Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Simulating Population Genetics of Pathogen Vectors in Changing Landscapes: Guidelines and Application with Triatoma brasiliensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

THE MAPPING IN THE CONTINUING EDUCATION OF TEACHERS: AN EXPERIENCE THROUGH DISTANCE LEARNING

In this work, we show the experience of continuing teacher education in Cartography in the period from 03/11/2009 to 03/11/2010, it was held by the Center for Continuing Education in Mathematics Education, Science and Environment (CECEMCA) - UNESP - Rio Claro, in DL (Distance Learning). This experience was through the extension course set in TelEduc platform. The course was titled Introduction to Cartography and aimed primarily: Present concepts of systematic and thematic mapping and its potential application in teaching practices, increase knowledge in the areas of Geography, Cartography and Environment; Offer alternatives for implementing content mapping in the classroom.

SEQUENTIAL SAMPLING AND MICROSATELLITES FOR EVALUATION OF THE GENETIC QUALITY IN CORN SEEDS LOTS

In the seed production system, genetic purity is one of the fundamental requirements for its commercialization. The present work had the goal of determined the sample size for genetic purity evaluation, in order to protect the seed consumer and the producer and to evaluate the sensitivity of microsatellite technique for discriminating hybrids from their respective relatives and for detecting mixtures when they are present in small amounts in the samples. For the sequential sampling, hybrid seeds were marked and mixed in with the seed lots, simulating the following levels of contamination: 0.25, 0.5, 1.0, 2.0, 4.0, and 6.0%. After this, groups of 40 seeds were taken in sequence, up to a maximum of 400 seeds, with the objective of determining the quantity of seeds necessary to detect the percentage of mixture mentioned above. The sensitivity of microsatellite technique was evaluated by mixing different proportions of DNA from the hybrids with their respective seed lines. For the level of mixture was higher than 1:8 (1P1:8P2; 8P1:1P2), the sensitivity of the marker in detecting different proportions of the mixture varied according to the primer used. In terms of the sequential sampling, it was verified that in order to detect mixture levels higher than 1% within the seed lot- with a risk level for both the producer and the consumer of 0.05- the size of the necessary sample was smaller than the size needed for the fixed sample size. This also made it possible to reduce costs, making it possible to use microsatellites to certify the genetic purity of corn seeds lots.

Patch size, shape and edge distance influences seed predation in a keystone palm in tropical rainforests

Pós-graduação em Ciências Biológicas (Zoologia) - IBRC

Online distance mathematics education in Brazil: research, practice and policy

In this article, we address online distance mathematics education research and practice in Brazil, which are relative newcomers to the educational scene. We present the national context of education in Brazil, highlighting the organization of the educational system, and also a summary of national legislation on distance education and an overview of digital inclusion in the country. We outline the potential and relevance of distance education for the Brazilian educational system and show how it could intervene in the system. With respect to research and practice in online mathematics education, we present support for research, examples of studies and highlight different aspects being addressed, including its essential components. In addition, we discuss the synergy between distance education and teacher education, and mathematics distance education and modeling, as well as other initiatives in the national scenario.

Determination of lead in eye shadow and blush by high-resolution continuum source graphite furnace atomic absorption spectrometry employing directSolid sampling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Simultaneous determination of chromium and nickel in medicinal plants by slurry sampling graphite furnace atomic absorption spectrometry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Allelopathic potential and survey of natural seed bank under the canopy of Copaifera Langsdorffii Desf

The aim of this study was to evaluate the allelopathic effect of soil samples collected under the canopies of three specimens of Copaifera langsdorffii the germination of Lactuca sativa and survey the natural seed bank according to seasonality. To test the allelopathic effect was carried experiments of pre and post-emergence with seeds of L. sativa and to quantify the stock of seeds, soil samples were collected from three specimens at three distances from the stem (1, 2 and 3 m) and at three depths (0-5, 5-10 and 10-15cm) in the region of savanna in the dry and wet seasons. The samples tested in bioassay of pre-emergence no significant influence on germinability, mean germination time and mean germination speed, but showed a difference in the synchronism of germination, these data were independent of sampling station. In test for post-emergence was observed statistical difference in the parameters evaluate (length of primary roots and hypocotyls) in both seasons. To quantify the natural seed bank were macroscopic analysis of each soil sample with the help of stereoscopic microscope. The analysis of the natural seed bank showed a larger number of seeds in the 0-5cm and in distance of 2m for both seasons. The results suggest the presence of allelochemical substances in soil samples collected under the canopy of Copaifera langsdorffii.

Gestão democrática na escola: as impressões dos participantes do programa progestão

This paper is a sampling of an extensive research which analyzed and assessed the Distance Learning Program for Qualification of School Managers (Progestão) carried out in three schools, which preserved the same management team during the program. Progestão provided continuing and inservice development for public school managers by means of distance and presential types of learning. This paper deals with the concept of democratic management understood by the proponents of Progestão, the training team (trainers and multipliers), and the managers assisting the course (principals, vice principals, and pedagogical supervisors). Three issues that check the understanding of the democratic management concept were analyzed, as well as how those participants implement it in schools. The research is based on the qualitative approach, which has an evaluating character. It discusses the profile assigned to school management since the amendment of the State and the passing of the Law of Policies and Principles of Education (LDB)/96, besides pointing out the difficulties to support democratic management dissociated from other school practices.

Distance exercised during submaximal training on race winnings for Thoroughbred racehorses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The effect of gastrointestinal nematode infection level on grazing distance from dung

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The steady-state behavior of the synthetic and side-sensitive synthetic double sampling (X)over-bar charts

The steady-state average run length is used to measure the performance of the recently proposed synthetic double sampling (X) over bar chart (synthetic DS chart). The overall performance of the DS X chart in signaling process mean shifts of different magnitudes does not improve when it is integrated with the conforming run length chart, except when the integrated charts are designed to offer very high protection against false alarms, and the use of large samples is prohibitive. The synthetic chart signals when a second point falls beyond the control limits, no matter whether one of them falls above the centerline and the other falls below it; with the side-sensitive feature, the synthetic chart does not signal when they fall on opposite sides of the centerline. We also investigated the steady-state average run length of the side-sensitive synthetic DS X chart. With the side-sensitive feature, the overall performance of the synthetic DS X chart improves, but not enough to outperform the non-synthetic DS X chart. Copyright (C) 2014 John Wiley &Sons, Ltd.

A new sampling strategy for the Shewhart control chart monitoring a process with wandering mean

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparative abundance and diversity of Dryininae (Hymenoptera, Dryinidae) in three savannah phytophysiognomies in southeastern Brazil, under three sampling methods

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)