446 research outputs found

    Towards frameworks for large scale ensemble-based execution patterns

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    Towards Frameworks for Large Scale Ensemble-based Execution Patterns by Vivekanandan Balasubramanian Thesis Director: Dr. Shantenu Jha A major challenge in the field of chemical sciences is to bridge the gap between the ability to study matter at an atomic scale and to predict how these details behave and impact at a macroscopic scale. Molecular Dynamics (MD) simulations are a powerful tool for the study of macromolecular systems as they provide the ability to compute thermodynamic and kinetic parameters accurately. In order for MD simulations to be effective, they must adequately sample, e.g., effi- ciently and accurately sample all conformational space for a molecule. A long standing debate in the MD community has been around approaches to effective sampling: for a given amount of compute time, which is likely to guarantee better sampling: a single long-running simulation or multiple smaller simulations? In this project, we provide support for the scenario when multiple small simulations are to be used. Another important requirement faced by MD community is the need for iterative simulation and analysis stages, from which data can be extracted and, based on prob- ability densities and weights, new set of trajectories can be generated. These scenarios result in the following computational challenges: (i) Executing large number of tasks concurrently, (ii) Support for heterogeneous resource, (iii) Effective data movement that is correlated with stage transitions. iiTo address these requirements, we developed the Ensemble MD Toolkit (EnMDTK). The EnMDTK has three primary design features: (1) Fundamental support for multiple concurrent simulations, (2) Support for different ensemble-based execution patterns, and (3) Execution Plugins which abstract, from the user the challenges /difficulties of managing the execution of these patterns on heterogeneous systems. The toolkit enables scientists to easily and scalably develop their own applications using pre-determined patterns supported by the EnMDTK. Our contribution to this project is the development, testing and documentation of the specific iterative Simulation-Analysis pattern of EnMDTK. The development re- quired extensive study and testing of the underlying RADICAL-Pilot framework in order to use it in the most effective form. Knowledge of the individual kernels, work- ing and their specific dependencies were required for their deployment on the various resources. Testing revealed certain optimizations that could be done with the data movement. Performance characterization of the final toolkit was also done.M.S.Includes bibliographical referencesby Vivekanandan Balasubramania

    Polarimetric Radar Studies of Atmospheric Ice Particles.

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    Single scattering properties of ice crystals are described at microwave frequencies using discrete dipole approximations and Rayleigh scattering techniques. For a given shape, the average bulk densities of ice crystals can be estimated using the ratio of the copolarized radar signal in a linear (horizontal, vertical) polarization basis. Reflectivity depends on the ice content (g • m-3), and also on both size distribution parameters and average bulk density of the scatterers. Differential propagation phase is primarily a function of shape, ice water content, and is independent of size distribution parameters. Thus, by using a combination of polarimetric radar measurements, average ice content, bulk density, and shape of distributed scatterers can be inferred. These techniques become quite complex in the case of a winter storm where scatterers can exist with varying shape and bulk densities. Polarimetric radar properties of such complex distributed scatterers are modeled. Physical variations in the relation among ice water content, reflectivity, and differential propagation phase are considered with respect to change in the shape of size distribution, bulk density, and average shape of the scatterers. Also, simultaneous polarimetric radar observations and in situ aircraft measurements are shown to demonstrate practical applicability of the techniques.This work was supported under FAA Contract DTFA01-90-Z-02005. The work of J. Vivekanandan and V. N. Bringi was supported by the National Science Foundation under Grants ATM-8915141 and ATM-9214864

    Marine fisheries along the southwest coast of India

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    Marine fisheries production in India has increased from 0.5 million t in 1950 to 2.47 million t in 1997. The gross value of fisheries landings in India was US$2.37 billion in 1997. The contribution of fisheries to the Gross Domestic Product (GDP) has risen from 0.7% in 1980 - 81 to 1.2% in 1994 - 95. The contribution to agricultural GDP has risen from 1.9% to 4%. Fisheries production also plays a critical role in food security and livelihood in rural areas. The southwest (SW) coast, while only 16% of the Indian coastline, is an important area for marine fisheries production, contributing 31.7% (0.74 million t) in 1993 - 98. This production is dominated by pelagic (59% of landings) and demersal species (23%). However, the open access system has resulted in rapid increases in fishing effort, particularly in the coastal areas. The density of fishers inshore has increased from 3.6 to 8.5 fishers per km2 in the past four decades. This excess effort has resulted in overfishing of the stocks and lower economic rent from the fishery. The overall objective of coastal fisheries management along the southwest coast of India is sustainable coastal fisheries development. This requires key ecological, social, economic and administrative issues to be addressed. Ecological sustainability requires the reduction of the excess effort through limited entry and effort reduction schemes, appropriate exploitation patterns through improved gear selectivity and restoration of the degraded coastal environment through integrated coastal zone management initiatives. Key social interventions include: creation of alternative employment to reduce fisher numbers, prevention/management of increasing intra- and inter-sectoral conflicts and empowerment of artisanal fishers through co-management schemes, social legislation and improved support/welfare schemes. The key economic issues include declining earnings, particularly of artisanal fishers, which requires; optimizing fleet composition for economic returns, improvement of the marketing system and cold storage chains, improvement of post-harvest processes to increase product value. The key administrative needs are a strong fisheries policy that balances welfare concerns with sustainability, effective implementation of regulations, and increased government resources for fisheries management. Project briefs covering the key interventions are provided, however these require further review and improvement in collaboration with concerned stakeholders.Fishery resources, Catch/effort, Population characteristics, Coastal fisheries, Marine fisheries, Ecosystems, Economic benefits, Fishery industry, Capture fishery economics, Fish consumption, Fishery policy, Legislation, Fishery management, Flood plains, Demersal fisheries, Pelagic fisheries, Socioeconomic aspects, Surveys, Marketing, Fish storage, Fishing gear, ISW, India,

    Active and passive remote sensing of precipitating storms during CaPE. Part I: Advanced Microwave Precipitation Radiometer and polarimetric radar measurements and models

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    The Advanced Microwave Precipitation Radiometer (AMPR), an across-track scanning, four-channel (10.7, 19.35, 37.1, 85.5 GHz) total-power radiometer system, was instrumented aboard a NASA ER-2 aircraft during the 1991 CaPE (Convection and Precipitation/Electrification) project in central Florida. At a 20 km flight altitude, the AMPR provides fine-scale microwave imagery of Earth surfaces and its atmosphere, and is well-suited for diverse hydrological applications. During overflights of precipitation, coincident ground-based radar measurements were taken with the NCAR CP-2 dual-frequency, dual-polarization radar system. After remapping the radar data into a format compatible with the AMPR scanning geometry, the radar-derived profiles of rain, melting, and frozen hydrometeors are compared against the AMPR equivalent blackbody brightness temperature (T B) imagery. Microwave radiative transfer modeling procedures incorporating the radar-derived hydrometeor profiles were used to simulated the multifrequency AMPR imagery over both land and ocean background ER-2 flights. Within storm cores over land, columnar ice water paths up to 20 kgm–2 gradually depressed the 85 GHzT B as low as 100 K. The presence of tall vertical reflectivity columns encompassing > 20 kgm–2 columnar ice water path often produced 37 GHzT BT B directly over the core. Over ocean, the 10 GHz channel provided the clearest correlation with the rainfall amounts, whereas the 19 GHz channel saturated near 260 K past 10–15 mm hr–1 rain rate as determined by radar. Scattering by ice and melting ice at 37 GHz producedT B ambiguities over both raining and clear-ocean regions. Sensitivity to the columnar mixed phase region via the intermediate frequencies (19 and 37 GHz) is demonstrated and explained with the radar-derivedT B modeling. By superimposing vertical profiles of cloud liquid water (which this radar cannot measure) upon the radarinferred hydrometeor structure, additional information on the location of the peak cloud water and its amount relative to the vertical ice structure can be noted, along with a possible inference of the dominant ice particle size within the upper storm core. These results suggest that as the resolution of passive radiometric measurements approaches dimensions where the antenna beams become increasingly filled by the cloud, precipitation retrieval via multifrequencyT B input is well-suited to a vertical profiling-type algorithm. This is further examined in Part II of this manuscript, where the radarderived vertical hydrometeor profiles are used to test the applicability of a multispectral cloud model-based approach to passive microwave precipitation retrieval from space

    Fishery - Related Mortality of Sea Turtles in India: An Overview

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    Coastal communities have exploited sea turtles for centuries. In the 1950s, organised fisheries were developed to capture turtles in many parts of the world; sea turtles were considered an important exploitable fishery resource due to their high commercial value. Turtle meat and eggs were seell as a basic protein source for coastal populations. In India, Jacob (1973) highlighted the potential of sea turtle resources. Organised trade in turtle products existed prior to the eighties (Dattatri 1984, Rajagopalan 1984, 2000). It is estimated that 50,000-80,000 adult olive ridleys were captured off the Gahirmatha coast every nesting season up to 1981-82 (Das 1985). In September 1977. the five species of sea turtles that occur in Indian waters were included in Schedule I of the Indian Wildlife (Protection) Act, 1972. As a consequence of the implementation of regulatory measures, organised capture and trade decreased, though illegal trade persisted till the mid-1980s. While the threat from targeted capture and trade decreased, incidental capture of sea turtles in gear operated for other species of fish and shellfish has become more significant over the years. The interaction of sea turtles with fisheries has become an area of critical importance in many parts of the world (Gerosa and Casale 1999, Vivekanandan 2002). In India tOO, incidental capture in gill nets and trawls has become a serious threat to sea turtle populations (Rajagopalan et a11996, 2001, Pandav and Choudhury 1999, Wright and Mohanty 2002). Due to an increase in the number of fishing units, and also improvement in technology, incidental bycatch has increased in recent years to the extent that it is the most significant cause of sea turtle mortality in Indian waters

    Fatal Case of Probable Invasive Aspergillosis after Five Years of Heart Transplant: A Case Report and Review of the Literature

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    Invasive fungal infections are very common in solid organ transplants and occur most frequently in the first three months after transplant. A 49-year-old female with a history of two remote heart transplants with the most recent one occurring 5 years ago was admitted for increasing shortness of breath, cough, and fever. Computerized tomography (CT) scan of the chest showed left lower lung ground-glass and tree-in-bud opacities. She was started on broad spectrum antibiotics along with ganciclovir and micafungin. Ganciclovir was added due to the patient’s past history of CMV infection and empiric fungal coverage with micafungin. Bronchoalveolar lavage (BAL) was performed as her respiratory status worsened and voriconazole was added for possible aspergillosis in combination therapy with micafungin. BAL galactomannan returned positive which was suggestive of aspergillosis. Patient worsened clinically and subsequently succumbed to cardiorespiratory arrest despite our best efforts. It is important to have a high degree of clinical suspicion for invasive aspergillosis in transplant patients even many years after transplant and initiate aggressive therapy due to poor outcomes

    Trophic model of the coastal fisheries ecosystem of the southwest coast of India

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    The Ecopath approach and software were used to construct a trophic model of the coastal fisheries ecosystem of the southwest (SW) coast of India. The model consisted of 11 ecological groups and used estimated landings from all areas along the southwest coast (based on the sample surveys conducted by Coastal Marine Fisheries Research Institute for the years 1994, 1995 and 1996). The trophic model suggests high catch levels, particularly for the large and medium predators, demersal feeders and detritivores. The biomass estimates in the trophic model were comparable to the biomass estimates from trawl surveys based on the swept area method for the southwest coast.Fishery resources, Demersal fisheries, Fishery surveys, Biomass, Population density, Shrimp fisheries, Catch/effort, Trawling, Mathematical models, Coastal fisheries, ISW, India,

    Vision-based Terrain Segmentation and Roughness Estimation: Application on the CENTAURO Robot

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    Intelligent terrain perception for search-and-rescue robotic applications, requires a high-level understanding of both the terrain type and its chief physical characteristics. Roughness is one such important terrain property, since it could play a key role in robot control/planning strategies, while navigatingin an unknown environment. In this paper, we present a single deep neural network architecture that predicts the pixel-wise terrain labels (i.e., sand, stone, wood, metal, road/sidewalk, and grass) and regresses their roughness from an input RGB image. Our approach, inspired by human analogy, leverages the basic image feature space from a pre-trained network (SegNet) to estimate the roughness. We experimentally validate our approach in real-world images, using RGB cameras. Moreover, we implement the algorithm on our four-legged centaur-like robot CENTAURO and demonstrate the use of our method inassuring the stability of the robot in real-world scenarios, where the robot is traversing terrains of varying roughness.Mechanical Engineerin
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