Diseño de pavimento rígido incorporando vidrio molido en el concreto 210 kg/cm2 en la Avenida 28 de Julio, Moquegua 2022

La presente investigación denominada “Diseño de Pavimento Rígido Incorporando Vidrio Molido en el Concreto 210 kg/cm2 en la Avenida 28 de Julio, Moquegua 2022”, teniendo como objetivo principal determinar la influencia que tiene el vidrio molido en el diseño de pavimento rígido en la Avenida 28 de Julio; utilizando materiales tales como el Cemento portland tipo I, agregado grueso y agregado fino para la elaboración del concreto f’c= 210 kg/cm2. Se han determinado propiedades mecánicas mediante ensayos (Resistencia a la compresión del concreto) con briquetas cilíndricas de dimensiones de 6” x 12”, realizando una sustitución porcentual en peso del cemento por vidrio, siendo los porcentajes de 5%, 10% y 15% respectivamente, obteniendo una dosificación óptima para la sustitución porcentual de 5% en peso de cemento por vidrio con una resistencia promedio de 221.10 kg/cm2 a los 28 días de curado. Así también para el diseño de pavimento rígido se utilizó la metodología AASHTO 93 determinando un espesor de losa de 17 cm y espesor de sub base de 15 cm. El presente proyecto de investigación a través la sustitución porcentual en peso de cemento por vidrio molido en el diseño de mezcla del concreto se busca la optimización de los materiales, de esta manera se reduce el uso del cemento siendo reemplazado por vidrio molido reciclado el cual es normalmente desechado y desperdiciad

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2

Background Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors. Results Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI. Conclusions HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection.

The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs). An optical map of the MB11 strain generated using the KpnI restriction enzyme showed that the approach used to assemble the genome was satisfactory, producing good alignment between the sequence observed in vitro and that obtained in silico. In the resulting Neighbor-Joining dendrogram, the C. pseudotuberculosis strains sequenced in this study were clustered into a single clade supported by a high bootstrap value. The structural analysis showed that the genomes of the MB11 and MB14 strains were very similar, while the MB30 and MB66 strains had several inverted regions. The observed genomic characteristics were similar to those described for other strains of the same species, despite the number of inversions found. These genomes will serve as a basis for determining the relationship between the genotype of the pathogen and the type of infection that it causes

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes

The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulceransFRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs. Availability All scripts are available at http://github.com/dcbmariano/maprepea

DISMIRA: Prioritization of disease candidates in miRNA-disease associations based on maximum weighted matching inference model and motif-based analysis

Background MicroRNAs (miRNAs) have increasingly been found to regulate diseases at a significant level. The interaction of miRNA and diseases is a complex web of multilevel interactions, given the fact that a miRNA regulates upto 50 or more diseases and miRNAs/diseases work in clusters. The clear patterns of miRNA regulations in a disease are still elusive. Methods In this work, we approach the miRNA-disease interactions from a network scientific perspective and devise two approaches - maximum weighted matching model (a graph theoretical algorithm which provides the result by solving an optimization equation of selecting the most prominent set of diseases) and motif-based analyses (which investigates the motifs of the miRNA-disease network and selects the most prominent set of diseases based on their maximum number of participation in motifs, thereby revealing the miRNA-disease interaction dynamics) to determine and prioritize the set of diseases which are most certainly impacted upon the activation of a group of queried miRNAs, in a miRNA-disease network. Results and Conclusion Our tool, DISMIRA implements the above mentioned approaches and presents an interactive visualization which helps the user in exploring the networking dynamics of miRNAs and diseases by analyzing their neighbors, paths and topological features. A set of miRNAs can be used in this analysis to get the associated diseases for the input group of miRs with ranks and also further analysis can be done to find key miRs or diseases, shortest paths etc

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.

The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi

Aprovechamiento de las galerías filtrantes de la Presa la Esperanza para el abastecimiento de la Parroquia Quiroga

The drinking water service of the Quiroga parish has drawbacks, because the water they use for treatment presents risks of contamination, high levels of turbidity, which causes a long delay in the purification process. The objective of the project consisted in the capture of raw water and its conduction to the treatment plant, the place chosen for the capture is 1500 m from the Quiroga parish within the La Esperanza dam. It should be noted that the reservoirs have a system for evacuating excess water within the main wall, called filtering galleries. The variables that were measured were the hydraulic ones. Finding a flow in these galleries of approximately 10 L / s that could supply water without interruption, projecting the Quiroga parish to a future population of 2358 inhabitants projected to 20 years, the average daily flow (Qmd) was 3 L / s. The maximum daily flow (QMD) was 4.50 L / s, the maximum hourly flow (QMH) was 6 L / s. The storage volume gave us an amount of 195 m ^ 3. The flow of the source was 9.01 L / s. The catchment flow was 5.40 L / s. The flow of the conduction was 4.95 L / s. The treatment plant will be able to supply 4.95 L / s. The study includes all the capture, conduction and interconnection processes with the existing treatment plant for which the necessary hydraulic calculations based on the standards were made.El servicio de agua potable de la parroquia Quiroga tiene inconvenientes, debido a que el agua que utilizan para el tratamiento presenta riesgos de contaminación, altos niveles de turbiedad lo que provoca un gran retraso en el proceso de potabilización. El objetivo del proyecto consistió en la captación de agua cruda y de su conducción hasta la planta de tratamiento, el lugar escogido para la captación está a 1500 m de la parroquia Quiroga dentro de los predios de la presa La Esperanza. Se debe indicar que los embalses tienen un sistema de evacuación del exceso de agua dentro del muro principal, llamadas galerías filtrantes. Las variables que se midieron fueron las hidráulicas. Encontrando un caudal en estas galerías de aproximadamente 10 L/s que podrían abastecer de agua sin interrupción proyectando a la parroquia Quiroga a una población futura de 2358 habitantes proyectado a 20 años, el caudal medio diario (Qmd) fue de 3 L/s. El caudal máximo diario (QMD) fue de 4.50 L/s, el Caudal máximo de horario (QMH) fue de 6 L/s.  El volumen de almacenamiento nos arrojó una cantidad de 195 m^3. El caudal de la fuente fue de 9.01 L/s.  El caudal de la captación fue de 5.40 L/s.  El caudal de la conducción fue de 4.95 L/s.  La Planta de tratamiento podrá abastecer 4.95 L/s. El estudio comprende todos los procesos de captación, conducción e interconexión con la planta de tratamiento existente para la cual se realizaron los cálculos hidráulicos necesarios basados en las normas