RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically generated PDF report using R, knitr, and LaTeX, as well as publication-ready table and figure files. A user-friendly configuration file handles sample metadata entry, processing, analysis, and reporting options. The configuration supports time series RNA-Seq experimental designs with at least one pre- and one post-treatment sample for each subject, as well as multiple treatment groups and specimen types. All RSEQREP analyses components are built using open-source R code and R/Bioconductor packages allowing for further customization. As a use case, we provide RSEQREP results for a trivalent influenza vaccine (TIV) RNA-Seq study that collected 1 pre-TIV and 10 post-TIV vaccination samples (days 1-10) for 5 subjects and two specimen types (peripheral blood mononuclear cells and B-cells)

La fauna de mamíferos fósiles del pleistoceno de jútua, municipio de soata (boyacá, colombia)

En las proximidades del  Núcleo Escolar de Jútua, 6 Km al NNE de Soatá, municipio de Boyacá, se han colectado restos de mamíferos fósiles pleistocénicos. A pesar de que la calidad del material no permite determinaciones seguras a nivel especifico, y en algunos casos ni siquiera a nivel genérico, la colección resulta importante puesto que incluye dos taxones hasta hoy no mencionados en el país: un Caninae indet. y un ?Neochoerus (Hydrochoeridae). Por otra parte, el descubrimiento de la fauna que se describe ha permitido aclarar lo relacionado con la procedencia de los fósiles de Soatá; ahora se sabe que estos provienen de por lo menos dos lugares diferentes: Portugalete y Jútua, ubicados al SSE y NNE, respect iva mente, de Soatá, y están separados entre si por 9 km.In the neighborhoods of the Primary School of Jútua, 6 kms to the NNW from the town of Soatá (Boyacá) have been collected some Pleistocene mammals. In spite of the not so good quality of the fossils, that prevents a clear determination at the species level, even in some cases at genus level, this collection is important, because it includes two taxons not previously reported from Colombia: Caninae indet. and?Neochoerus (Hydrochoeridae).  The discovery of this fauna clarifies the origin of the Soatá fossils; they stem from two different places: Portugalete and Jútua, SSE and NNE from Soatá, respectively, some 9 kms apart

Analysis and optimization of propagation losses in LiNbO3 optical waveguides produced by swift heavy-ion irradiation

The propagation losses (PL) of lithium niobate optical planar waveguides fabricated by swift heavy-ion irradiation (SHI), an alternative to conventional ion implantation, have been investigated and optimized. For waveguide fabrication, congruently melting LiNbO3 substrates were irradiated with F ions at 20 MeV or 30 MeV and fluences in the range 1013–1014 cm−2. The influence of the temperature and time of post-irradiation annealing treatments has been systematically studied. Optimum propagation losses lower than 0.5 dB/cm have been obtained for both TE and TM modes, after a two-stage annealing treatment at 350 and 375∘C. Possible loss mechanisms are discussed

Building extended resolvent of heat operator via twisting transformations

Twisting transformations for the heat operator are introduced. They are used, at the same time, to superimpose a` la Darboux N solitons to a generic smooth, decaying at infinity, potential and to generate the corresponding Jost solutions. These twisting operators are also used to study the existence of the related extended resolvent. Existence and uniqueness of the extended resolvent in the case of $N$ solitons with N "ingoing" rays and one "outgoing" ray is studied in details.Comment: 15 pages, 2 figure

A percentagem ideal de carneiros e o desempenho reprodutivo de ovelhas Corriedale submetidas à monta natural durante a estação reprodutiva no Sul do Brasil.

bitstream/item/64246/1/BP33.pd

Mitochondrial dysfunction in peripheral blood mononuclear cells in pediatric septic shock

OBJECTIVES: Mitochondrial dysfunction in peripheral blood mononuclear cells has been linked to immune dysregulation and organ failure in adult sepsis, but pediatric data are limited. We hypothesized that pediatric septic shock patients exhibit mitochondrial dysfunction within peripheral blood mononuclear cells which in turn correlates with global organ injury. DESIGN: Prospective observational study. SETTING: Academic PICU. PATIENTS: Thirteen pediatric patients with septic shock and greater than or equal to two organ failures and 11 PICU controls without sepsis or organ failure. INTERVENTIONS: Ex vivo measurements of mitochondrial oxygen consumption and membrane potential (DeltaPsim) were performed in intact peripheral blood mononuclear cells on day 1-2 and day 5-7 of septic illness and in controls. The Pediatric Logistic Organ Dysfunction score, inotrope score, and organ failure-free days were determined from medical records. MEASUREMENTS AND MAIN RESULTS: Spare respiratory capacity, an index of bioenergetic reserve, was lower in septic peripheral blood mononuclear cells on day 1-2 (median, 1.81; interquartile range, 0.52-2.09 pmol O2/s/10 cells) compared with controls (5.55; 2.80-7.21; p = 0.03). Spare respiratory capacity normalized by day 5-7. Patients with sepsis on day 1-2 exhibited a higher ratio of LEAK to maximal respiration than controls (17% vs \u3c 1%; p = 0.047) with normalization by day 5-7 (1%; p = 0.008), suggesting mitochondrial uncoupling early in sepsis. However, septic peripheral blood mononuclear cells exhibited no differences in basal or adenosine triphosphate-linked oxygen consumption or DeltaPsim. Oxygen consumption did not correlate with Pediatric Logistic Organ Dysfunction score, inotrope score, or organ failure-free days (all p \u3e 0.05). Although there was a weak overall association between DeltaPsim on day 1-2 and organ failure-free days (Spearman rho = 0.56, p = 0.06), patients with sepsis with normal organ function by day 7 exhibited higher DeltaPsim on day 1-2 compared with patients with organ failure for more than 7 days (p = 0.04). CONCLUSIONS: Mitochondrial dysfunction was present in peripheral blood mononuclear cells in pediatric sepsis, evidenced by decreased bioenergetic reserve and increased uncoupling. Mitochondrial membrane potential, but not respiration, was associated with duration of organ injury

Experimental study on styrene–butadiene–styrene-modified binders and fly ash micro-filler contributions for implementation in porous asphalt mixes

Styrene-butadiene-styrene copolymer (SBS) can be used to improve the mechanical and deformation properties of the binder used in its manufacture. However, the high cost of and variability in processing limit its performance. A secondary modifier to solve these problems is nano- and micromaterials that allow for the generation of unique properties in polymeric systems. Based on this, this study experimented with fly ash micro-filler (µFA) in low proportions as a binder modifier with SBS for use in PA mixes. The FA residue is considered in 3% and 5% dosages on a base binder with 5% SBS. Rheological results show that µFA improves classical, linear viscoelastic (LVE), and progressive damage properties compared with the modified binder. The PA blends with µFA reduce binder runout, resulting in a thicker film, thus showing better abrasion resistance in dry and wet conditions. Samples with µFA increase the post-cracking energy in indirect tension due to higher ductility. However, they decrease the fracture energy due to higher cracking before failure. In addition, µFA manages to decrease the difference between dry and wet ITS.Regular FONDECYT project 1201029 funded by the National Research and Development Agency of Chil

On the equivalence of different approaches for generating multisoliton solutions of the KPII equation

The unexpectedly rich structure of the multisoliton solutions of the KPII equation has been explored by using different approaches, running from dressing method to twisting transformations and to the tau-function formulation. All these approaches proved to be useful in order to display different properties of these solutions and their related Jost solutions. The aim of this paper is to establish the explicit formulae relating all these approaches. In addition some hidden invariance properties of these multisoliton solutions are discussed

Utilización del suero de queso en combinación con harina de arroz restringida para cerdos en crecimiento y acabado en pastoreo.

Arroz-Oryza sativ

DISCURSIVE PRACTICES OF STUDENTS AT THE FIFTH YEAR, OF THE OCCUPATIONAL THERAPY PROGRAM, UNIVERSITY OF CHILE, ABOUT OF CLINICAL TEACHING AND COMPETENCY-BASED EDUCATION

Background. The present research is an exploratory study on clinical teaching and competency-based education in the discursive practices of the fifth-level students of the Occupational Therapy program at the University of Chile Purpose. Describe and analyze the assessment made by students regarding the clinical teachings they receive in their professional practices. Methods. This work, from the theoretical and methodological points of view, assumes the critical analysis of the discourse, specifically, of the discursive practices that arise from the professional practices carried out by the students of the first innovated cohort, in 2017, of occupational oherapy in the clinical fields. It is based in a file body, which the students complete according to three periods during the academic year. Therefore, an analysis of the discursive practices is followed, which transcends the pure act of numerical and qualitative scores, to acquire all its subjective dimension as recognition of a multiplicity of meanings, which value and challenge the conditions of its own formative course. Results. Data and valuations are presented, where the scores mark repeatedly a positive evaluation of the teaching practice. For example, compliance with the agreements and established deadlines (84%); a respectful treatment with the student is maintained (77.8%); the necessary time is used to support and supervise the practice (92.9%); it is encouraged and generates spaces for the discussion of topics related to professional practice; the student is encouraged to work as a team (86.9%); among other things. Likewise, the students identify a series of topics, such as autonomy / autonomous work; feedback; teamwork; facilitation of teaching work, and, critical points in the teaching-learning process, such as participation; the administrative work of the teacher of practice and the lack of spaces for discussion. However, the different learning contexts in the different clinical fields are valued in a relevant way: conditions are facilitated to participate in various activities such as team meetings, home visits, instances of group and individual intervention, all of a practical nature; training focused on student learning, the issue of decision making an