Luciano Vieira Koenigkan

Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry.

ABSTRACT Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. The disease might present as different local infections or as septicemia. Here, we present the draft genome sequences of three Brazilian APEC strains isolated from different kinds of infections. The availability of these APEC genome sequences is important for gaining a thorough understanding of the genomic features of E. coli, particularly those of this pathotype.

3D Plant Modeling: Localization, Mapping and Segmentation for Plant Phenotyping Using a Single Hand-held Camera

Functional-structural modeling and high-throughput phenomics demand tools for 3D measurements of plants. In this work, structure from motion is employed to estimate the position of a hand-held camera, moving around plants, and to recover a sparse 3D point cloud sampling the plants’ surfaces. Multiple-view stereo is employed to extend the sparse model to a dense 3D point cloud. The model is automatically segmented by spectral clustering, properly separating the plant’s leaves whose surfaces are estimated by fitting trimmed B-splines to their 3D points. These models are accurate snapshots for the aerial part of the plants at the image acquisition moment and allow the measurement of different features of the specimen phenotype. Such state-of-the-art computer vision techniques are able to produce accurate 3D models for plants using data from a single free moving camera, properly handling occlusions and diversity in size and structure for specimens presenting sparse canopies. A data set formed by the input images and the resulting camera poses and 3D points clouds is available, including data for sunflower and soybean specimens.

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC) associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli) and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

Parallel DSP architecture for reconstruction of tomographic images using wavelets techniques

This paper describes a technique for reconstructing tomographic images generated by a minitomograph scanner for soil science developed by Embrapa Agricultural Instrumentation using a parallel DSP architecture with an HEPC2E board from Hunt Engineering with two TMS32OC40 processors from Texas Instruments. The software designed for visualization of bi- and tri-dimensional images uses code composer tool combined with Parallel C from 3L and Borland Builder C++. Reconstruction and interpolation tasks were distributed throughout the platform processors, using parallel algorithms in order to improve speed and processing power. The work resulted in an increase of about 15% in the system speed when compared with that reached using a classical platform at 200 MHz.

Perspectives on the use of unmanned aerial systems to monitor cattle

The use of unmanned aerial systems (UASs) in agriculture has been growing steadily in the last decade, but their use to monitor and count cattle has been very limited. This article analyses the reasons for this apparent lack of progress, considering both the technical challenges and the difficulties in defining target users who would benefit from a UAS-based system for monitoring cattle. Such an analysis is combined with the findings reported in several investigations dedicated to counting and monitoring wildlife to draw a comprehensive picture on the current situation, to suggest possible solutions to technical issues and to delineate applications that could be useful to both cattle farmers and governments. The text concludes by showing that there are unexplored viable uses for UAS in livestock monitoring, especially in countries like Brazil, where extensive stockbreeding prevails.

Visualizing Thermal Information and Knowledge Creation in Grain Storage Bin Based on Three-Dimensional (3D) Interface Model and Computer Graphic Techniques

This paper presents a new methodology for studying thermal behavior of grain storage bins through the use of intelligent instrumentation combined with an advanced three-dimensional (3D) interface model using computer graphic techniques, which is useful for increasing the safety margin of storage processes with consequent loss decrease. Result was obtained by incorporating into the automation process a vector regarding to spatial and temporal temperature variability in these bins, which is essential for decision-making in storage processes. The algorithm was developed as an integral part of an application system for IBM-PC computers with a Microsoft Windows platform. A Borland C++ Builder 6 was used in its development. The environment created, using the OpenGL Library and its auxiliary libraries, allows 3D data visualization, and simultaneous observation of temperatures in preprogrammed positions with their interaction with other planes or regions of interest.

NatData: A Platform to Integrate Geospatial Data from Natural Resources of the Brazilian Biomes

There are numerous challenges for sustainable agriculture. One of them is to provide an inventory of natural resources, to allow their evaluation for a sustainable use in production systems for food, fiber, essences and energy. The generation and maintenance of this inventory requires efforts of strategic innovation management in order to reduce errors, inconsistencies and unpredictability, replacing them with precise diagnosis, monitoring, early exploration of problems, needs and requirements. Then, it should act as a guide for investment in organization of knowledge and generation of technology flows. This requires an easier access to organized and integrated data about natural resources of different biomes. however, this access is often hampered by a number of reasons, mainly due to their volume and heterogeneity. This paper describes the NatData platform, which is under development at the Brazilian Agricultural Research Corporation (Embrapa). It intends to overcome the challenges, aiming to integrate data from Brazilian natural resources, preserving their semantic and allowing different users to access the data.