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Gene expression analysis of non-clinical strain of aspergillus fumigatus (LMB-35AA): Does biofilm affect virulence?
No full textAspergillus fumigatus LMB-35Aa, a saprophytic fungus, was used for cellulase production through biofilms cultures. Since biofilms usually favor virulence in clinical strains, the expression of the related genes of the LMB 35-Aa strain was analyzed by qPCR from the biomass of planktonic cultures and biofilms developed on polyester cloth and polystyrene microplates. For this, virulence-related genes reported for the clinical strain Af293 were searched in A. fumigatus LMB 35-Aa genome, and 15 genes were identified including those for the synthesis of cell wall components, hydrophobins, invasins, efflux transporters, mycotoxins and regulators. When compared with planktonic cultures at 37?C, invasin gene calA was upregulated in both types of biofilm and efflux transporter genes mdr4 and atrF were predominantly upregulated in biofilms on polystyrene, while aspHs and ftmA were upregulated only in biofilms formed on polyester. Regarding the transcription regulators, laeA was downregulated in biofilms, and medA did not show a significant change. The effect of temperature was also evaluated by comparing the biofilms grown on polyester at 37 vs. 28?C. Non-significant changes at the expression level were found for most genes evaluated, except for atrF, gliZ and medA, which were significantly downregulated at 37?C. According to these results, virulence appears to depend on the interaction of several factors in addition to biofilms and growth temperature. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity
No full textThe Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries. © 2020 Ramirez 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.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater
No full textKarst aquifers provide drinking water for 10% of the world’s population, support agriculture, groundwater-dependent activities, and ecosystems. These aquifers are characterised by complex groundwater-flow systems, hence, they are extremely vulnerable and protecting them requires an in-depth understanding of the systems. Poor data accessibility has limited advances in karst research and realistic representation of karst processes in large-scale hydrological studies. In this study, we present World Karst Spring hydrograph (WoKaS) database, a community-wide effort to improve data accessibility. WoKaS is the first global karst springs discharge database with over 400 spring observations collected from articles, hydrological databases and researchers. The dataset’s coverage compares to the global distribution of carbonate rocks with some bias towards the latitudes of more developed countries. WoKaS database will ensure easy access to a large-sample of good quality datasets suitable for a wide range of applications: comparative studies, trend analysis and model evaluation. This database will largely contribute to research advancement in karst hydrology, supports karst groundwater management, and promotes international and interdisciplinary collaborations. © 2020, The Author(s).Fondo Nacional de Desarrollo Científico y Tecnológico - Fondecy
Numerical analysis of bonding between masonry and steel reinforced grout using a plastic–damage model for lime–based mortar
No full textThis paper shows a numerical investigation with single-lap shear bond tests between Peruvian brick masonry and SRG system. For this purpose, the finite element method, elements and constitutive models implemented in ABAQUS library were used. Eight-node continuum elements were employed for modelling mortar, masonry and steel fibers assuming a linear-elastic behaviour for the last two materials. Eight-node cohesive elements with zero-thickness were used to model substrate-mortar and steel-mortar interfaces. Due to experimental results showed the detachment of the steel fiber from the mortar accompanied by cracking of the outer mortar layer, the non-linearity of the mortar was also considered by using a Concrete Damage Plasticity constitutive model. The effect of the mortar non-linearity was compared with other models assuming a linear and rigid material for mortar, as recommended by literature. This shows that modelling a non-linear mortar leads to more accurate results for future design and strengthening purposes, thus, its implementation is encouraged. A comparison in time between Bond–Slip Law (BSL) at steel–mortar interface and mortar constitutive law is analysed in order to investigate the stress-transfer mechanism during single–lap shear tests.Fondo Nacional de Desarrollo Científico y Tecnológico - Fondecy
System identification models' fit using error histogram analysis and the Hampel filter as computational tools
No full textIn the present investigation, we use the error histogram analysis as a computational tool to define whether the model resulting from a system identification process should continue to be fitted, and the Hampel filter for the elimination of outliers as a tool that also avoids on model over-parameterization. To do this, we use three data sets from a four-cylinder BMW diesel engine, to identify a linear model, and then, with that model, analyze the error and its histogram in a data set (without noise, with noise and with outliers). The analysis of the histogram of the error was found to be a useful tool for detecting white noise and helps to avoid overfitting, in addition to the fact that the Hampel filter allowed detecting and eliminating atypical samples. The software used was MATLAB. © 2020 IEEE.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
Magnetic fields in food processing perspectives, applications and action models
No full textMagnetic fields (MF) are increasingly being applied in food processing to preserve food quality. They can be static (SMF), oscillating (OMF) or pulsed (PMF) depending on the type of equipment. The food characteristics can be influenced by several configurations of the applied magnetic field as its flux density, frequency, polarity and exposure time. Several mechanisms have been proposed to explain the eects of magnetic fields on foods. Some of them propose interactions at the subatomic particle level that show quantum behavior, such as the radical pair and cyclotron resonance mechanisms. Other proposals are at the level of DNA, compounds, subcellular organelles and cells. The interactions between food and magnetic fields are addressed in a general way in this work, highlighting the applications and action models involved and their eects on the physicochemical, enzymatic and microbiological characteristics of food. © 2020 by the authors.Fondo Nacional de Desarrollo Científico y Tecnológico - Fondecy
Regional mapping and spatial distribution analysis of Canopy palms in an Amazon forest using deep learning and VHR images
No full textMapping plant species at the regional scale to provide information for ecologists and forest managers is a challenge for the remote sensing community. Here, we use a deep learning algorithm called U-net and very high-resolution multispectral images (0.5 m) from GeoEye satellite to identify, segment and map canopy palms over ~3000 km2 of Amazonian forest. The map was used to analyse the spatial distribution of canopy palm trees and its relation to human disturbance and edaphic conditions. The overall accuracy of the map was 95.5% and the F1-score was 0.7. Canopy palm trees covered 6.4% of the forest canopy and were distributed in more than two million patches that can represent one or more individuals. The density of canopy palms is affected by human disturbance. The post-disturbance density in secondary forests seems to be related to the type of disturbance, being higher in abandoned pasture areas and lower in forests that have been cut once and abandoned. Additionally, analysis of palm trees' distribution shows that their abundance is controlled naturally by local soil water content, avoiding both flooded and waterlogged areas near rivers and dry areas on the top of the hills. They show two preferential habitats, in the low elevation above the large rivers, and in the slope directly below the hill tops. Overall, their distribution over the region indicates a relatively pristine landscape, albeit within a forest that is critically endangered because of its location between two deforestation fronts and because of illegal cutting. New tree species distribution data, such as the map of all adult canopy palms produced in this work, are urgently needed to support Amazon species inventory and to understand their distribution and diversity. © 2020 by the authors.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
Development and characterization of an allergic asthma rat model for interventional studies
No full textAllergic asthma is one of the most common chronic diseases of the airways, however it still remains underdiagnosed and hence undertreated. Therefore, an allergic asthma rat model would be useful to be applied in future therapeutic strategy studies. The aim of the present study was to develop an objective model of allergic asthma in atopic rats that allows the induction and quantification of anaphylactic shock with quantitative variables. Female Brown Norway rats were intraperitoneally sensitized with ovalbumin (OVA), alum and Bordetella pertussis toxin and boosted a week later with OVA in alum. At day 28, all rats received an intranasal challenge with OVA. Anaphylactic response was accurately assessed by changes in motor activity and body temperature. Leukotriene concentration was determined in the bronchoalveolar lavage fluid (BALF), and total and IgE anti-OVA antibodies were quantified in blood and BALF samples. The asthmatic animals’ motility and body temperature were reduced after the shock for at least 20 h. The asthmatic animals developed anti-OVA IgE antibodies both in BALF and in serum. These results show an effective and relatively rapid model of allergic asthma in female Brown Norway rats that allows the quantification of the anaphylactic response.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
Biomechanical study of proximal femur for designing stems for total hip replacement
No full textInnovative hip implants should be designed in accordance with biomechanical models of the proximal femur and take into account both body weight and muscle action in order to improve usability and biomimetic performance. This article proposes a finite element analysis of the proximal femur using both cortical and trabecular regions and employing transverse isotropic properties with standardized loads taken from active and young patients. Maximum principal stresses are plotted to show the mechanical behavior of the femur and grouped to evaluate stress shielding. Tsai-Wu and the maximum principal stress fields are useful for finding the areas more prone to failure and analyzing the influence of the stems on femoral mechanics. Other parameters, such as the stem material, absence of neck and osteotomy level, are explained. This paper is expected to provide a guide for designers and surgeons of femoral stems for assessing qualitatively and quantitatively the risks of stress shielding. © 2020 by the authors.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte
Characteristics of Tsunami Fragility Functions Developed Using Different Sources of Damage Data from the 2018 Sulawesi Earthquake and Tsunami
No full textWe developed tsunami fragility functions using three sources of damage data from the 2018 Sulawesi tsunami at Palu Bay in Indonesia obtained from (i) field survey data (FS), (ii) a visual interpretation of optical satellite images (VI), and (iii) a machine learning and remote sensing approach utilized on multisensor and multitemporal satellite images (MLRS). Tsunami fragility functions are cumulative distribution functions that express the probability of a structure reaching or exceeding a particular damage state in response to a specific tsunami intensity measure, in this case obtained from the interpolation of multiple surveyed points of tsunami flow depth. We observed that the FS approach led to a more consistent function than that of the VI and MLRS methods. In particular, an initial damage probability observed at zero inundation depth in the latter two methods revealed the effects of misclassifications on tsunami fragility functions derived from VI data; however, it also highlighted the remarkable advantages of MLRS methods. The reasons and insights used to overcome such limitations are discussed together with the pros and cons of each method. The results show that the tsunami damage observed in the 2018 Sulawesi event in Indonesia, expressed in the fragility function developed herein, is similar in shape to the function developed after the 1993 Hokkaido Nansei-oki tsunami, albeit with a slightly lower damage probability between zero-to-five-meter inundation depths. On the other hand, in comparison with the fragility function developed after the 2004 Indian Ocean tsunami in Banda Aceh, the characteristics of Palu structures exhibit higher fragility in response to tsunamis. The two-meter inundation depth exhibited nearly 20% probability of damage in the case of Banda Aceh, while the probability of damage was close to 70% at the same depth in Palu. © 2020, The Author(s).Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - Concyte