Software Tools For Large Scale Interactive Hydrodynamic Modeling

Running hydrodynamic models interactively allows both visual exploration and change of model state during simulation. One of the main characteristics of an interactive model is that it should provide immediate feedback to the user, for example respond to changes in model state or view settings. For this reason, such features are usually only available for models with a relatively small number of computational cells, which are used mainly for demonstration and educational purposes. It would be useful if interactive modeling would also work for models typically used in consultancy projects involving large scale simulations. This results in a number of technical challenges related to the combination of the model itself and the visualisation tools (scalability, implementation of an appropriate API for control and access to the internal state). While model parallelisation is increasingly addressed by the environmental modeling community, little effort has been spent on developing a high-performance interactive environment. What can we learn from other high-end visualisation domains such as 3D animation, gaming, virtual globes (Autodesk 3ds Max, Second Life, Google Earth) that also focus on efficient interaction with 3D environments? In these domains high efficiency is usually achieved by the use of computer graphics algorithms such as surface simplification depending on current view, distance to objects, and efficient caching of the aggregated representation of object meshes. We investigate how these algorithms can be re-used in the context of interactive hydrodynamic modeling without significant changes to the model code and allowing model operation on both multi-core CPU personal computers and high-performance computer clusters.

Large scale laboratory cultures of Ankistrodesmus gracilis (Reisch) Korsikov (Chlorophyta) and Diaphanosoma biergei Korinek, 1981 (Cladocera)

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

Performance and economic indicators of a large scale fish farming in Mato Grosso, Brazil

Performance and economic indicators of a large scale fish farm that produces round fish, located in Mato Grosso State, Brazil, were evaluated. The 130.8 ha-water surface area was distributed in 30 ponds. Average total production costs and the following economic indicators were calculated: gross income (GI), gross margin (GM), gross margin index (GMI), profitability index (PI) and profit (P) for the farm as a whole and for ten ponds individually. Production performance indicators were also obtained, such as: production cycle (PC), apparent feed conversion (FC), average biomass storage (ABS), survival index (SI) and final average weight (FAW). The average costs to produce an average 2.971 kg.ha-1 per year were: R$ 2.43, R$ 0.72 and R$ 3.15 as average variable, fixed and total costs, respectively. Gross margin and profit per year per hectare of water surface were R$ 2,316.91 and R$ 180.98, respectively. The individual evaluation of the ponds showed that the best pond performance was obtained for PI 38%, FC 1.7, ABS 0.980 kg.m-2, TS 56%, FAW 1.873 kg with PC of 12.3 months. The worst PI was obtained for the pond that displayed losses of 138%, FC 2.6, ABS 0.110 kg.m-2, SI 16% and FAW 1.811 kg. However, large scale production of round-fish in farms is economically feasible. The studied farm displays favorable conditions to improve performance and economic indicators, but it is necessary to reproduce the breeding techniques and performance indicators achieved in few ponds to the entire farm.

A novel system for large-scale gene expression analysis: bacterial colonies array

In the present work, we report the use of bacterial colonies to optimize macroarray technique. The devised system is significantly cheaper than other methods available to detect large-scale differential gene expression. Recombinant Escherichia coli clones containing plasmid-encoded copies of 4,608 individual expressed sequence tag (ESTs) were robotically spotted onto nylon membranes that were incubated for 6 and 12 h to allow the bacteria to grow and, consequently, amplify the cloned ESTs. The membranes were then hybridized with a beta-lactamase gene specific probe from the recombinant plasmid and, subsequently, phosphorimaged to quantify the microbial cells. Variance analysis demonstrated that the spot hybridization signal intensity was similar for 3,954 ESTs (85.8%) after 6 h of bacterial growth. Membranes spotted with bacteria colonies grown for 12 h had 4,017 ESTs (87.2%) with comparable signal intensity but the signal to noise ratio was fivefold higher. Taken together, the results of this study indicate that it is possible to investigate large-scale gene expression using macroarrays based on bacterial colonies grown for 6 h onto membranes.

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. In addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.

Interior point method for long-term generation scheduling of large-scale hydrothermal systems

This paper presents an interior point method for the long-term generation scheduling of large-scale hydrothermal systems. The problem is formulated as a nonlinear programming one due to the nonlinear representation of hydropower production and thermal fuel cost functions. Sparsity exploitation techniques and an heuristic procedure for computing the interior point method search directions have been developed. Numerical tests in case studies with systems of different dimensions and inflow scenarios have been carried out in order to evaluate the proposed method. Three systems were tested, with the largest being the Brazilian hydropower system with 74 hydro plants distributed in several cascades. Results show that the proposed method is an efficient and robust tool for solving the long-term generation scheduling problem.

Are large-scale distributional shifts of the blue-winged macaw (Primolius maracana) related to climate change?

Aim To evaluate whether observed geographical shifts in the distribution of the blue-winged macaw (Primolius maracana) are related to ongoing processes of global climate change. This species is vulnerable to extinction and has shown striking range retractions in recent decades, withdrawing broadly from southern portions of its historical distribution. Its range reduction has generally been attributed to the effects of habitat loss; however, as this species has also disappeared from large forested areas, consideration of other factors that may act in concert is merited.Location Historical distribution of the blue-winged macaw in Brazil, eastern Paraguay and northern Argentina.Methods We used a correlative approach to test a hypothesis of causation of observed shifts by reduction of habitable areas mediated by climate change. We developed models of the ecological niche requirements of the blue-winged macaw, based on point-occurrence data and climate scenarios for pre-1950 and post-1950 periods, and tested model predictivity for anticipating geographical distributions within time periods. Then we projected each model to the other time period and compared distributions predicted under both climate scenarios to assess shifts of habitable areas across decades and to evaluate an explanation for observed range retractions.Results Differences between predicted distributions of the blue-winged macaw over the twentieth century were, in general, minor and no change in suitability of landscapes was predicted across large areas of the species' original range in different time periods. No tendency towards range retraction in the south was predicted, rather conditions in the southern part of the species' range tended to show improvement for the species.Main conclusions Our test permitted elimination of climate change as a likely explanation for the observed shifts in the distribution of the blue-winged macaw, and points rather to other causal explanations (e.g. changing regional land use, emerging diseases).

Cosmic microwave background and large-scale structure constraints on a simple quintessential inflation model

We derive constraints on a simple quintessential inflation model, based on a spontaneously broken Phi(4) theory, imposed by the Wilkinson Microwave Anisotropy Probe three-year data (WMAP3) and by galaxy clustering results from the Sloan Digital Sky Survey (SDSS). We find that the scale of symmetry breaking must be larger than about 3 Planck masses in order for inflation to generate acceptable values of the scalar spectral index and of the tensor-to-scalar ratio. We also show that the resulting quintessence equation of state can evolve rapidly at recent times and hence can potentially be distinguished from a simple cosmological constant in this parameter regime.

Managing large scale virtual environments using portals

This article describes a technique for Large Scale Virtual Environments (LSVEs) partitioning in hexagon cells and using portal in the cell interfaces to reduce the number of messages on the network and the complexity of the virtual world. These environments usually demand a high volume of data that must be sent only to those users who needs the information [Greenhalgh, Benford 1997].

Geotechnical and structural behavior of the railroad track in large-scale apparatus

This paper analyses the static and dynamic behavior of the railroad track model in laboratory. Measurements of stresses and strains on a large-scale railroad track apparatus were studied. The model includes: compacted soil, representing the final layers of platform, ballast layer, and ties (steel, wooden, and pre-stressed concrete). The soil and soil ballast interface were instrumented with pneumatic stress gauge. Settlement measurement device were positioned at the same levels as the load cells. Loads were applied by hydraulic actuators, statically and dynamically. After the prescribed number of load cycles, in pre-determined intervals, stresses and strains were measured. Observations indicate that stress and strain distributions, transmitted by wooden or steel ties, behave similarly. A more favorable behavior was observed with pre-stressed concrete mono block ties. Non-linear response was observed after a threshold numbers of cycles were surpassed, showing that the strain modulus increases with the numbers of cycles. © 2009 IOS Press.

Large-Scale Water Productivity Assessments with MODIS Images in a Changing Semi-Arid Environment: A Brazilian Case Study

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

Large-scale analysis of the SDSS-III DR8 photometric luminous galaxies angular correlation function

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A test of large-scale reproductive migration in females of the amphidromous shrimp Macrobrachium acanthurus (Caridea : Palaemonidae) from south-eastern Brazil

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