Three-dimensional reconstruction of coronary arteries and plaque morphology using CT angiography - comparison and registration with IVUS

BACKGROUND: The aim of this study is to present a new methodology for three-dimensional (3D) reconstruction of coronary arteries and plaque morphology using Computed Tomography Angiography (CTA). METHODS: The methodology is summarized in six stages: 1) pre-processing of the initial raw images, 2) rough estimation of the lumen and outer vessel wall borders and approximation of the vessel’s centerline, 3) manual adaptation of plaque parameters, 4) accurate extraction of the luminal centerline, 5) detection of the lumen - outer vessel wall borders and calcium plaque region, and 6) finally 3D surface construction. RESULTS: The methodology was compared to the estimations of a recently presented Intravascular Ultrasound (IVUS) plaque characterization method. The correlation coefficients for calcium volume, surface area, length and angle vessel were 0.79, 0.86, 0.95 and 0.88, respectively. Additionally, when comparing the inner and outer vessel wall volumes of the reconstructed arteries produced by IVUS and CTA the observed correlation was 0.87 and 0.83, respectively. CONCLUSIONS: The results indicated that the proposed methodology is fast and accurate and thus it is likely in the future to have applications in research and clinical arena

Formation of Lipofuscin-Like Autofluorescent Granules in the Retinal Pigment Epithelium Requires Lysosome Dysfunction

PURPOSE: We aim to characterize the pathways required for autofluorescent granule (AFG) formation by RPE cells using cultured monolayers. METHODS: We fed RPE monolayers in culture with a single pulse of photoreceptor outer segments (POS). After 24 hours the cells started accumulating AFGs that were comparable to lipofuscin in vivo. Using this model, we used a variety of light and electron microscopical techniques, flow cytometry and Western blot to analyze the formation of AFGs. We also generated a mutant RPE line lacking cathepsin D by gene editing. RESULTS: AFGs seem to derive from incompletely digested POS-containing phagosomes and after 3 days are surrounded by a single membrane positive for lysosome markers. We show by various methods that lysosome-phagosome fusion is required for AFG formation, and that impairment of lysosomal pH or catalytic activity, particularly cathepsin D activity, enhances AF accumulation. CONCLUSIONS: We conclude that lysosomal dysfunction results in incomplete POS degradation and enhanced AFG accumulation

Mechanisms for collaboration: a design and evaluation framework for multi-user interfaces

Multi-user interfaces are said to provide “natural” interaction in supporting collaboration, compared to individual and noncolocated technologies. We identify three mechanisms accounting for the success of such interfaces: high awareness of others' actions and intentions, high control over the interface, and high availability of background information. We challenge the idea that interaction over such interfaces is necessarily “natural” and argue that everyday interaction involves constraints on awareness, control, and availability. These constraints help people interact more smoothly. We draw from social developmental psychology to characterize the design of multi-user interfaces in terms of how constraints on these mechanisms can be best used to promote collaboration. We use this framework of mechanisms and constraints to explain the successes and failures of existing designs, then apply it to three case studies of design, and finally derive from them a set of questions to consider when designing and analysing multi-user interfaces for collaboration

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in Brazilian Plasmodium vivax populations.

Background. Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII), which is the most variable segment of the protein. Methods. To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results. The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii) PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions. This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion

New Results in Sasaki-Einstein Geometry

This article is a summary of some of the author's work on Sasaki-Einstein geometry. A rather general conjecture in string theory known as the AdS/CFT correspondence relates Sasaki-Einstein geometry, in low dimensions, to superconformal field theory; properties of the latter are therefore reflected in the former, and vice versa. Despite this physical motivation, many recent results are of independent geometrical interest, and are described here in purely mathematical terms: explicit constructions of infinite families of both quasi-regular and irregular Sasaki-Einstein metrics; toric Sasakian geometry; an extremal problem that determines the Reeb vector field for, and hence also the volume of, a Sasaki-Einstein manifold; and finally, obstructions to the existence of Sasaki-Einstein metrics. Some of these results also provide new insights into Kahler geometry, and in particular new obstructions to the existence of Kahler-Einstein metrics on Fano orbifolds.Comment: 31 pages, no figures. Invited contribution to the proceedings of the conference "Riemannian Topology: Geometric Structures on Manifolds"; minor typos corrected, reference added; published version; Riemannian Topology and Geometric Structures on Manifolds (Progress in Mathematics), Birkhauser (Nov 2008

Termos técnicos úteis na catalogação de datasets ômicos no Repositório de Dados de Pesquisa da Embrapa: uma compilação de definições.

Este trabalho de compilação de termos é fruto de esforços conjuntos realizados no escopo da Ação Gerencial Local (AGL), intitulada "Implantar a gestão de dados de pesquisa na Embrapa Informática Agropecuária", alinhada ao Programa de Governança de Dados de Pesquisa. Desses esforços participaram ativamente membros da equipe do Laboratório Multiusuário de Bioinformática da Embrapa (LMB) e do Grupo de Pesquisa em Computação Científica, Engenharia da Informação e Automação (GCIA), da Embrapa Agricultura Digital. Trata-se de um documento de natureza terminológica indispensável à ampliação e à popularização do vocabulário técnico associado à Biblioteconomia aplicada a dados, em especial, na catalogação de datasets ômicos no Repositório de Dados de Pesquisa da Embrapa (Redape). Neste documento estão reunidos os principais termos catalográficos utilizados na linguagem corrente e empregados por catalogadores. A publicação tem o propósito de apoiar os catalogadores - autores de datasets e bibliotecários, entre outros atores -, na compreensão e apropriação dos principais conceitos e definições, sobretudo no processo de representação descritiva. Além de contribuir para o mapeamento da linguagem corrente praticada pelos catalogadores e demais interessados na catalogação de datasets ômicos, a obra beneficiará diretamente a implementação de boas práticas de catalogação. Ademais, esta compilação de termos é uma contribuição efetiva para a implementação do processo de gestão de dados biológicos na Embrapa, pois além do seu valor intrínseco, é também um documento complementar às orientações para catalogação de datasets no Redape, publicadas na série Documentos, pela Embrapa Agricultura Digital. Destaca-se, ainda, a contribuição desta compilação de termos técnicos para o processo de gestão de dados de pesquisa na Embrapa, visto que oferece um recurso adicional no apoio a ações de capacitação e divulgação, previstas na Política de Governança de Dados, Informação e Conhecimento da Embrapa (PGDIC)