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Ítem Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónBackground: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).Ítem Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).Ítem Effect of medium components and culture conditions in Bacillus subtilis EA-CB0575 spore production(Springer Berlin Heidelberg, 2015-10-01) Posada-Uribe, Luisa F.; Romero-Tabarez, Magally; Villegas-Escobar, Valeska; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Bacillus subtilis spores have important biotechnological applications; however, achieving both, high spore cell densities and sporulation efficiencies in fermentation, is poorly reported. In this study, medium components and culture conditions were optimized with different statistical methods to increase spore production of the plant growth promoting rhizobacteria B. subtilis EA-CB0575. Key medium components were determined with Plackett-Burman (PB) design, and the optimum concentration levels of two components (glucose, MgSO4·7H2O) were optimized with a full factorial and central composite design, achieving 1.37 × 10(9) CFU/mL of spore cell density and 93.5 % of sporulation efficiency in shake flask. The optimized medium was used to determine the effect of culture conditions on spore production at bioreactor level, finding that maintaining pH control did not affect significantly spore production, while the interaction of agitation and aeration rates had a significant effect on spore cell density. The overall optimization generated a 17.2-fold increase in spore cell density (8.78 × 10(9) CFU/mL) and 1.9-fold increase in sporulation efficiency (94.2 %) compared to that of PB design. These results indicate the potential of B. subtilis EA-CB0575 to produce both, high spore cell densities and sporulation efficiencies, with very low nutrient requirements and short incubation period which can represent savings of process production.Ítem Efficient use of mobile devices for quantification of pressure injury images(IOS Press, 2018-01-01) Garcia-Zapirain B; Sierra-Sosa D; Ortiz P D; Isaza-Monsalve M; Elmaghraby A; Garcia-Zapirain B; Sierra-Sosa D; Ortiz P D; Isaza-Monsalve M; Elmaghraby A; Universidad EAFIT. Departamento de Ciencias; Modelado MatemáticoPressure Injuries are chronic wounds that are formed due to the constriction of the soft tissues against bone prominences. In order to assess these injuries, the medical personnel carry out the evaluation and diagnosis using visual methods and manual measurements, which can be inaccurate and may generate discomfort in the patients. By using segmentation techniques, the Pressure Injuries can be extracted from an image and accurately parameterized, leading to a correct diagnosis. In general, these techniques are based on the solution of differential equations and the involved numerical methods are demanding in terms of computational resources. In previous work, we proposed a technique developed using toroidal parametric equations for image decomposition and segmentation without solving differential equations. In this paper, we present the development of a mobile application useful for the non-contact assessment of Pressure Injuries based on the toroidal decomposition from images. The usage of this technique allows us to achieve an accurate segmentation almost 8 times faster than Active Contours without Edges (ACWE) and Dynamic Contours methods.We describe the techniques and the implementation for Android devices using Python and Kivy. This application allows for the segmentation and parameterization of injuries, obtain relevant information for the diagnosis and tracking the evolution of patient's injuries. © 2018 - IOS Press and the authors.Ítem Remote sensing-based measurement of Living Environment Deprivation: Improving classical approaches with machine learning(Public Library of Science, 2017-05-02) Arribas-Bel D; Patino JE; Duque JC; Universidad EAFIT. Departamento de Economía y Finanzas; Research in Spatial Economics (RISE)This paper provides evidence on the usefulness of very high spatial resolution (VHR) imagery in gathering socioeconomic information in urban settlements. We use land cover, spectral, structure and texture features extracted from a Google Earth image of Liverpool (UK) to evaluate their potential to predict Living Environment Deprivation at a small statistical area level. We also contribute to the methodological literature on the estimation of socioeconomic indices with remote-sensing data by introducing elements from modern machine learning. In addition to classical approaches such as Ordinary Least Squares (OLS) regression and a spatial lag model, we explore the potential of the Gradient Boost Regressor and Random Forests to improve predictive performance and accuracy. In addition to novel predicting methods, we also introduce tools for model interpretation and evaluation such as feature importance and partial dependence plots, or cross-validation. Our results show that Random Forest proved to be the best model with an R2 of around 0.54, followed by Gradient Boost Regressor with 0.5. Both the spatial lag model and the OLS fall behind with significantly lower performances of 0.43 and 0.3, respectively. © 2017 Arribas-Bel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Ítem A unified model framework for the multiattribute consistent periodic vehicle routing problem(Public Library of Science, 2020-01-01) Baldoquin M.G.; Martine J.A.; Diaz-Ramirez J.; Baldoquin M.G.; Martine J.A.; Diaz-Ramirez J.; Universidad EAFIT. Departamento de Ciencias; Matemáticas y AplicacionesModeling real-life transportation problems usually require the simultaneous incorporation of different variants of the classical vehicle routing problem (VRP). The periodic VRP (PVRP) is a classical extension in which routes are determined for a planning period of several days and each customer has an associated set of allowable visit schedules. This work proposes a unified model framework for PVRP that consists of multiple attributes or variants not previously addressed simultaneously, such as time-windows, time-dependence, and consistency-which guarantees the visits to customer by the same vehicle-, together with three objective functions that respond to the needs of practical problems. The numerical experimentation is focused on the effects of three factors: frequency, depot centrality, and the objective function on the performance of a general-purpose MILP solver, through the analysis of the achieved relative gaps. Results show higher sensitivity to the objective functions and to the problem sizes. © 2020 Baldoquin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Ítem Upper limb posture estimation in robotic and virtual reality-based rehabilitation(HINDAWI PUBLISHING CORPORATION, 2014-07-08) Cortés C; Ardanza A; Molina-Rueda F; Cuesta-Gómez A; Unzueta L; Epelde G; Ruiz OE; De Mauro A; Florez J; Universidad EAFIT. Departamento de Ingeniería Mecánica; Laboratorio CAD/CAM/CAENew motor rehabilitation therapies include virtual reality (VR) and robotic technologies. In limb rehabilitation, limb posture is required to (1) provide a limb realistic representation in VR games and (2) assess the patient improvement. When exoskeleton devices are used in the therapy, the measurements of their joint angles cannot be directly used to represent the posture of the patient limb, since the human and exoskeleton kinematic models differ. In response to this shortcoming, we propose a method to estimate the posture of the human limb attached to the exoskeleton. We use the exoskeleton joint angles measurements and the constraints of the exoskeleton on the limb to estimate the human limb joints angles. This paper presents (a) the mathematical formulation and solution to the problem, (b) the implementation of the proposed solution on a commercial exoskeleton system for the upper limb rehabilitation, (c) its integration into a rehabilitation VR game platform, and (d) the quantitative assessment of the method during elbow and wrist analytic training. Results show that this method properly estimates the limb posture to (i) animate avatars that represent the patient in VR games and (ii) obtain kinematic data for the patient assessment during elbow and wrist analytic rehabilitation. © 2014 Camilo Cortés et al.