VR Based Visualization and Exploration of Plant Biological Data

This paper investigates the use of virtual reality (VR) technologies to facilitate the analysis of plant biological data in distinctive steps in the application pipeline. Reconstructed three-dimensional biological models (primary polygonal models) transferred to a virtual environment support scientists' collaborative exploration of biological datasets so that they obtain accurate analysis results and uncover information hidden in the data. Examples of the use of virtual reality in practice are provided and a complementary user study was performed.

Design and implementation of a windows-based parallel computing environment for large scale optimization

A parallel computing environment to support optimization of large-scale engineering systems is designed and implemented on Windows-based personal computer networks, using the master-worker model and the Parallel Virtual Machine (PVM). It is involved in decomposition of a large engineering system into a number of smaller subsystems optimized in parallel on worker nodes and coordination of subsystem optimization results on the master node. The environment consists of six functional modules, i.e. the master control, the optimization model generator, the optimizer, the data manager, the monitor, and the post processor. Object-oriented design of these modules is presented. The environment supports steps from the generation of optimization models to the solution and the visualization on networks of computers. User-friendly graphical interfaces make it easy to define the problem, and monitor and steer the optimization process. It has been verified by an example of a large space truss optimization. (C) 2004 Elsevier Ltd. All rights reserved.

ImageSpace: An Environment for Image Ontology Management

More and more researchers have realized that ontologies will play a critical role in the development of the Semantic Web, the next generation Web in which content is not only consumable by humans, but also by software agents. The development of tools to support ontology management including creation, visualization, annotation, database storage, and retrieval is thus extremely important. We have developed ImageSpace, an image ontology creation and annotation tool that features (1) full support for the standard web ontology language DAML+OIL; (2) image ontology creation, visualization, image annotation and display in one integrated framework; (3) ontology consistency assurance; and (4) storing ontologies and annotations in relational databases. It is expected that the availability of such a tool will greatly facilitate the creation of image repositories as islands of the Semantic Web.

3D Environment for Virtual Collections

This paper describes a framework for building virtual collections of several digital objects and presenting them in an interactive 3D environment, rendered in a web browser. Using that environment, the website visitor can examine a given collection from a first-person perspective by walking around and inspecting each object in detail by viewing it from any angle. The rendering and visualization of the models is done solely by the web browser with the use of HTML5 and the Three.js JavaScript library, without any additional requirements.

A large-scale dynamic vector and raster data visualization geographic information system based on parallel map tiling

With the exponential increasing demands and uses of GIS data visualization system, such as urban planning, environment and climate change monitoring, weather simulation, hydrographic gauge and so forth, the geospatial vector and raster data visualization research, application and technology has become prevalent. However, we observe that current web GIS techniques are merely suitable for static vector and raster data where no dynamic overlaying layers. While it is desirable to enable visual explorations of large-scale dynamic vector and raster geospatial data in a web environment, improving the performance between backend datasets and the vector and raster applications remains a challenging technical issue. This dissertation is to implement these challenging and unimplemented areas: how to provide a large-scale dynamic vector and raster data visualization service with dynamic overlaying layers accessible from various client devices through a standard web browser, and how to make the large-scale dynamic vector and raster data visualization service as rapid as the static one. To accomplish these, a large-scale dynamic vector and raster data visualization geographic information system based on parallel map tiling and a comprehensive performance improvement solution are proposed, designed and implemented. They include: the quadtree-based indexing and parallel map tiling, the Legend String, the vector data visualization with dynamic layers overlaying, the vector data time series visualization, the algorithm of vector data rendering, the algorithm of raster data re-projection, the algorithm for elimination of superfluous level of detail, the algorithm for vector data gridding and re-grouping and the cluster servers side vector and raster data caching.

Developing a Theory of Pervasive Information Capture, Processing, Visualization and Documentation

Developing a theoretical framework for pervasive information environments is an enormous goal. This paper aims to provide a small step towards such a goal. The following pages report on our initial investigations to devise a framework that will continue to support locative, experiential and evaluative data from ‘user feedback’ in an increasingly pervasive information environment. We loosely attempt to outline this framework by developing a methodology capable of moving from rapid-deployment of software and hardware technologies, towards a goal of realistic immersive experience of pervasive information. We propose various technical solutions and address a range of problems such as; information capture through a novel model of sensing, processing, visualization and cognition.

Subjective comparison of consumer television technologies for 3D visualization

This paper presents a comparison among different consumer 3D display technologies by means of a subjective assessment test. Therefore, four 55-in displays have been considered: one autostereoscopic display, one stereoscopic with polarized passive glasses, and two with active shutter glasses. In addition, a high-quality 3D video database has been used to show diverse material with both views in high definition. To carry out the test, standard recommendations have been followed considering also some modifications looking for a test environment more similar to real home viewing conditions, with the objective of obtaining more representative conclusions. Moreover, several perceptual factors have been considered to study the performance of the displays, such as picture quality, depth perception, and visual discomfort. The obtained results show interesting issues, like the performance improvement of active shutter glasses technology, the high performance of the polarized glasses technology in terms of quality and comfort, and the need of improvement of the autostereoscopic displays to complement the visual comfort to reach a global high-quality visual experience.

Laying the path to consumer-level immersive simulation environment

Since the end of the long winter of virtual reality (VR) at the beginning of the 2010 decade, many improvements have been made in terms of hardware technologies and software platforms performances and costs. Many expect such trend will continue, pushing the penetration rate of virtual reality headsets to skyrocket at some point in the future, just as mobile platforms did before. In the meantime, virtual reality is slowly transitioning from a specialized laboratory-only technology, to a consumer electronics appliance, opening interesting opportunities and challenges. In this transition, two interesting research questions amount to how 2D-based content and applications may benefit (or be hurt) by the adoption of 3D-based immersive environments and to how to proficiently support such integration. Acknowledging the relevance of the former, we here consider the latter question, focusing our attention on the diversified family of PC-based simulation tools and platforms. VR-based visualization is, in fact, widely understood and appreciated in the simulation arena, but mainly confined to high performance computing laboratories. Our contribution here aims at characterizing the simulation tools which could benefit from immersive interfaces, along with a general framework and a preliminary implementation which may be put to good use to support their transition from uniquely 2D to blended 2D/3D environments.

Direct Visualization Of The Action Of Triton X-100 On Giant Vesicles Of Erythrocyte Membrane Lipids.

The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their compositions. In fact, the impact of detergents in membrane organization is still controversial. Here, we use phase contrast and fluorescence microscopy to observe giant unilamellar vesicles (GUVs) made of erythrocyte membrane lipids (erythro-GUVs) when exposed to the detergent Triton X-100 (TX-100). We clearly show that TX-100 has a restructuring action on biomembranes. Contact with TX-100 readily induces domain formation on the previously homogeneous membrane of erythro-GUVs at physiological and room temperatures. The shape and dynamics of the formed domains point to liquid-ordered/liquid-disordered (Lo/Ld) phase separation, typically found in raft-like ternary lipid mixtures. The Ld domains are then separated from the original vesicle and completely solubilized by TX-100. The insoluble vesicle left, in the Lo phase, represents around 2/3 of the original vesicle surface at room temperature and decreases to almost 1/2 at physiological temperature. This chain of events could be entirely reproduced with biomimetic GUVs of a simple ternary lipid mixture, 2:1:2 POPC/SM/chol (phosphatidylcholine/sphyngomyelin/cholesterol), showing that this behavior will arise because of fundamental physicochemical properties of simple lipid mixtures. This work provides direct visualization of TX-100-induced domain formation followed by selective (Ld phase) solubilization in a model system with a complex biological lipid composition.

The Influence Of The Environment On The Development Of Thyroid Tumors: A New Appraisal.

Most epidemiological studies concerning differentiated thyroid cancers (DTC) indicate an increasing incidence over the last two decades. This increase might be partially explained by the better access to health services worldwide, but clinicopathological analyses do not fully support this hypothesis, indicating that there are carcinogenetic factors behind this noticeable increasing incidence. Although we have undoubtedly understood the biology and molecular pathways underlying thyroid carcinogenesis in a better way, we have made very little progresses in identifying a risk profile for DTC, and our knowledge of risk factors is very similar to what we knew 30-40 years ago. In addition to ionizing radiation exposure, the most documented and established risk factor for DTC, we also investigated the role of other factors, including eating habits, tobacco smoking, living in a volcanic area, xenobiotics, and viruses, which could be involved in thyroid carcinogenesis, thus, contributing to the increase in DTC incidence rates observed.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Obesogenic Environment By Excess Of Dietary Fats In Different Phases Of Development Reduces Spermatic Efficiency Of Wistar Rats At Adulthood: Correlations With Metabolic Status.

This study compares the impact of obesogenic environment (OE) in six different periods of development on sperm parameters and the testicular structure of adult rats and their correlations with sex steroid and metabolic scenario. Wistar rats were exposed to OE during gestation (O1), during gestation/lactation (O2), from weaning to adulthood (O3), from lactation to adulthood (O4), from gestation to sexual maturity (O5), and after sexual maturation (O6). OE was induced by a 20% fat diet, and control groups were fed a balanced diet (4% fat). Serum leptin levels and adiposity index indicate that all groups were obese, except for O1. Three progressive levels of impaired metabolic status were observed: O1 presented insulin resistance, O2 were insulin resistant and obese, and groups O3, O4, and O5 were insulin resistant, obese, and diabetic. These three levels of metabolic damage were proportional to the increase of leptin and decreased circulating testosterone. The impairment in the daily sperm production (DSP) paralleled these three levels of metabolic and hormonal damage being marginal in O1, increasing in O2, and being higher in groups O3, O4, O5, and O6. None of the OE periods affected the sperm transit time in the epididymis, and the lower sperm reserves were caused mainly by impaired DSP. In conclusion, OE during sexual maturation markedly reduces the DSP at adulthood in the rat. A severe reduction in the DSP also occurs in OE exposure during gestation/lactation but not in gestation, indicating that breast-feeding is a critical period for spermatogenic impairment under obesogenic conditions.

The Environment Of Professional Practice And Burnout In Nurses In Primary Healthcare.

to assess how nurses perceive autonomy, control over the environment, the professional relationship between nurses and physicians and the organizational support and correlate them with burnout, satisfaction at work, quality of work and the intention to quit work in primary healthcare. cross-sectional and correlation study, using a sample of 198 nurses. The tools used were the Nursing Work Index Revised, Maslach Burnout Inventory and a form to characterize the nurses. To analyze the data, descriptive statistics were applied and Spearman's correlation coefficient was used. the nurses assessed that the environment is partially favorable for: autonomy, professional relationship and organizational support and that the control over this environment is limited. Significant correlations were evidenced between the Nursing Work Index Revised, Maslach Burnout Inventory and the variables: satisfaction at work, quality of care and the intent to quit the job. the nurses' perceptions regarding the environment of practice are correlated with burnout, satisfaction at work, quality of care and the intent to quit the job. This study provides support for the restructuring of work processes in the primary health care environment and for communication among the health service management, human resources and occupational health areas.

Fracture Of Distal Humerus: Mipo Technique With Visualization Of The Radial Nerve.

To evaluate the outcomes in patients treated for humerus distal third fractures with MIPO technique and visualization of the radial nerve by an accessory approach, in those without radial palsy before surgery. The patients were treated with MIPO technique. The visualization and isolation of the radial nerve was done by an approach between the brachialis and the brachiorradialis, with an oblique incision, in the lateral side of the arm. MEPS was used to evaluate the elbow function. Seven patients were evaluated with a mean age of 29.8 years old. The average follow up was 29.85 months. The radial neuropraxis after surgery occurred in three patients. The sensorial recovery occurred after 3.16 months on average and also of the motor function, after 5.33 months on average, in all patients. We achieved fracture consolidation in all patients (M=4.22 months). The averages for flexion-extension and prono-supination were 112.85° and 145°, respectively. The MEPS average score was 86.42. There was no case of infection. This approach allowed excluding a radial nerve interposition on site of the fracture and/or under the plate, showing a high level of consolidation of the fracture and a good evolution of the range of movement of the elbow. Level of Evidence IV, Case Series.

The Role Of Edaphic Environment And Climate In Structuring Phylogenetic Pattern In Seasonally Dry Tropical Plant Communities.

Seasonally dry tropical plant formations (SDTF) are likely to exhibit phylogenetic clustering owing to niche conservatism driven by a strong environmental filter (water stress), but heterogeneous edaphic environments and life histories may result in heterogeneity in degree of phylogenetic clustering. We investigated phylogenetic patterns across ecological gradients related to water availability (edaphic environment and climate) in the Caatinga, a SDTF in Brazil. Caatinga is characterized by semiarid climate and three distinct edaphic environments - sedimentary, crystalline, and inselberg -representing a decreasing gradient in soil water availability. We used two measures of phylogenetic diversity: Net Relatedness Index based on the entire phylogeny among species present in a site, reflecting long-term diversification; and Nearest Taxon Index based on the tips of the phylogeny, reflecting more recent diversification. We also evaluated woody species in contrast to herbaceous species. The main climatic variable influencing phylogenetic pattern was precipitation in the driest quarter, particularly for herbaceous species, suggesting that environmental filtering related to minimal periods of precipitation is an important driver of Caatinga biodiversity, as one might expect for a SDTF. Woody species tended to show phylogenetic clustering whereas herbaceous species tended towards phylogenetic overdispersion. We also found phylogenetic clustering in two edaphic environments (sedimentary and crystalline) in contrast to phylogenetic overdispersion in the third (inselberg). We conclude that while niche conservatism is evident in phylogenetic clustering in the Caatinga, this is not a universal pattern likely due to heterogeneity in the degree of realized environmental filtering across edaphic environments. Thus, SDTF, in spite of a strong shared environmental filter, are potentially heterogeneous in phylogenetic structuring. Our results support the need for scientifically informed conservation strategies in the Caatinga and other SDTF regions that have not previously been prioritized for conservation in order to take into account this heterogeneity.