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Multiscale integration schemes for jump-diffusion systems

Description: We study a two-time-scale system of jump-diffusion stochastic differential equations. We analyze a class of multiscale integration methods for these systems, which, in the spirit of [1], consist of a hybridization between a standard solver for the slow components and short runs for the fast dynamics, which are used to estimate the effect that the fast components have on the slow ones. We obtain explicit bounds for the discrepancy between the results of the multiscale integration method and the slow components of the original system.
Date: December 9, 2008
Creator: Givon, D. & Kevrekidis, I.G.
Partner: UNT Libraries Government Documents Department

DNA-DNA Hybridization of Methane Oxidizing Bacteria

Description: Bacteria classified in the family Methylomonadaceae must derive their carbon from one-carbon compounds. They are characterized by the possession of internal membranes of two types. Type I membranes are layered and fill the middle of the cells while type II membranes form concentric layers around the periphery of the cells. Also, there are two metabolic pathways by which the methylobacteria assimilate one-carbon compounds. Further evidence of this dichotomy was sought by DNA-DNA saturation hybridization of DNAs from both types of methylobacteria. Very low DNA-DNA homology was seen between types I and II or within the types. It was not possible, therefore, to correlate the degree of genetic relatedness with either the nature of the internal membranes or the pathway of carbon assimilation.
Date: December 1976
Creator: Ackerson, Jill W.
Partner: UNT Libraries

Final Report on ``Theories of Strong Electron Correlations in Molecules and Solids’’ - DE-FG02-97ER45640

Description: The PI led theoretical studies of correlated hybridization in transition metal complexes, compounds, and molecules, and of electron transport in DNA associated with nanoelectronic conformations attached to gold electrodes and in the presence of DNA repair proteins.
Date: April 15, 2013
Creator: Cox, Daniel L.
Partner: UNT Libraries Government Documents Department

Novel Fabrication and Simple Hybridization of Exotic Material MEMS

Description: Work in materials other than silicon for MEMS applications has typically been restricted to metals and metal oxides instead of more ''exotic'' semiconductors. However, group III-V and II-VI semiconductors form a very important and versatile collection of material and electronic parameters available to the MEMS and MOEMS designer. With these materials, not only are the traditional mechanical material variables (thermal conductivity, thermal expansion, Young's modulus, etc.) available, but also chemical constituents can be varied in ternary and quaternary materials. This flexibility can be extremely important for both friction and chemical compatibility issues for MEMS. In addition, the ability to continually vary the bandgap energy can be particularly useful for many electronics and infrared detection applications. However, there are two major obstacles associated with alternate semiconductor material MEMS. The first issue is the actual fabrication of non-silicon devices and the second impediment is communicating with these novel devices. We will describe an essentially material independent fabrication method that is amenable to most group III-V and II-VI semiconductors. This technique uses a combination of non-traditional direct write precision fabrication processes such as diamond turning, ion milling, laser ablation, etc. This type of deterministic fabrication approach lends itself to an almost trivial assembly process. We will also describe in detail the mechanical, electrical, and optical self-aligning hybridization technique used for these alternate-material MEMS.
Date: November 13, 1999
Creator: Datskos, P.G. & Rajic, S.
Partner: UNT Libraries Government Documents Department

Oncogene mRNA Imaging with Radionuclide-PNA-Peptides

Description: New cancer gene hybridization probes to carry radionuclides were made. Noninvasive technetium-99m gamma imaging of CCND1 cancer gene activity in human breast cancer tumors in mice was demonstrated, followed by noninvasive technetium-99m imaging of MYC cancer gene activity. Noninvasive imaging of CCND1 cancer gene activity in human breast cancer tumors in mice was demonstrated with a positron-emitting copper-64 probe, followed by noninvasive positron imaging of IRS1 cancer gene activity.
Date: March 19, 2008
Creator: Wickstrom, Eric
Partner: UNT Libraries Government Documents Department

Biosystematic Study of a Desmodium Complex

Description: An examination of the Desmodium canescens complex (D. canescens; D. tweedyi; D. illinoense) has resulted in the delimitation of a previously unreported alliance between D. canescens and D. tweedyi. The following points support this view: (a) morphological data taken from herbarium and garden specimens indicate that for many characters, the mean values of D. canescens and D. tweedy are not significantly different (b) breeding experiments have shown that artificial interspecific hybridization is possible between D. canescens and D. tweedyi (c) cytological studies have shown that D. canescens and D. tweedyi have a base number of x = 11, while D. illinoense has a base number of x = 10. A new combination is suggested: Desmodium canescens var. tweedyi (Britt.) Williams.
Date: December 1977
Creator: Williams, John G., 1949-
Partner: UNT Libraries

A common allele on chromosome 9 associated with coronary heartdisease

Description: Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.
Date: March 1, 2007
Creator: McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R. et al.
Partner: UNT Libraries Government Documents Department

Terahertz spectroscopy of two-dimensional subwavelength plasmonic structures

Description: The fascinating properties of plasmonic structures have had significant impact on the development of next generation ultracompact photonic and optoelectronic components. We study two-dimensional plasmonic structures functioning at terahertz frequencies. Resonant terahertz response due to surface plasmons and dipole localized surface plasmons were investigated by the state-of-the-art terahertz time domain spectroscopy (THz-TDS) using both transmission and reflection configurations. Extraordinary terahertz transmission was demonstrated through the subwavelength metallic hole arrays made from good conducting metals as well as poor metals. Metallic arrays m!lde from Pb, generally a poor metal, and having optically thin thicknesses less than one-third of a skin depth also contributed in enhanced THz transmission. A direct transition of a surface plasmon resonance from a photonic crystal minimum was observed in a photo-doped semiconductor array. Electrical controls of the surface plasmon resonances by hybridization of the Schottkey diode between the metallic grating and the semiconductor substrate are investigated as a function of the applied reverse bias. In addition, we have demonstrated photo-induced creation and annihilation of surface plasmons with appropriate semiconductors at room temperature. According to the Fano model, the transmission properties are characterized by two essential contributions: resonant excitation of surface plasmons and nonresonant direct transmission. Such plasmonic structures may find fascinating applications in terahertz imaging, biomedical sensing, subwavelength terahertz spectroscopy, tunable filters, and integrated terahertz devices.
Date: January 1, 2009
Creator: Azad, Abul K; Chen, Houtong; Taylor, Antoinette; O' Hara, John F; Han, Jiaguang; Lu, Xinchao et al.
Partner: UNT Libraries Government Documents Department

Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

Description: The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.
Date: January 15, 2008
Creator: Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M. et al.
Partner: UNT Libraries Government Documents Department

Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

Description: Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.
Date: December 16, 2008
Creator: Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly & Weier, Heinz-Ulli
Partner: UNT Libraries Government Documents Department

Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

Description: Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.
Date: December 4, 2008
Creator: Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F. & Weier, Heinz-Ulli G.
Partner: UNT Libraries Government Documents Department

Chromosomal mosaicism in mouse two-cell embryos after paternal exposure to acrylamide

Description: Chromosomal mosaicism in human preimplantation embryos is a common cause ofspontaneous abortions, however, our knowledge of its etiology is limited. We used multicolor fluorescence in situ hybridization (FISH) painting to investigate whether paternally-transmitted chromosomal aberrations result in mosaicism in mouse 2-cell embryos. Paternal exposure to acrylamide, an important industrial chemical also found in tobacco smoke and generated during the cooking process of starchy foods, produced significant increases in chromosomally defective 2-cell embryos, however, the effects were transient primarily affecting the postmeiotic stages of spermatogenesis. Comparisons with our previous study of zygotes demonstrated similar frequencies of chromosomally abnormal zygotes and 2-cell embryos suggesting that there was no apparent selection against numerical or structural chromosomal aberrations. However, the majority of affected 2-cell embryos were mosaics showing different chromosomal abnormalities in the two blastomeric metaphases. Analyses of chromosomal aberrations in zygotes and 2-cell embryos showed a tendency for loss of acentric fragments during the first mitotic division ofembryogenesis, while both dicentrics and translocations apparently underwent propersegregation. These results suggest that embryonic development can proceed up to the end of the second cell cycle of development in the presence of abnormal paternal chromosomes and that even dicentrics can persist through cell division. The high incidence of chromosomally mosaic 2-cell embryos suggests that the first mitotic division of embryogenesis is prone to missegregation errors and that paternally-transmitted chromosomal abnromalities increase the risk of missegregation leading to embryonic mosaicism.
Date: October 14, 2008
Creator: Marchetti, Francesco; Bishop, Jack; Lowe, Xiu & Wyrobek, Andrew J
Partner: UNT Libraries Government Documents Department

Design and analysis of mismatch probes for long oligonucleotide microarrays

Description: Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.
Date: August 15, 2008
Creator: Deng, Ye; He, Zhili; Van Nostrand, Joy D. & Zhou, Jizhong
Partner: UNT Libraries Government Documents Department

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

Description: The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation
Date: June 1, 2004
Creator: Chen, Chung, H.
Partner: UNT Libraries Government Documents Department

Highly specific electronic signal transduction mediated by DNA/metal self-assembly.

Description: Highly specific interactions between DNA could potentially be amplified if the DNA interactions were utilized to assemble large scale parts. Fluidic assembly of microsystem parts has the potential for rapid and accurate placement of otherwise difficult to handle pieces. Ideally, each part would have a different chemical interaction that allowed it to interact with the substrate only in specific areas. One easy way to obtain a multiple chemical permutations is to use synthetic DNA oligomers. Si parts were prepared using silicon-on-insulator technology microfabrication techniques. Several surface chemistry protocols were developed to react commercial oligonucleotides to the parts. However, no obvious assembly was achieved. It was thought that small defects on the surface did not allow the microparts to be in close enough proximity for DNA hybridization, and this was. in part, confirmed by interferometry. To assist in the hybridization, plastic, pliable parts were manufactured and a new chemistry was developed. However, assembly was still absent even with the application of force. It is presently thought that one of three mechanisms is preventing the assembly. The surfaces of the two solid substrates can not get in close enough proximity, the surface chemistry lacks sufficient density to keep the parts from separating, or DNA interactions in close proximity on solid substrates are forbidden. These possibilities are discussed in detail.
Date: November 1, 2003
Creator: Dentinger, Paul M. & Pathak, Srikant
Partner: UNT Libraries Government Documents Department