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The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to beta-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.

The densest network for measuring air pollutant concentrations in Colombia is in Medellin, where most sensors are located in the heavily polluted lower parts of the valley. Measuring stations in the higher elevations on the mountains surrounding the valley are not available, which limits our understanding of the valley’s pollutant dynamics and hinders the effectiveness of data assimilation studies using chemical transport models such as LOTOS-EUROS. To address this gap in measurements, we have designed a new network of low-cost sensors to be installed at altitudes above 2000 m.a.s.l. The network consists of custom-built, solar-powered, and remotely connected sensors. Locations were strategically selected using the LOTOS-EUROS model driven by diverse meteorology-simulated fields to explore the effects of the valley wind representation on the transport of pollutants. The sensors transmit collected data to internet gateways for posterior analysis. Various tests to verify the critical characteristics of the equipment, such as long-range transmission modeling and experiments with an R score of 0.96 for the best propagation model, energy power system autonomy, and sensor calibration procedures, besides case exposure to dust and water experiments, to ensure IP certifications. An inter-calibration procedure was performed to characterize the sensors against reference sensors and describe the observation error to provide acceptable ranges for the data assimilation algorithm (<10% nominal). The design, installation, testing, and implementation of this air quality network, oriented towards data assimilation over the Aburrá Valley, constitute an initial experience for the simulation capabilities toward the system’s operative capabilities. Our solution approach adds value by removing the disadvantages of low-cost devices and offers a viable solution from a developing country’s perspective, employing hardware explicitly designed for the situation., Mathematical Physics

This work proposes a robust and non-Gaussian version of the shrinkage-based knowledge-aided EnKF implementation called Ensemble Time Local H∞ Filter Knowledge-Aided (EnTLHF-KA). The EnTLHF-KA requires a target covariance matrix to integrate previously obtained information and knowledge directly into the data assimilation (DA). The proposed method is based on the robust H∞ filter and on its ensemble time-local version the EnTLHF, using an adaptive inflation factor depending on the shrinkage covariance estimated matrix. This implies a theoretical and solid background to construct robust filters from the well-known covariance inflation technique. The proposed technique is implemented in a synthetic assimilation experiment, and in an air quality application using the LOTOS-EUROS model over the Aburrá Valley to evaluate its potential for non-linear and non-Gaussian large systems. In the spatial distribution of the PM2.5 concentrations along the valley, the method outperforms the well-known Local Ensemble Transform Kalman Filter (LETKF), and the non-robust knowledge-aided Ensemble Kalman filter (EnKF-KA). In contrast to the other simulations, the ability to issue warnings for high concentration events is also increased. Finally, the simulation using EnTLHF-KA has lower error values than using EnKF-KA, indicating the advantages of robust approaches in high uncertainty systems., Mathematical Physics

El comercio informal callejero se ubica en múltiples y variados espacios citadinos, principalmente en las calles céntricas. Allí emergen manifestaciones discursivas que permiten interpretar y analizar las complejas redes que enmarcan su realidad. En sus textualidades fundamentadas por la oralidad, es posible identificar huellas de tradiciones y de simbolizaciones del intercambio mercantil, incluso de aquel que ha sido institucionalizado por los procesos identitarios de la ciudad. Igualmente, en sus discursos se manifiesta la lucha diaria por la sobrevivencia. En las puestas en escena se advierten prácticas y estrategias vinculadas a la cultura de la cual se reciben tradiciones, fórmulas lingüísticas y modalizaciones que inciden, de manera significativa, en el sostenimiento del comercio informal en las vías citadinas y de las personas que lo ejercen. En esta obra, se expone parte de los resultados de la investigación titulada: “Rituales y estrategias de sobrevivencia ciudadana en espacios urbanos: un estudio semiótico-discursivo del comercio informal”, desarrollada por el Grupo Estudios del Lenguaje y la Educación (avalado por la Universidad Tecnológica de Pereira y la Universidad Colegio Mayor de Cundinamarca), la cual se propuso reconocer los procesos simbólicos que operan en el comercio informal callejero y la manera cómo representan la situación sociocultural de grupos y personas marginados de territorios, empleos y mejores oportunidades de vida. Finalmente, se reflexiona en torno al panorama actual y futuro del comercio informal que se ha constituido en un recurso paliativo de las crisis económicas, en este caso, con el agravante de “la peste” del Covid 19., Informal street trade is located in multiple and varied city spaces, mainly in downtown streets. There, discursive manifestations emerge that allow interpreting and analyzing the complex networks that frame their reality. In its textualities based on orality, it is possible to identify traces of traditions and symbolizations of commercial exchange, including that which has been institutionalized by the identity processes of the city. Likewise, in their speeches the daily struggle for survival is manifested. In the staging, practices and strategies linked to the culture from which traditions, linguistic formulas and modalities are received are observed that have a significant impact on the maintenance of informal commerce in city streets and of the people who exercise it. In this work, part of the results of the research entitled: "Rituals and strategies of citizen survival in urban spaces: a semiotic-discursive study of informal commerce", developed by the Language and Education Studies Group (endorsed by the Universidad Tecnológica de Pereira and Universidad Colegio Mayor de Cundinamarca), which set out to recognize the symbolic processes that operate in informal street trade and how they represent the sociocultural situation of groups and people marginalized from territories, jobs and better life opportunities. Finally, it reflects on the current and future panorama of informal commerce that has become a palliative resource for economic crises, in this case, with the aggravating circumstance of the "plague" of Covid 19.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In

Particulate matter (PM) is one of the most problematic pollutants in urban air. The effects of PM on human health, associated especially with PM of ≤2.5μm in diameter, include asthma, lung cancer and cardiovascular disease. Consequently, major urban centers commonly monitor PM2.5 as part of their air quality management strategies. The Chemical Transport models allow for a permanent monitoring and prediction of pollutant behavior for all the regions of interest, different to the sensor network where the concentration is just available in specific points. In this chapter a data assimilation system for the LOTOS-EUROS chemical transport model has been implemented to improve the simulation and forecast of Particulate Matter in a densely populated urban valley of the tropical Andes. The Aburrá Valley in Colombia was used as a case study, given data availability and current environmental issues related to population expansion. Using different experiments and observations sources, we shown how the Data Assimilation can improve the model representation of pollutants., Mathematical Physics

In this work, we present the development of a 4D-Ensemble-Variational (4DEnVar) data assimilation technique to estimate NOx top-down emissions using the regional chemical transport model LOTOS-EUROS with the NO2 observations from the TROPOspheric Monitoring Instrument (TROPOMI). The assimilation was performed for a domain in the northwest of South America centered over Colombia, and includes regions in Panama, Venezuela and Ecuador. In the 4DEnVar approach, the implementation of the linearized and adjoint model are avoided by generating an ensemble of model simulations and by using this ensemble to approximate the nonlinear model and observation operator. Emission correction parameters’ locations were defined for positions where the model simulations showed significant discrepancies with the satellite observations. Using the 4DEnVar data assimilation method, optimal emission parameters for the LOTOS-EUROS model were estimated, allowing for corrections in areas where ground observations are unavailable and the region’s emission inventories do not correctly reflect the current emissions activities. The analyzed 4DEnVar concentrations were compared with the ground measurements of one local air quality monitoring network and the data retrieved by the satellite instrument Ozone Monitoring Instrument (OMI). The assimilation had a low impact on NO2 surface concentrations reducing the Mean Fractional Bias from 0.45 to 0.32, primordially enhancing the spatial and temporal variations in the simulated NO2 fields., Atmospheric Remote Sensing, Mathematical Physics

The use of low air quality networks has been increasing in recent years to study urban pollution dynamics. Here we show the evaluation of the operational Aburrá Valley’s low-cost network against the official monitoring network. The results show that the PM2.5 low-cost measurements are very close to those observed by the official network. Additionally, the low-cost allows a higher spatial representation of the concentrations across the valley. We integrate low-cost observations with the chemical transport model Long Term Ozone Simulation-European Operational Smog (LOTOS-EUROS) using data assimilation. Two different configurations of the low-cost network were assimilated: using the whole low-cost network (255 sensors), and a high-quality selection using just the sensors with a correlation factor greater than 0.8 with respect to the official network (115 sensors). The official stations were also assimilated to compare the more dense low-cost network’s impact on the model performance. Both simulations assimilating the low-cost model outperform the model without assimilation and assimilating the official network. The capability to issue warnings for pollution events is also improved by assimilating the low-cost network with respect to the other simulations. Finally, the simulation using the high-quality configuration has lower error values than using the complete low-cost network, showing that it is essential to consider the quality and location and not just the total number of sensors. Our results suggest that with the current advance in low-cost sensors, it is possible to improve model performance with low-cost network data assimilation., Mathematical Physics

In order to avoid the adverse effects of air pollution, efforts have been made to monitor when air pollution reaches dangerous levels. A Chemical Transport Model (CTM) can simulate trace gases and particles concentration in specific areas. These models are not entirely reliable, owing to incomplete knowledge about emissions and meteorological conditions. Explaining and predicting variability in air quality models remains a challenge. In this thesis we want to demonstrate that data assimilation (DA) can reduce uncertainty in the model process. DA is a mathematical family of techniques in which observed values are combined with a dynamic model to improve the accuracy of the model. Standard DA methods have limitations when there is not a complete characterization of the uncertainties. In air quality applications, emission inventories’ accuracy is often low, and weather models often do not predict events very well. The problem is worse in developing countries where the knowledge available is sparse and of relatively low quality. The thesis’s main contribution is the development of a DA systems for improving the behavior of complex models in the presence of high uncertainty. The proposed methods and developments have been tested in the framework of the LOTOS-EUROS CTM with applications to forecast particular matter in the Aburrá Valley in Colombia. The use of a less expensive monitoring network is also discussed. The Aburrá valley represents a good testing scenario because of its current air quality issues, the difficulty of its terrain, the lack of a detailed emission inventory, and the operational availability of a low-cost monitoring network. Our first step was to apply the Ensemble Kalman Filter (EnKF) to assimilate the official air quality monitoring network. Evaluations of the system were performed by varying values of the covariance localization influence area. Moreover, various inheritance strategies were evaluated to optimize the assimilation window’s estimated, Mathematical Physics

This chapter book presents Medellín Air qUality Initiative or MAUI Project; it tells a brief story of this teamwork, their scientific and technological directions. The modeling work focuses on the ecosystems and human health impact due to the exposition of several pollutants transported from long-range places and deposited. For this objective, the WRF and LOTOS-EUROS were configurated and implemented over the región of interest previously updating some input conditions like land use and orography. By other side, a spinoff initiative named SimpleSpace was also born during this time, developing, through this instrumentation branch a very compact and modular low-cost sensor to deploy in new air quality networks over the study domain. For testing this instrument and find an alternative way to measure pollutants in the vertical layers, the Helicopter In-Situ Pollution Assessment Experiment HIPAE misión was developed to take data through the overflight of a helicopter over Medellín. From the data obtained from the Simple units and other experiments in the payload, a citogenotoxicity analysis quantify the cellular damage caused by the exposition of the pollutants., Mathematical Physics

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In th

In this paper, we propose an efficient and practical implementation of the ensemble Kalman filter via shrinkage covariance matrix estimation. Our filter implementation combines information brought by an ensemble of model realizations, and that based on our prior knowledge about the dynamical system of interest. We perform the combination of both sources of information via optimal shrinkage factors. The method exploits the rank-deficiency of ensemble covariance matrices to provide an efficient and practical implementation of the analysis step in EnKF based formulations. Localization and inflation aspects are discussed, as well. Experimental tests are performed to assess the accuracy of our proposed filter implementation by employing an Advection Diffusion Model and an Atmospheric General Circulation Model. The experimental results reveal that the use of our proposed filter implementation can mitigate the impact of sampling noise, and even more, it can avoid the impact of spurious correlations during assimilation steps., Mathematical Physics

Unfortunately, the corresponding author name was incorrectly spelled as ‘‘Simán Polanía-Restrepo’’ instead of ‘Simón Polania-Restrepo” in the original publication. © 2020, Springer-Verlag France SAS, part of Springer Nature.

Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa; 20Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark; 21Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt; 22Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran; 23Department of Medical Microbiology, King's College Hospital, London, UK;24Department of Infectious Diseases, Imperial College London, London, UK;25Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine; 26Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa; 27School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA; 28Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC