Data Mining of the Coffee Rust Genome

The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the genomic data

Probabilistic Measures for Biological Adaptation and Resilience

The importance of understanding and predicting biological resilience is growing as we become increasingly aware of the consequences of changing climatic conditions. However, various approaches to operationalize resilience have been proposed. Here, we adapt a statistical mechanical framework for the time dependent dynamics of biological systems that offers a powerful conceptualization of systems whose response share similarities with heterogeneous forced/dissipative physical systems. In this framework we are concerned with the dynamics of a probabilistic description of observables. In this study we propose and derive a quantitative measure of adaptive resilience. Unlike more common resilience measures, ours takes into account the variability of the time history of the dynamics and the heterogeneity of the organism. Once a measure of success is proposed it quantifies the degree to which a biological system succeeds to adapt to new conditions after being stressed

Mechanical Investigation of Phase-Transforming Cellular and Origami Materials

Cellular materials, such as honeycombs and metallic foams, have attracted much attention due to their exceptional ability to absorb and diffuse mechanical energy. These materials have a wide range of applications, such as improving vehicle crash safety and helmet impact resistance. However, many of these materials are rendered unusable after one application. Phase-transforming cellular materials (PXCMs) utilize a reversible bistable mechanism to facilitate energy absorption from one-dimensional impacts and loads. These mechanisms have the added benefit over other cell structures of reusability. In this study, various PXCM designs are discussed and examined to determine their energy absorption capabilities. Three different designs were tested: the common bending straw’s ribbed mechanism, the Kresling pattern cylinder, and a sinusoidal beam mechanism. These designs underwent cyclic compression-tension load tests and their force-displacement curves were examined. These tests showed that all three designs exhibit significant energy absorption behaviors. Each design shows promise, warranting further detailed study of their full properties

DIET OF BARN OWL (TYTO ALBA), SPECTACLED OWL (PULSATRIX PERSPICILLATA) AND RUFOUS-BANDED OWL (STRIX ALBITARSIS) IN THE WESTERN ANDES OF COLOMBIA

Abstract · Dietary studies are one of the most developed research areas in biology and ecology studies of Neotropical owls, but most of these studies have focused on few species. Our study describes the diet of Barn Owl (Tyto alba), Spectacled Owl (Pulsatrix perspicillata), and Rufous-banded Owl (Strix albitarsis) in Jardin and Ciudad Bolivar, western Andes of Colombia. The diet of T. alba, based on 495 prey items consisted 98.6% of vertebrates, the main food items being rodents (66%) and shrews (21.4%). Out of 142 prey items identified from P. perspicillata fractured pellets, the main prey species were Artibeus lituratus (23.9%), Rattus norvegicus (21.8%), and Didelphis sp. (16.1%), species of small and medium-sized mammals that tolerate environmental changes and often live in urban areas. Pulsatrix perspicillata preyed also on at least 14 bird species including hummingbirds and migratory birds. Based on 165 prey items S. albitarsis consumed more invertebrates (57.7%) than vertebrates (42.3%). Among the insects, the main preys were Coleoptera beetles and Orthoptera crickets. Among the vertebrates, the main prey species included mammals such as Thomasomys aureus, Marmosops sp., Marmosa sp., and Reithrodontomys mexicanus. These scansorial species are likely to be vulnerable to aerial predators such as S. albitarsis which hunt from a perchs. According to standardized Levins index values T. alba was the most selective in its food habits, P. perspicillata had intermediate values, while S. albitarsis showed the least selective diet.RESUMEN · Dieta de la Lechuza Común (Tyto alba), el Búho de Anteojos (Pulsatrix perspicillata) y el Búho Ocelado (Strix albitarsis) en la cordillera Occidental de Colombia Los estudios sobre hábitos tróficos constituyen la línea de investigación más desarrollada dentro de la biología y ecología de los búhos Neotropicales, pero la mayoría de esos estudios se han centrado en pocas especies. El propósito de este estudio es describir la dieta de la Lechuza Común (Tyto alba), el Búho de Anteojos (Pulsatrix perspicillata) y el Búho Ocelado (Strix albitarsis), en Jardín y Ciudad Bolívar, cordillera Occidental de Colombia. Identificamos 495 presas consumidas por T. alba. Su dieta estuvo compuesta en un 98.7% de vertebrados, principalmente roedores (66%) y musarañas (21.4%). De 142 presas de P. perspicillata, las presas principales, Artibeus lituratus (23.9%), Rattus norvegicus (21.8%) y Didelphis sp. (16.1%), son especies tolerantes a los ambientes intervenidos y hacen parte de los ensamblajes de pequeños mamíferos encontrados en ambientes urbanos. Pulsatrix perspicillata consumió también al menos 14 especies de aves incluyendo colibríes y aves migratorias. En base a 165 presas S. albitarsis consumió más invertebrados (57.7%) que vertebrados (42.3%). Entre los insectos depredó en mayor porcentaje los ordenes Coleoptera y Orthoptera, mientras que entre los vertebrados predominaron los de hábitos escansoriales (Thomasomys aureus, Marmosops sp., Marmosa sp. y Reithrodontomys mexicanus). Estos vertebrados serían más vulnerables a depredadores aéreos como S. albitarsis, la cual caza desde perchas en árboles. De acuerdo a los valores obtenidos para el índice estandarizado de Levins, T. alba fue más selectiva en el consumo de las presas, seguida por P. perspicillata, mientras que S. albitarsis tiene la dieta menos selectiva

Evidence for subaerial development of the Caribbean oceanic plateau in the Late Cretaceous and palaeo-environmental implications

The formation of oceanic plateaus in the Pacific in the Mesozoic has been proposed to create major environmental impacts, including global anoxic events OAE-1 in the Aptian (ca. 120 Ma) and OAE-2 in the Cenomanian–Turonian (ca. 90 Ma). However, our understanding of the formation of these large volcanic systems and their environmental effects are strongly limited by difficulties in accessing them and characterising their volcanic evolution. In particular, it remains significant to determine whether Pacific oceanic plateaus experience a phase of subaerial volcanic activity as this has critical implications in terms of their environmental impacts. Herein we provide the first unequivocal evidence for an emergent volcanic phase of the Caribbean oceanic plateau in the Late Cretaceous. This subaerial phase is evidenced by accreted oceanic sequences in Colombia that include fallout tuffs with accretionary lapilli and lahar deposits. This facies assemblage, recognised for the first time in an oceanic plateau, reflects phreatomagmatic eruptions coeval with subaerial erosion on an oceanic island. This result, combined with previous evidence of subaerial development of the Ontong Java Plateau and Shatsky Rise, suggests that syn-volcanic emergence of oceanic plateaus was common in the Pacific during the Mesozoic. Although temporal and spatial scales of these emergences remain poorly constrained it confirms that emergence of the Caribbean plateau in the Late Cretaceous (ca. 90 Ma) could have actively contributed to atmospheric changes and the establishment of OAE-2. Significantly, emergence of the Caribbean plateau occurred synchronously to the beginning of its tectonic displacement between the Americas. We propose that this unusual volcanic and tectonic evolution led to drastic reduction of the flow of Pacific oxygenated bottom waters into the early Atlantic basin, leading to a series of regional anoxic events previously documented between the Coniacian and Santonian (OAE-3, ca. 89 to 84 Ma). In addition, emergence of the Caribbean Plateau in the early inter-American seaway could have facilitated migration of terrestrial organisms between the Americas in the Late Cretaceous. The formation of the Caribbean plateau had therefore a large range of possible environmental effects, from atmospheric to palaeo-oceanographic and biotic impacts

Evaluación de diluyentes para la refrigeración de semen de conejo (Oryctolagus cuniculus)

The aim of this research was to evaluate the use of different extenders for cooling of rabbit semen and its effect on sperm quality. Thirty semen samples from 10 sexually mature rabbits (Oryctolagus cuniculus) were used. Each sample was diluted separately in a 1:10 ratio in four extenders, composed of skim milk and sugars (T1); dextrose, sodium citrate, and potassium acetate (T2); sodium caseinates, phosphates and sugars (T3); and tris-citric acid and egg yolk (T4). The semen was kept at 16 °C for 72 hours. At the time of dilution and every 24 hours, total motility (MT), progressive motility (MP) and sperm kinetics were evaluated with the Sperm Class Analyzer® system, and vitality and morphology were evaluated by the eosin-nigrosin staining. Statistical analysis was performed using mixed models and the comparison of means by the Duncan test. At the time of dilution (0 h), a lower MT for T2 and T4 was observed (p<0.05). This same effect at 24 h of cooling was observed, while at 48 h the MT was lower for T2, compared to T1, T3 and T4 (p <0.05). The MP was equally higher for T1 and T3 at 0, 24 and 48 h (p<0.05). A decrease in normal morphology at 72 h for T4 was found (p<0.05). Greater preservation of the viability over time for T1 and T3 was observed (p<0.05). It is concluded that the extenders composed by skim milk or caseinates, and sugars, protect more efficiently the rabbit semen preserved by refrigeration.El objetivo de esta investigación fue evaluar el uso de diferentes diluyentes para la refrigeración de semen de conejo y su efecto sobre la calidad espermática. Se utilizaron 30 muestras de semen de 10 conejos (Oryctolagus cuniculus) sexualmente maduros. Cada muestra se diluyó separadamente en proporción 1:10 en cuatro diluyentes, compuestos por leche descremada y azucares (T1); dextrosa, citrato sódico y acetato potásico (T2); caseinatos de sodio, fosfatos y azúcares (T3); y tris-ácido cítrico y yema de huevo (T4). El semen se mantuvo a 16 °C durante 72 horas. Al momento de la dilución y cada 24 horas se evaluó la movilidad total (MT), la movilidad progresiva (MP) y la cinética espermática con el sistema Sperm Class Analizer®, y la viabilidad y la morfología mediante la tinción con eosina-nigrosina. El análisis estadístico se realizó mediante modelos mixtos y la comparación de medias por la prueba de Duncan. Al momento de la dilución (0 h), se observó una MT inferior para T2 y T4 en comparación con T1 y T3 (p<0.05). Este mismo efecto se observó a las 24 h de refrigeración, mientras a las 48 h la MT fue inferior para T2, respecto a T1, T3 y T4 (p<0.05). La MP fue igualmente superior para T1 y T3 a las 0, 24 y 48 h (p<0.05). Se halló un descenso en la morfología normal a las 72 h para T4 (p<0.05). Se observó una mayor conservación de la viabilidad en el tiempo para T1 y T3 (p<0.05). Se concluye que los diluyentes compuestos por leche descremada o caseinatos con azucares protegen de forma más eficiente los espermatozoides de conejo conservados mediante refrigeración

Understanding water and energy fluxes in the Amazonia: Lessons from an observation-model intercomparison

Tropical forests are an important part of global water and energy cycles, but the mechanisms that drive seasonality of their land-atmosphere exchanges have proven challenging to capture in models. Here, we (1) report the seasonality of fluxes of latent heat (LE), sensible heat (H), and outgoing short and longwave radiation at four diverse tropical forest sites across Amazonia—along the equator from the Caxiuanã and Tapajós National Forests in the eastern Amazon to a forest near Manaus, and from the equatorial zone to the southern forest in Reserva Jaru; (2) investigate how vegetation and climate influence these fluxes; and (3) evaluate land surface model performance by comparing simulations to observations. We found that previously identified failure of models to capture observed dry-season increases in evapotranspiration (ET) was associated with model overestimations of (1) magnitude and seasonality of Bowen ratios (relative to aseasonal observations in which sensible was only 20%–30% of the latent heat flux) indicating model exaggerated water limitation, (2) canopy emissivity and reflectance (albedo was only 10%–15% of incoming solar radiation, compared to 0.15%–0.22% simulated), and (3) vegetation temperatures (due to underestimation of dry-season ET and associated cooling). These partially compensating model-observation discrepancies (e.g., higher temperatures expected from excess Bowen ratios were partially ameliorated by brighter leaves and more interception/evaporation) significantly biased seasonal model estimates of net radiation (Rn), the key driver of water and energy fluxes (LE ~ 0.6 Rn and H ~ 0.15 Rn), though these biases varied among sites and models. A better representation of energy-related parameters associated with dynamic phenology (e.g., leaf optical properties, canopy interception, and skin temperature) could improve simulations and benchmarking of current vegetation–atmosphere exchange and reduce uncertainty of regional and global biogeochemical models

LA HIDROGENACION SELECTIVA DE ACEITES NATURALES A TRAVES DE CATALIZADORES HETEROGENEOS

En este artículo se presenta una revisión bibliográfica sobre los procesos y los catalizadores heterogéneos que permiten hidrogenar selectivamente el grupo carbonilo de sustratos insaturados presentes en aceites vegetales tales como ácidos y ésteres grasos con el fin de sintetizar productos de la química fina. Se discuten además algunos resultados importantes relacionados con los mecanismos que se han propuesto recientemente para la reacción de hidrogenación selectiva, así como algunas pautas para trabajos futuros

Multidimensional Machine Learning Model to Calculate a COVID-19 Vulnerability Index

In Colombia, the first case of COVID-19 was confirmed on 6 March 2020. On 13 March 2023, Colombia registered 6,360,780 confirmed positive cases of COVID-19, representing 12.18% of the total population. The National Administrative Department of Statistics (DANE) in Colombia published in 2020 a COVID-19 vulnerability index, which estimates the vulnerability (per city block) of being infected with COVID-19. Unfortunately, DANE did not consider multiple factors that could increase the risk of COVID-19 (in addition to demographic and health), such as environmental and mobility data (found in the related literature). The proposed multidimensional index considers variables of different types (unemployment rate, gross domestic product, citizens’ mobility, vaccination data, and climatological and spatial information) in which the incidence of COVID-19 is calculated and compared with the incidence of the COVID-19 vulnerability index provided by DANE. The collection, data preparation, modeling, and evaluation phases of the Cross-Industry Standard Process for Data Mining methodology (CRISP-DM) were considered for constructing the index. The multidimensional index was evaluated using multiple machine learning models to calculate the incidence of COVID-19 cases in the main cities of Colombia. The results showed that the best-performing model to predict the incidence of COVID-19 in Colombia is the Extra Trees Regressor algorithm, obtaining an R-squared of 0.829. This work is the first step toward a multidimensional analysis of COVID-19 risk factors, which has the potential to support decision making in public health programs. The results are also relevant for calculating vulnerability indexes for other viral diseases, such as dengue