The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have ...been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). This new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.
Se determinó el perfil de sensibilización a aeroalérgenos más comunes en la población de Portoviejo, durante el periodo noviembre 2017 - noviembre 2018. Se llevó a cabo un estudio observacional, ...descriptivo, de carácter retrospectivo y corte transversal, cuyos resultados se obtuvieron de la base de datos del Laboratorio Gamma de la ciudad de Portoviejo. La muestra poblacional estuvo conformada por 112 pacientes que se realizaron el test de RAST, RIDA qLine® Allergy de alérgenos inhalantes. Los resultados obtenidos muestran que el 63,4 % presentó algún tipo de sensibilización. La mayoría de estos casos se produjeron durante el verano (96 %), en total fueron 19 aeroalérgenos que produjeron dicha sensibilización, siendo los de mayor frecuencia, Dermatophagoides pteranyssinus y Dermatophagoides farinae, seguido por polen, donde se destacaron el centeno, roble y mezclas de hierbas, con animales y hongos. Se demostró que en adultos y tercera edad existe una mayor frecuencia de sensibilización al polen de centeno comparados con los ácaros domésticos, mientras que en rango de edad infantil a adulto joven se encontró un predominio de sensibilización a ácaros de la familia Dermatophagoides.
Palabras clave: sensibilización; aeroalérgenos; RAST; alergia; mastocitos.
Abstract
Metagenomics combined with 16S rRNA gene sequence analyses was applied to unveil the taxonomic composition and functional diversity of the farmed adult turbot gastrointestinal (GI) ...microbiome. Proteobacteria and Firmicutes which existed in both GI content and mucus were dominated in the turbot GI microbiome. 16S rRNA gene sequence analyses also indicated that the turbot GI tract may harbor some bacteria which originated from associated seawater. Functional analyses indicated that the clustering-based subsystem and many metabolic subsystems were dominant in the turbot GI metagenome. Compared with other gut metagenomes, quorum sensing and biofilm formation was overabundant in the turbot GI metagenome. Genes associated with quorum sensing and biofilm formation were found in species within Vibrio, including Vibrio vulnificus,Vibrio cholerae and Vibrio parahaemolyticus. In farmed fish gut metagenomes, the stress response and protein folding subsystems were over-represented and several genes concerning antibiotic and heavy metal resistance were also detected. These data suggested that the turbot GI microbiome may be affected by human factors in aquaculture. Additionally, iron acquisition and the metabolism subsystem were more abundant in the turbot GI metagenome when compared with freshwater fish gut metagenome, suggesting that unique metabolic potential may be observed in marine animal GI microbiomes.
Se estudiaron 30 pacientes con reacciones alérgicas a J3 - Lactámicos claramente demostrados por las manifestaciones clínicas. El objetivo de este trabajo fue determinar la importancia del núcleo (3 ...-Lactúmico y las cadenas laterales en la inducción de IgE específica para BPO, Ax y Anip por medio de las pruebas cutáneas y el RA ST para estos determinantes. Este grupo se dividió previamente por historia clínica en: 1 - Acelerados (n: 19); 2 - Inmediatos (n:11). Las pruebas del Prick se realizaron con BPO-PL, Ax-PL, Amp-PL, MDM de BR MDM de Ax y MDM de Amp. Presentando en el grupo acelerado: 2 (-1-) a 13P0,4(+) Ax/Amp, 13(+) a todos los reactivos (BPO- Ax - Amp - MDM BP/Ax/Amp). Los pacientes con reacción inmediata: ¡Ocasos (+) a MDM -BPy l(-1-) MDM -Amp. Estos pacientes fueron estudiados con la técnica del RAST para BPO - PL, Ax-PL, Amp PL y PL. Se consideró como línea de corte positiva al nivel ~ a 1524 cpm, tomado tic la curva estandar de Pharniacia Los pacientes con reacción acelerada presentaron en 13/19 casos RAST (+) a BPO- PL, 1/19 (+) BPO- Ax/PL, 3 /19(4) Ax-PL. 1/19 (4-) Am/PL y 1 negativo para todos los reactivos estudiados. Los pacientes con reación inmediata (n: II) en todos los casos lueron negativos para todos los reactivos estudiados. El grupo control (1):20) presentó en 1/20 casos positividad por Prick a Ax- PL y 19 casos negatividad total a todos los reactivos. Los RAST a todos los reactivos fueron negativos en todos los individuos estudiados. Estos resultados indican que la bencilpenicilina (BPO) es el más importante determinante y las cadenas laterales (Ax y Amp) son otros determinantes antigéntcos en -los (3-Lactúmicos, siendo cada uno tIc ellos inductores de un tipo de IgL específica y que raramente aparece una respuesta ¡gE a dos determinantes diferentes en un mismo sujeto. Las pruebas cutáneas son el método de elección para el estudio de alergia a penicilina ya que con el método in vitro se cubre un espectro menor (le reactivos que los que producen reacción acelerada (MDM).
The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ...ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.
Microbial communities are essential for nutrient cycling in ecosystems. Disturbance, such as tilling, alters the composition of microbial communities in corn and soy agroecosystems. The changes in these communities affect their composition and function, thus changing the ecosystem services they perform, such as cycling nitrogen.
•Development of multigroup advanced semi analytic nodal method solver for HTGR analysis.•Analysis of MHTGR-350 benchmark.•Verification of the developed solver with commercial neutronics codes.
This ...study introduces the multigroup advanced semi-analytic nodal method (A-SANM) tailored for the high-temperature gas-cooled reactor (HTGR) analysis. The A-SANM has been crafted specifically for reactors with hexagonal geometries, such as the Vodo-Vodyanoi energetichesky reactor (VVER) and HTGR. A triangular node was constructed with a 12-term basis to delineate the flux by integrating both the polynomial and hyperbolic functions. The multigroup calculation kernel of this approach was embedded in the nodal diffusion code, RAST-V. To evaluate the computational efficiency of the A-SANM, we employed the MHTGR-350 benchmark. This benchmark, associated with a modular high-temperature gas-cooled reactor, was established by the OECD/NEA under the NGNP Project in 2021. In this study, we conducted the Phase I calculations to evaluate the performance of the neutronics code. Key parameters including the multiplication factor, rod worth, and axial and radial power distributions were meticulously assessed. When juxtaposed with the Monte Carlo code MCS, the A-SANM exhibited a deviation of –97 pcm. Differences in the axial and radial power were ± 4 and ± 3 %, respectively. Furthermore, the rod worth discrepancy was –6 pcm when set against the MCS. In summary, this study effectively elucidates the potential and precision of the multigroup A-SANM for the HTGR evaluations.
The study aimed to investigate the anaerobic performance with laboratory and field tests in youth athletes in different sports. One-hundred four athletes between the ages of 10 and 16, minimum age of ...training of one year in different sports voluntarily participated in the study. Anthropometric measurements of participants were measured. Wingate Anaerobic Test (WAnT) using Monark cycle ergometer (Monark-Crescent AB, Sweden), Running-based Anaerobic Sprint Test (RAST), and pediatric RAST using photocell advice (Newtest 2000) were performed to determine anaerobic performance. Peak power (PP), average power (AP), minimum power (MP) and fatigue index (FI) were determined for each test. Absolute and relative power outputs, FI, and total exercise time (TED) values of WAnT, RAST, and PRAST were significantly different (p<0.01). The absolute peak, average and minimum power of PRAST were significantly higher than WAnT and RAST. According to test-retest results of WAnT, RAST, and PRAST, ICC 95% CI values have a high-reliability coefficient for all variables. It was found there is a positive correlation statistically between WAnT and RAST for all variables (p<0.01). Besides, there were also positive correlations statistically between WAnT-PRAST and RAST-PRAST excluding fatigue index (p<0.01). As a result of this study, it was determined WAnT, RAST, and PRAST have high reliability and are appropriate for child and adolescent athletes in that age group to evaluate anaerobic performance. Although tests have different motion properties, it was determined they have similar results when performed. High correlations between tests and variables support this determination.
The study aimed to investigate the anaerobic performance with laboratory and field tests in youth athletes in different sports. One-hundred four athletes between the ages of 10 and 16, minimum age of ...training of one year in different sports voluntarily participated in the study. Anthropometric measurements of participants were measured. Wingate Anaerobic Test (WAnT) using Monark cycle ergometer (Monark-Crescent AB, Sweden), Running-based Anaerobic Sprint Test (RAST), and pediatric RAST using photocell advice (Newtest 2000) were performed to determine anaerobic performance. Peak power (PP), average power (AP), minimum power (MP) and fatigue index (FI) were determined for each test. Absolute and relative power outputs, FI, and total exercise time (TED) values of WAnT, RAST, and PRAST were significantly different (p<0.01). The absolute peak, average and minimum power of PRAST were significantly higher than WAnT and RAST. According to test-retest results of WAnT, RAST, and PRAST, ICC 95% CI values have a high-reliability coefficient for all variables. It was found there is a positive correlation statistically between WAnT and RAST for all variables (p<0.01). Besides, there were also positive correlations statistically between WAnT-PRAST and RAST-PRAST excluding fatigue index (p<0.01). As a result of this study, it was determined WAnT, RAST, and PRAST have high reliability and are appropriate for child and adolescent athletes in that age group to evaluate anaerobic performance. Although tests have different motion properties, it was determined they have similar results when performed. High correlations between tests and variables support this determination.
This book will appeal to scholars and policymakers who deal with and/or are conducting research on the factors of economic growth. At present, there is no unified growth model that is feasible for ...every investigation. As such, this volume offers key insights into the factors that are most relevant in explaining growth variation at country, regional and metropolitan levels. In order to acquaint the reader with the concepts related to the subject, two theoretical chapters detail the schools of thought and the models that were formulated in the past. Three empirical chapters then present an up-to-date and a multi-level investigation, using the most comprehensive models, for the European Union. The results of this book are policy-oriented and will serve to help close the gaps between EU countries and regions.
The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial ...composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.
•River Ganga harbored broad range of carbohydrate and energy metabolism genes.•Enzymes involved in reverse TCA, Calvin-Benson cycle enzyme RuBisCO were prevalent.•Sulfur metabolism enzymes such as EC:2.7.7.4 and EC:1.8.1.2 were prevalent river.•Proteobacteria, Actinobacteria and Bacteroidetes were the highly abundant phyla.•Various purple sulfur and purple non sulfur bacteria were also detected.