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Transgenic Medicago truncatula plants obtained from Agrobacterium tumefaciens-transformed roots and Agrobacterium rhizogenes-transformed hairy roots

Description: Article on transgenic Medicago truncatula plants obtained from Agrobacterium tumefaciens-transformed roots and Agrobacterium rhizogenes-transformed hairy roots.
Date: January 9, 2006
Creator: Crane, Cynthia; Wright, Elane; Dixon, R. A. & Wang, Z.-Y. (Zeng-Yu), 1963-
Partner: UNT College of Arts and Sciences

The Decomposition of Human-Written Book Summaries

Description: In this paper, the authors evaluate the extent to which human-written book summaries can be obtained through cut-and-paste operations from the original book. The authors analyze the effect of the parameters involved in the decomposition algorithm, and highlight the distinctions in coverage obtained for different summary types.
Date: March 2009
Creator: Ceylan, Hakan & Mihalcea, Rada, 1974-
Partner: UNT College of Engineering

Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters

Description: This paper discusses expressed sequence tag sequencing over grid and cloud computing clusters, specifically for biological applications. In this paper, the authors propose a Web service framework for high-level job scheduling that is developed for scientific applications.
Date: September 2009
Creator: Pallickara, Sangmi Lee; Pierce, Marlon; Dong, Qunfeng & Kong, ChinHua
Partner: UNT College of Arts and Sciences

Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula

Description: Article on methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula.
Date: March 1, 2005
Creator: Suzuki, Hideyuki; Reddy, M. S. Srinivasa; Naoumkina, Marina A.; Aziz, Naveed; May, Gregory D.; Huhman, David et al.
Partner: UNT College of Arts and Sciences

Volume visualization of multiple alignment of large genomicDNA

Description: Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.
Date: July 25, 2005
Creator: Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H. & Hamann, Bernd
Partner: UNT Libraries Government Documents Department


Description: Transition metal carbides and phosphides have shown tremendous potential as highly active catalysts. At a microscopic level, it is not well understood how these new catalysts work. Their high activity is usually attributed to ligand or/and ensemble effects. Here, we review recent studies that examine the chemical activity of metal carbide and phosphides as a function of size, from clusters to extended surfaces, and metal/carbon or metal/phosphorous ratio. These studies reveal that the C and P sites in these compounds cannot be considered as simple spectators. They moderate the reactivity of the metal centers and provide bonding sites for adsorbates.
Date: July 1, 2007
Partner: UNT Libraries Government Documents Department

Aberration-Coreected Electron Microscopy at Brookhaven National Laboratory

Description: The last decade witnessed the rapid development and implementation of aberration correction in electron optics, realizing a more-than-70-year-old dream of aberration-free electron microscopy with a spatial resolution below one angstrom [1-9]. With sophisticated aberration correctors, modern electron microscopes now can reveal local structural information unavailable with neutrons and x-rays, such as the local arrangement of atoms, order/disorder, electronic inhomogeneity, bonding states, spin configuration, quantum confinement, and symmetry breaking [10-17]. Aberration correction through multipole-based correctors, as well as the associated improved stability in accelerating voltage, lens supplies, and goniometers in electron microscopes now enables medium-voltage (200-300kV) microscopes to achieve image resolution at or below 0.1nm. Aberration correction not only improves the instrument's spatial resolution but, equally importantly, allows larger objective lens pole-piece gaps to be employed thus realizing the potential of the instrument as a nanoscale property-measurement tool. That is, while retaining high spatial resolution, we can use various sample stages to observe the materials response under various temperature, electric- and magnetic- fields, and atmospheric environments. Such capabilities afford tremendous opportunities to tackle challenging science and technology issues in physics, chemistry, materials science, and biology. The research goal of the electron microscopy group at the Dept. of Condensed Matter Physics and Materials Science and the Center for Functional Nanomaterials, as well as the Institute for Advanced Electron Microscopy, Brookhaven National Laboratory (BNL), is to elucidate the microscopic origin of the physical- and chemical-behavior of materials, and the role of individual, or groups of atoms, especially in their native functional environments. We plan to accomplish this by developing and implementing various quantitative electron microscopy techniques in strongly correlated electron systems and nanostructured materials. As a first step, with the support of Materials Science Division, Office of Basic Energy Science, US Department of Energy, and the New York State Office of Science, Technology, ...
Date: April 1, 2008
Creator: Zhu,Y. & Wall, J.
Partner: UNT Libraries Government Documents Department

Evaluation Strategies for Bitmap Indices with Binning

Description: Bitmap indices are efficient data structures for querying read-only data with low attribute cardinalities. To improve the efficiency of the bitmap indices on attributes with high cardinalities, we present a new strategy to evaluate queries using bitmap indices. This work is motivated by a number of scientific data analysis applications where most attributes have cardinalities in the millions. On these attributes, binning is a common strategy to reduce the size of the bitmap index. In this article we analyze how binning affects the number of pages accessed during query processing, and propose an optimal way of using the bitmap indices to reduce the number of pages accessed. Compared with two basic strategies the new algorithm reduces the query response time by up to a factor of two. On a set of 5-dimensional queries on real application data, the bitmap indices are on average 10 times faster than the projection index.
Date: June 3, 2004
Creator: Stockinger, Kurt; Wu, Kesheng & Shoshani, Arie
Partner: UNT Libraries Government Documents Department

A Survey of High-Quality Computational Libraries and their Impactin Science and Engineering Applications

Description: Recently, a number of important scientific and engineering problems have been successfully studied and solved by means of computational modeling and simulation. Many of these computational models and simulations benefited from the use of available software tools and libraries to achieve high performance and portability. In this article, we present a reference matrix of the performance of robust, reliable and widely used tools mapped to scientific and engineering applications that use them. We aim at regularly maintaining and disseminating this matrix to the computational science community. This matrix will contain information on state-of-the-art computational tools, their applications and their use.
Date: September 20, 2004
Creator: Drummond, L.A.; Hernandez, V.; Marques, O.; Roman, J.E. & Vidal, V.
Partner: UNT Libraries Government Documents Department