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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

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

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


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

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

Criticality safety evaluation - an endusers's perspective

Description: This paper presents criticality safety evaluations from an enduser's perspective. Overall issues related to a criticality safety evaluation in an operations support setting are discussed. A work flow process is presented which shows the key steps in conducting an effective criticality evaluation. Finally, a few suggestions are given to assist newcomers to this field.
Date: May 6, 1999
Creator: Huang, S T
Partner: UNT Libraries Government Documents Department

Feature article: adoption of an official ISEA glossary

Description: The International Society for Exposure Analysis (ISEA) and its Nomenclature Committee have been involved since the mid-1990s in an intermittent but ongoing effort to develop an official ISEA glossary. Several related activities have stimulated greater interest and discussion nationally and internationally on a common exposure language. Among these activities are a 1997 Journal of Exposure Analysis and Environmental Epidemiology feature article on exposure and dose definitions and a 1999-initiated project of the International Programme on Chemical Safety (IPCS) (WHO/ILO/UNEP) to confront terminology issues hindering harmonization in the area of exposure assessment. Recently the ISEA members voted in support of adopting the IPCS glossary as the official ISEA glossary, and the ISEA Executive Board agreed to accept this recommendation. In this feature article we (1) describe the process through which the ISEA adopted the IPCS glossary as the official ISEA glossary, (2) present the joint IPC S/ISEA glossary of terms and their definitions, and (3) discuss plans for how the glossary can be used by ISEA and updated over time by ISEA and IPCS. The glossary is intended to be a living document that reflects the latest usage and maintains international harmonization of exposure terminology that can be practically applied to improve communication in exposure and related fields.
Date: September 15, 2004
Creator: Zartarian, Valerie; Bahadori, Tina & McKone, Thomas
Partner: UNT Libraries Government Documents Department

Three Dimensional Molecular Imaging for Lignocellulosic Materials

Description: The development of high efficiency, inexpensive processing protocols to render biomass components into fermentable substrates for the sequential processing of cell wall components into fuels and important feedstocks for the biorefinery of the future is a key goal of the national roadmap for renewable energy. Furthermore, the development of such protocols depends critically on detailed knowledge of the spatial and temporal infiltration of reagents designed to remove and separate the phenylpropenoid heteropolymer (lignin) from the processable sugar components sequestered in the rigid cell walls of plants. A detailed chemical and structural understanding of this pre-enzymatic processing in space and time was the focus of this program. We worked to develop new imaging strategies that produce real-time molecular speciation information in situ; extract sub-surface information about the effects of processing; and follow the spatial and temporal characteristics of the molecular species in the matrix and correlate this complex profile with saccharification. Spatially correlated SIMS and Raman imaging were used to provide high quality, high resolution subcellular images of Miscanthus cross sections. Furthermore, the combination of information from the mass spectrometry and Raman scattering allows specific chemical assignments of observed structures, difficult to assign from either imaging approach alone and lays the foundation for subsequent heterocorrelated imaging experiments targeted at more challenging biological systems, such as the interacting plant-microbe systems relevant to the rhizosphere.
Date: June 9, 2011
Creator: Bohn, Paul W. & Sweedler, Jonathan V.
Partner: UNT Libraries Government Documents Department

Computation of Confidence Limits for Linear Functions of the Normal Mean and Variance

Description: A program is described that calculates exact and optimal (uniformly most accurate unbiased) confidence limits for linear functions of the normal mean and variance. The program can therefore also be used to calculate confidence limits for monotone transformations of such functions (e.g., lognormal means). The accuracy of the program has been thoroughly evaluated in terms of coverage probabilities for a wide range of parameter values.
Date: September 1, 1999
Creator: Land, C.E. & Lyon, B.F.
Partner: UNT Libraries Government Documents Department

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

Description: Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.
Date: July 15, 2010
Creator: Callister, S.J.; Wilkins, M.J.; Nicora, C.D.; Williams, K.H.; Banfield, J.F.; VerBerkmoes, N.C. et al.
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