyceride content in the liver of endoglin heterozygous mice fed a high fat diet in comparison to their wild type littermates. Overall, our findings indicate that endoglin is a potentially important physiological mediator of insulin levels and hepatic lipid metabolism

The Sustainable Development Goals as frame for action and social and environmental intervention

El cambio climático se ha erigido como uno de los mayores riesgos para la ciudanía a nivel planetario y, especialmente, para el ser humano que a su vez es el principal causante. Esta investigación ha pretendido analizar el papel de los objetivos de desarrollo sostenible para la acción y la intervención social y ambiental y el papel que la educomunicación ambiental tiene ante el reto del cambio climático, como uno de los fenómenos que, por su urgencia, está en la agenda ambiental, social, económica y política, para ello se ha realizado una revisión bibliográfica actual de las principales investigaciones en el área. A lo largo de esta revisión se ha observado que el cambio climático y los objetivos de desarrollo sostenible, definidos por entidades supranacionales, no están presente en la educación ambiental y que en la comunicación ambiental solo se cuenta con especial interés las catástrofes y situaciones extremas. En tiempos de redes sociales e informaciones falsases necesario la recuperación de enfoques críticos e ideológicos de la educación para los medios, para el desarrollo de la educación mediática y de la competencia digital para ser capaces de construir nuevas narrativas a través de los medios digitales para formas nuevas ecociudadanías capaces de provocar un cambio necesario y transformador en el sistema.Climate change has emerged as one of the greatest risks for citizenship at the planetary level and especially for the human being which in turn is the main cause. This research has sought to analyse the role of sustainable development objectives for action and social and environmental intervention and the role that environmental educommunication has faced with the challenge of climate change, as one of the phenomena that, by its Urgency, it is on the environmental, social, economic and political agenda,for this has been carried out a current bibliographical review of the main investigations in the area. Throughout this review, it has been observed that climate change and the objectives of sustainable development, defined by supranational entities, are not present in environmental education and that in environmental communication only special interest is given to the Catastrophes and extreme situations. In times of social networking and false information necessary the recovery of critical and ideological approaches to media education, for the development of media education and digital competence to be able to build new narratives to through digital media for new forms of ecocitizenship capable of causing a necessary change and transformer in the system.&nbsp

Characterization of Artifact Influence on the Classification of Glucose Time Series Using Sample Entropy Statistics

[EN] This paper analyses the performance of SampEn and one of its derivatives, Fuzzy Entropy (FuzzyEn), in the context of artifacted blood glucose time series classification. This is a difficult and practically unexplored framework, where the availability of more sensitive and reliable measures could be of great clinical impact. Although the advent of new blood glucose monitoring technologies may reduce the incidence of the problems stated above, incorrect device or sensor manipulation, patient adherence, sensor detachment, time constraints, adoption barriers or affordability can still result in relatively short and artifacted records, as the ones analyzed in this paper or in other similar works. This study is aimed at characterizing the changes induced by such artifacts, enabling the arrangement of countermeasures in advance when possible. Despite the presence of these disturbances, results demonstrate that SampEn and FuzzyEn are sufficiently robust to achieve a significant classification performance, using records obtained from patients with duodenal-jejunal exclusion. The classification results, in terms of area under the ROC of up to 0.9, with several tests yielding AUC values also greater than 0.8, and in terms of a leave-one-out average classification accuracy of 80%, confirm the potential of these measures in this context despite the presence of artifacts, with SampEn having slightly better performance than FuzzyEn.The Czech partners were supported by DROIKEM000023001 and RVOVFN64165. No funding was received to support this research work by the Spanish partners.Cuesta Frau, D.; Novák, D.; Burda, V.; Molina Picó, A.; Vargas-Rojo, B.; Mraz, M.; Kavalkova, P.... (2018). Characterization of Artifact Influence on the Classification of Glucose Time Series Using Sample Entropy Statistics. Entropy. 20(11):1-18. https://doi.org/10.3390/e20110871S118201

Angolan vegetable crops have unique genotypes of potential value for future breeding programmes

[EN] A survey was carried out in Angola with the aim of collecting vegetable crops. Collecting expeditions were conducted in Kwanza-Sul, Benguela, Huila and Namibe Provinces and a total of 80 accessions belonging to 22 species was collected from farmers and local markets. Species belonging to the Solanaceae (37 accessions) and Cucurbitaceae (36 accessions) families were the most frequently found with pepper and eggplant being the predominant solanaceous crops collected. Peppers were sold in local markets as a mixture of different types, even different species: Capsicum chinense, C. baccatum, C. frutescens and C. pubescens. Most of the eggplant accessions collected belonged to Solanum aethiopicum L. Gilo Group, the so-called 'scarlet eggplant'. Cucurbita genus was better represented than the other cucurbit crops. A high morphological variation was present in the Cucurbita maxima and C. moschata accessions. A set of 22 Cucurbita accessions from Angola, along with 32 Cucurbita controls from a wide range of origins, was cultivated in Valencia, Spain and characterised based on morphology and molecularity using a set of 15 microsatellite markers. A strong dependence on latitude was found in most of the accessions and as a result, many accessions did not set fruit. The molecular analysis showed high molecular variability and uniqueness in the collected accessions, as shown by their segregation from the set of global controls. In summary, the material collected is quite valuable because of its uniqueness and the potential of the breeding characteristics it possesses.This work, project A1/039611/11, was funded by the Agencia Espanola de Cooperacion Internacional para el Desarrollo (Spanish Agency of International Cooperation for the Development).Domingos, J.; Fita, A.; Picó Sirvent, MB.; Sifres Cuerda, AG.; Daniel, IH.; Salvador, J.; Pedro, J.... (2016). Angolan vegetable crops have unique genotypes of potential value for future breeding programmes. South African Journal of Science. 112(3):114-125. http://hdl.handle.net/10251/97771S114125112

MELOGEN: an EST database for melon functional genomics

<p>Abstract</p> <p>Background</p> <p>Melon (<it>Cucumis melo </it>L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions.</p> <p>Results</p> <p>We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes.</p> <p>Conclusion</p> <p>The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based microarray for melon that is being used in experiments to further analyse the melon transcriptome.</p

Transcriptome sequencing for SNP discovery across Cucumis melo

Background: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD¿ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species.Results: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes.Conclusions: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties. © 2012 Blanca et al.; licensee BioMed Central Ltd.This project was carried out in the frame of the MELONOMICS project (2009-2012) of the Fundacion Genoma Espana.Blanca Postigo, JM.; Esteras Gómez, C.; Ziarsolo Areitioaurtena, P.; Perez, D.; Fernández-Pedrosa, V.; Collado, C.; Rodríguez De Pablos, R.... (2012). Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics. 13(280):1-18. doi:10.1186/1471-2164-13-280S1181328

Angolan vegetable crops have unique genotypes of potential value for future breeding programmes

A survey was carried out in Angola with the aim of collecting vegetable crops. Collecting expeditions were conducted in Kwanza-Sul, Benguela, Huíla and Namibe Provinces and a total of 80 accessions belonging to 22 species was collected from farmers and local markets. Species belonging to the Solanaceae (37 accessions) and Cucurbitaceae (36 accessions) families were the most frequently found with pepper and eggplant being the predominant solanaceous crops collected. Peppers were sold in local markets as a mixture of different types, even different species: Capsicum chinense, C. baccatum, C. frutescens and C. pubescens. Most of the eggplant accessions collected belonged to Solanum aethiopicum L. Gilo Group, the so-called ‘scarlet eggplant’. Cucurbita genus was better represented than the other cucurbit crops. A high morphological variation was present in the Cucurbita maxima and C. moschata accessions. A set of 22 Cucurbita accessions from Angola, along with 32 Cucurbita controls from a wide range of origins, was cultivated in Valencia, Spain and characterised based on morphology and molecularity using a set of 15 microsatellite markers. A strong dependence on latitude was found in most of the accessions and as a result, many accessions did not set fruit. The molecular analysis showed high molecular variability and uniqueness in the collected accessions, as shown by their segregation from the set of global controls. In summary, the material collected is quite valuable because of its uniqueness and the potential of the breeding characteristics it possesses

Thomas Decomposition and Nonlinear Control Systems

This paper applies the Thomas decomposition technique to nonlinear control systems, in particular to the study of the dependence of the system behavior on parameters. Thomas' algorithm is a symbolic method which splits a given system of nonlinear partial differential equations into a finite family of so-called simple systems which are formally integrable and define a partition of the solution set of the original differential system. Different simple systems of a Thomas decomposition describe different structural behavior of the control system in general. The paper gives an introduction to the Thomas decomposition method and shows how notions such as invertibility, observability and flat outputs can be studied. A Maple implementation of Thomas' algorithm is used to illustrate the techniques on explicit examples