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CAGE100: Real-Time Multi-Port Packet Capture System for 100 Gigabit Ethernet Traffic

Description: Future large scale sciences are anticipated to use massive amount of data in their experiments. DOE’s ESnet (Energy Science Network) is developing a 100 Gbps backbone based on this state-of-the-art 100 Gigabit Ethernet standard. ESnet will serve thousands of DOE and non-DOE scientists with its high bandwidth backbone, and connect several national laboratories. Current Ethernet test and debug solutions, such as network traffic capturer/analyzer tools, support up to 10 Gbps speed, and the very few capable of handling 100 Gbps are extremely costly. Such tools are essential in the development of high speed devices and routers, and ultimately the success of 100 Gigabit Ethernet.
Date: June 14, 2012
Creator: Farrokhnia, Shahin; Namazi, Ali; Azimi-Sadjadi, Babak & Lin, Chujen
Partner: UNT Libraries Government Documents Department

Genome-wide analysis of promoter architecture in Drosophila melanogaster

Description: Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLMRACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysis indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.
Date: October 20, 2010
Creator: Hoskins, Roger A.; Landolin, Jane M.; Brown, James B.; Sandler, Jeremy E.; Takahashi, Hazuki; Lassmann, Timo et al.
Partner: UNT Libraries Government Documents Department


Description: The theory of tomographical imaging with limited-angular input is discussed , from which two reconstruction algorithms are derived. The existence of missing information due to incomplete angular coverage is demonstrated. and an iteration algorithm to recover this information from a priori knowledge on the finite extent of the object developed. Smoothing algorithms to stabilize reconstructions in the presence of noise are given. The effects of digitization and finite truncation of the reconstruction region in numerical computation are also analysed. It is shown that the limited-angle problem is governed by a set of eigenvalues whose spectrum is determined by the imaging angle and the finite extent of the object. The distortion on a point source caused by the missing information is calculated; from the results some properties of the iteration scheme, such as spatial uniformity, are derived.
Date: September 1, 1980
Creator: Tam, K. C. & Perez-Mendez, V.
Partner: UNT Libraries Government Documents Department

Oncology Center

Description: Efforts by the Hollings Cancer Center to earn a designation as a National Cancer Center are outlined.
Date: September 21, 2009
Creator: Kraft, Andrew S.
Partner: UNT Libraries Government Documents Department

SARC: Development and Support of a Sarcoma Research Consortium Infrastructure

Description: SARC is a non-for-profit organization whose mission and vision is to advocate for the collaboration on the design of clinical trials on sarcoma, to further the knowledge regarding the diagnosis and treatment of sarcoma and provide accurate and up to date information to physicians, patients and families. The objectives are to assist in the development of the infrastructure for the continued growth and spectrum of clinical research, to facilitate biannual meeting of investigators, and to develop a preclinical research base that would design and conduct research that would improve the process of drug treatments selected for clinical research trials.
Date: October 29, 2007
Creator: Arkison, Jim
Partner: UNT Libraries Government Documents Department

Regeneration of Tissues and Organs Using Autologous Cells

Description: The proposed work aims to address three major challenges to the field of regenerative medicine: 1) the growth and expansion of regenerative cells outside the body in controlled in vitro environments, 2) supportive vascular supply for large tissue engineered constructs, and 3) interactive biomaterials that can orchestrate tissue development in vivo. Toward this goal, we have engaged a team of scientists with expertise in cell and molecular biology, physiology, biomaterials, controlled release, nanomaterials, tissue engineering, bioengineering, and clinical medicine to address all three challenges. This combination of resources, combined with the vast infrastructure of the WFIRM, have brought to bear on projects to discover and test new sources of autologous cells that can be used therapeutically, novel methods to improve vascular support for engineered tissues in vivo, and to develop intelligent biomaterials and bioreactor systems that interact favorably with stem and progenitor cells to drive tissue maturation. The Institute’s ongoing programs are aimed at developing regenerative medicine technologies that employ a patient’s own cells to help restore or replace tissue and organ function. This DOE program has provided a means to solve some of the vexing problems that are germane to many tissue engineering applications, regardless of tissue type or target disease. By providing new methods that are the underpinning of tissue engineering, this program facilitated advances that can be applied to conditions including heart disease, diabetes, renal failure, nerve damage, vascular disease, and cancer, to name a few. These types of conditions affect millions of Americans at a cost of more than $400 billion annually. Regenerative medicine holds the promise of harnessing the body’s own power to heal itself. By addressing the fundamental challenges of this field in a comprehensive and focused fashion, this DOE program has opened new opportunities to treat conditions where other approaches have failed.
Date: October 11, 2012
Creator: Anthony Atala, M.D.
Partner: UNT Libraries Government Documents Department

Corn Storage Protein - A Molecular Genetic Model

Description: Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to ...
Date: May 31, 2013
Creator: Messing, Joachim
Partner: UNT Libraries Government Documents Department

Development of a System for Rapid Detection of Contaminants in Water Supplies Using Magnetic Resonance and Nanoparticles

Description: To keep the water supply safe and to ensure a swift and accurate response to a water supply contamination event, rapid and robust methods for microbial testing are necessary. Current technologies are complex, lengthy and costly and there is a need for rapid, reliable, and precise approaches that can readily address this fundamental security and safety issue. T2 Biosystems is focused on providing solutions to this problem by making breakthroughs in nanotechnology and biosensor techniques that address the current technical restrictions facing rapid, molecular analysis in complex samples. In order to apply the T2 Biosystems nucleic acid detection procedure to the analysis of nucleic acid targets in unprocessed water samples, Bacillus thuringeinsis was selected as a model organism and local river water was selected as the sample matrix. The initial assay reagent formulation was conceived with a manual magnetic resonance reader, was optimized using a high throughput system, and transferred back to the MR reader for potential field use. The final assay employing the designed and manufactured instruments was capable of detecting 10 CFU/mL of B. thuringiensis directly within the environmental water sample within 90 minutes. Further, discrimination of two closely related species of Bacilli was accomplished using the methods of this project; greater than 3-fold discrimination between B. cereus and B. thuringiensis at a concentrations spanning 10 CFU/mL to 10{sup 5} CFU/mL was observed.
Date: September 14, 2010
Creator: Lowery, Thomas J; Neely, Lori; Chepin, James; Wellman, Parris; Toso, Ken; Murray, Paul et al.
Partner: UNT Libraries Government Documents Department

Characterization of the effects of x-ray irradiation on the hierarchical structure and mechanical properties of human cortical bone

Description: Bone comprises a complex structure of primarily collagen, hydroxyapatite and water, where each hierarchical structural level contributes to its strength, ductility and toughness. These properties, however, are degraded by irradiation, arising from medical therapy or bone-allograft sterilization. We provide here a mechanistic framework for how irradiation affects the nature and properties of human cortical bone over a range of characteristic (nano to macro) length-scales, following x-­ray exposures up to 630 kGy. Macroscopically, bone strength, ductility and fracture resistance are seen to be progressively degraded with increasing irradiation levels. At the micron-­scale, fracture properties, evaluated using in-situ scanning electron microscopy and synchrotron x-ray computed micro-tomography, provide mechanistic information on how cracks interact with the bone-matrix structure. At sub-micron scales, strength properties are evaluated with in-situ tensile tests in the synchrotron using small-/wide-angle x-ray scattering/diffraction, where strains are simultaneously measured in the macroscopic tissue, collagen fibrils and mineral. Compared to healthy bone, results show that the fibrillar strain is decreased by ~40% following 70 kGy exposures, consistent with significant stiffening and degradation of the collagen. We attribute the irradiation-­induced deterioration in mechanical properties to mechanisms at multiple length-scales, including changes in crack paths at micron-­scales, loss of plasticity from suppressed fibrillar sliding at sub-­micron scales, and the loss and damage of collagen at the nano-­scales, the latter being assessed using Raman and Fourier-Transform-Infrared spectroscopy and a fluorometric assay.
Date: August 19, 2011
Creator: Barth, Holly; Zimmermann, Elizabeth; Schaible, Eric; Tang, Simon; Alliston, Tamara & Ritchie, Robert
Partner: UNT Libraries Government Documents Department

CRADA No. BNL-C-97-10 between BNL and Cotton, Inc. Final abstract and final report [Final Report of Research carried out under DOE CRADA No. BNL-C-97-10 - "Prediction of Yield in Cotton"]

Description: The objectives of this work were to determine if the numbér of fiber cell initials varied genetically and to compare the number of initials with that of mature fibers obtained at harvest time. The method used to count the number of fiber cell initials is direct, simple, quick and done while the plant is growing. In contrast, the currently used commercial process is indirect and needs large amount mature fibers gathered at harvest time. However, all current work on cotton yield is based on fiber numbers obtained by the indirect commercial process. Consequently, it was necessary to compare results obtained from the two methods using the same plants as the source of material. The results show that the number of fiber initials per ovule differed significantly (P>0.05) for seven cultivars in 1995 and 1996. AIso, a 1997 study shows the number of fiber initials varied by 15% over boll positions and environments, with rankings among cultivars generally consistent across boll positions and sampling times. Finally, although there were differences among cultivars for initial fiber cell number, all cultivars had nearly the same number of mature lint fibers per seed. This last finding is significant. It indicates that the rate of fiber cell initiation varies among cultivars; the lower the rate, the greater the difference between the number of initials and the number of mature fiber cells. If the rate of fiber initiation is relatively high, the number of initials and mature fibers differs by about 11%; if it is low, the difference is as high as 31%. Cotton breeders may be able to use genetic differences for the number of fiber initials and/or the rate of fiber cell initiation in crop improvement programs.
Date: January 3, 2000
Partner: UNT Libraries Government Documents Department

Radiolabeled Monoclonal Antibodies and Hyperthermia. Final Progress Report for November 1, 1998 - April 30, 2003

Description: The overall objective of this project was to investigate the use of local hyperthermia as a means for improving the potential utility of radiolabeled monoclonal antibodies for tumor therapy. Hyperthermia not only can alter tumor hemodynamics but also can affect antigen expression, catabolism and cytotoxicity. These studies were performed with the human/mouse chimeric anti-tenascin 81C6 antibody in an athymic mouse xenograft model. Variables that were found to be important included the duration and temperature of heating, as well as the timing of the hyperthermia relative to the time of labeled antibody administration.
Date: June 23, 2004
Creator: Zalutsky, M. R.
Partner: UNT Libraries Government Documents Department

Metabolic Engineering VII Conference

Description: The aims of this Metabolic Engineering conference are to provide a forum for academic and industrial researchers in the field; to bring together the different scientific disciplines that contribute to the design, analysis and optimization of metabolic pathways; and to explore the role of Metabolic Engineering in the areas of health and sustainability. Presentations, both written and oral, panel discussions, and workshops will focus on both applications and techniques used for pathway engineering. Various applications including bioenergy, industrial chemicals and materials, drug targets, health, agriculture, and nutrition will be discussed. Workshops focused on technology development for mathematical and experimental techniques important for metabolic engineering applications will be held for more in depth discussion. This 2008 meeting will celebrate our conference tradition of high quality and relevance to both industrial and academic participants, with topics ranging from the frontiers of fundamental science to the practical aspects of metabolic engineering.
Date: December 4, 2012
Creator: Korpics, Kevin
Partner: UNT Libraries Government Documents Department

Cellular membrane trafficking of mesoporous silica nanoparticles

Description: This dissertation mainly focuses on the investigation of the cellular membrane trafficking of mesoporous silica nanoparticles. We are interested in the study of endocytosis and exocytosis behaviors of mesoporous silica nanoparticles with desired surface functionality. The relationship between mesoporous silica nanoparticles and membrane trafficking of cells, either cancerous cells or normal cells was examined. Since mesoporous silica nanoparticles were applied in many drug delivery cases, the endocytotic efficiency of mesoporous silica nanoparticles needs to be investigated in more details in order to design the cellular drug delivery system in the controlled way. It is well known that cells can engulf some molecules outside of the cells through a receptor-ligand associated endocytosis. We are interested to determine if those biomolecules binding to cell surface receptors can be utilized on mesoporous silica nanoparticle materials to improve the uptake efficiency or govern the mechanism of endocytosis of mesoporous silica nanoparticles. Arginine-glycine-aspartate (RGD) is a small peptide recognized by cell integrin receptors and it was reported that avidin internalization was highly promoted by tumor lectin. Both RGD and avidin were linked to the surface of mesoporous silica nanoparticle materials to investigate the effect of receptor-associated biomolecule on cellular endocytosis efficiency. The effect of ligand types, ligand conformation and ligand density were discussed in Chapter 2 and 3. Furthermore, the exocytosis of mesoporous silica nanoparticles is very attractive for biological applications. The cellular protein sequestration study of mesoporous silica nanoparticles was examined for further information of the intracellular pathway of endocytosed mesoporous silica nanoparticle materials. The surface functionality of mesoporous silica nanoparticle materials demonstrated selectivity among the materials and cancer and normal cell lines. We aimed to determine the specific organelle that mesoporous silica nanoparticles could approach via the identification of harvested proteins from exocytosis process. Based on the study of endo- and exocytosis behavior ...
Date: June 21, 2012
Creator: Fang, I-Ju
Partner: UNT Libraries Government Documents Department

Succinic Acid as a Byproduct in a Corn-based Ethanol Biorefinery

Description: MBI endeavored to develop a process for succinic acid production suitable for integration into a corn-based ethanol biorefinery. The project investigated the fermentative production of succinic acid using byproducts of corn mill operations. The fermentation process was attuned to include raw starch, endosperm, as the sugar source. A clean-not-sterile process was established to treat the endosperm and release the monomeric sugars. We developed the fermentation process to utilize a byproduct of corn ethanol fermentations, thin stillage, as the source of complex nitrogen and vitamin components needed to support succinic acid production in A. succinogenes. Further supplementations were eliminated without lowering titers and yields and a productivity above 0.6 g l-1 hr-1was achieved. Strain development was accomplished through generation of a recombinant strain that increased yields of succinic acid production. Isolation of additional strains with improved features was also pursued and frozen stocks were prepared from enriched, characterized cultures. Two recovery processes were evaluated at pilot scale and data obtained was incorporated into our economic analyses.
Date: December 31, 2007
Creator: International, MBI
Partner: UNT Libraries Government Documents Department

Carbon Sequestration in Dryland and Irrigated Agroecosystems: Quantification at Different Scales for Improved Prediction

Description: The overall objective of this research is to improve our basic understanding of the biophysical processes that govern C sequestration in major rainfed and irrigated agroecosystems in the north-central USA.
Date: September 14, 2012
Creator: Verma, Shashi B.; Cassman, Kenneth G.; Arkebauer, Timothy J.; Hubbard, Kenneth G.; Knops, Johannes M. & Suyker, Andrew E.
Partner: UNT Libraries Government Documents Department

Modeling daily flow patterns individuals to characterize disease spread

Description: The effect of an individual's travels throughout a day on the spread of disease is examined using a deterministic SIR model. We determine which spatial and demographic characteristics most contribute to the disease spread and whether the progression of the disease can be slowed by appropriate vaccination of people belonging to a specific location-type.
Date: November 17, 2002
Creator: Smallwood, J. (Jeanine); Hyman, J. M. (James M.) & Mirchandani, Pitu B.
Partner: UNT Libraries Government Documents Department

Coupling of Realistic Rate Estimates with Genomics for Assessing Contaminant Attenuation and Long-Term Plume Containment

Description: Acceptance of monitored natural attenuation (MNA) as a preferred treatment technology saves significant site restoration costs for DOE. However, in order to be accepted MNA requires direct evidence of which processes are responsible for the contaminant loss and also the rates of the contaminant loss. Our proposal aims to: 1) provide evidence for one example of MNA, namely the disappearance of the dissolved trichloroethylene (TCE) from the Snake River Plain aquifer (SRPA) at the Idaho National Laboratory’s Test Area North (TAN) site, 2) determine the rates at which aquifer microbes can co-metabolize TCE, and 3) determine whether there are other examples of natural attenuation of chlorinated solvents occurring at DOE sites. To this end, our research has several objectives. First, we have conducted studies to characterize the microbial processes that are likely responsible for the co-metabolic destruction of TCE in the aquifer at TAN (University of Idaho and INL). Second, we are investigating realistic rates of TCE co-metabolism at the low catabolic activities typical of microorganisms existing under aquifer conditions (INL). Using the co-metabolism rate parameters derived in low-growth bioreactors, we will complete the models that predict the time until background levels of TCE are attained in the aquifer at TAN and validate the long-term stewardship of this plume. Coupled with the research on low catabolic activities of co-metabolic microbes we are determining the patterns of functional gene expression by these cells, patterns that may be used to diagnose the co-metabolic activity in the SRPA or other aquifers. Third, we have systematically considered the aquifer contaminants at different locations in plumes at other DOE sites in order to determine whether MNA is a broadly applicable remediation strategy for chlorinated hydrocarbons (North Wind Inc.). Realistic terms for co-metabolism of TCE will provide marked improvements in DOE’s ability to predict and monitor ...
Date: September 1, 2005
Creator: Colwell, F. S.; Crawford, R. L. & Sorenson, K.
Partner: UNT Libraries Government Documents Department

Report on the Imaging Workshop for the Genomes to Life Program, April 16-18, 2002

Description: This report is a result of the Imaging Workshop for the Genomes to Life (GTL) program held April 16-19, 2002, in Charlotte, North Carolina. The meeting was sponsored by the Office of Biological and Environmental Research and the Office of Advanced Scientific Computing Research of the U.S. Department of Energy's (DOE) Office of Science. The purpose of the workshop was to project a broad vision for future needs and determine the value of imaging to GTL program research. The workshop included four technical sessions with plenary lectures on biology and technology perspectives and technical presentations on needs and approaches as they related to the following areas of the GTL program: (1) Molecular machines (protein complexes); (2) Intracellular and cellular structure, function, and processes; (3) Multicellular: Monoclonal and heterogeneous multicellular systems, cell-cell signaling, and model systems; and (4) Cells in situ and in vivo: Bacteria in the natural environment, microenvironment, and in vivo systems.
Date: August 4, 2003
Creator: Colson, STEVEN
Partner: UNT Libraries Government Documents Department