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Time-windows-based filtering method for near-surface detection of leakage from geologic carbon sequestration sites

Description: We use process-based modeling techniques to characterize the temporal features of natural biologically controlled surface CO{sub 2} fluxes and the relationships between the assimilation and respiration fluxes. Based on these analyses, we develop a signal-enhancing technique that combines a novel time-window splitting scheme, a simple median filtering, and an appropriate scaling method to detect potential signals of leakage of CO{sub 2} from geologic carbon sequestration sites from within datasets of net near-surface CO{sub 2} flux measurements. The technique can be directly applied to measured data and does not require subjective gap filling or data-smoothing preprocessing. Preliminary application of the new method to flux measurements from a CO{sub 2} shallow-release experiment appears promising for detecting a leakage signal relative to background variability. The leakage index of ?2 was found to span the range of biological variability for various ecosystems as determined by observing CO{sub 2} flux data at various control sites for a number of years.
Date: February 28, 2010
Creator: Pan, L.; Lewicki, J.L.; Oldenburg, C.M. & Fischer, M.L.
Partner: UNT Libraries Government Documents Department

Measurement of background translocation frequencies in individuals with clones

Description: In the leukemia case the unseparated B and T lymphocytes had a high translocation frequency even after 0.0014, respectively. After purging all clones from the data, the translocation frequencies for Bio 8 and Bio 23 were 0.00750.0014 and 0.0073 metaphases were scored for chromosomal aberrations,, specifically reciprocal translocations, using fluorescence in situ hybridization (FISH). Metaphase spreads were used from two healthy, unexposed individuals (not exposed to radiation, chemotherapy or radiotherapy) and one early B- precursor acute lymphocytic leukemia (ALL) patient (metaphase spreads from both separated T lymphocytes and unseparated B and T lymphocytes were scored). All three individuals had an abnormally high translocation frequency. The high translocation frequencies resulted from clonal expansion of specific translocated chromosomes. I show in this thesis that by purging (discounting or removing) clones from the data of unexposed individuals, one can obtain true background translocation frequencies. In two cases, Bio 8 and Bio 23, the measured translocation frequency for chromosomes 1, 2 and 4 was 0.0124 purging all of the clones from the data. This high translocation frequency may be due to a low frequency of some clones and may not be recognized. The separated T lymphocytes had a higher translocation frequency than expected.
Date: August 1, 1996
Creator: Wade, M.J.
Partner: UNT Libraries Government Documents Department

A test of aquatic macroinvertebrate sub-sampling using a gridded screen

Description: The Biological Resource Evaluations Team of Los Alamos National Laboratories assessed the reliability of a gridded screen sub-sampling technique to estimate aquatic macroinvertebrates in total samples. Benthic macroinvertebrates were collected by kick sampling three riffles areas in Guaje Canyon, Los Alamos County, New Mexico during July and August, 1994. The study included 4,144 macroinvertebrates from samples consisting of 442 to 1005 individuals. The entire samples were spread onto a gridded screen, and 100 macroinvertebrates were randomly selected for identification. To simplify the results, identified macroinvertebrates were assigned to one of six categories: plecoptera, ephemeroptera, trichoptera, coleoptera, diptera, and non-insects. Three sub-samples were taken from each of six full samples. These counts were used as predicted values, while the total sample counts were used as actual values. Single-factor ANOVA tests showed no significant differences between predicted to actual (PTA) values. However, PTA differences indicated that lab-sorting was a more reliable method than live-sorting without a narcotizing agent. Large samples and large numbers in macroinvertebrate categories were tentatively linked with greater PTA differences. PTA differences were less than 5% in 80% of our trials and less than 10% in 95% of our trials. Despite the relatively small size of sub-samples, sub-samples included 60% of taxa found in the total samples. This sub-sampling technique provides accurate estimates of total sample composition in stream reaches rich enough to easily yield the required 100 individuals.
Date: December 31, 1994
Creator: Cross, S. P.
Partner: UNT Libraries Government Documents Department

Rates of ingestion and their variability between individual calanoid copepods: Direct observations

Description: The goals of this study were to determine rates of ingestion and fecal pellet release, and their variability, for individual planktonic copepods over extended periods of time (>20 min). Ingestions and rejections of individual cells of the diatom Thalassiosira eccentrica by a adult females of the calanoid Paracalanus aculeatus were directly quantified by observing individual copepods continuously at cell concentrations ranging from 0.1 to 1.2 mm{sup 3} l{sup {minus}1}. Average ingestion rates increased with increasing food concentration, but were not significantly different between 0.3 and 1.0 mm{sup 3} l{sup {minus}1} (9.8 and 32.7 {mu}g Cl{sup {minus}1}) of T.eccentrica. Rates of cell rejections were low and similar at 0.1 and 0.3. but were significantly higher at 1.0 mm{sup 3} l{sup {minus}1}. The coefficients of variation for average ingestion rates of individual copepods hardly differed between food concentrations, ranging from 17 to 22%, and were close to those for average fecal pellet release intervals which ranged from 15 to 21%. A comparison between individuals at each food concentration found no significant differences at 1.0; at 0.1 and 0.3 mm{sup 3} l{sup {minus}1}, respectively, ingestion rates of four out of five females did not differ significantly from each other. Average intervals between fecal pellet releases were similar at 0.3 and 1.0 mm{sup 3} l{sup {minus}1}. Fecal pellet release intervals between individuals were significantly different at each food concentration; these significant differences were attributed to rather narrow ranges of pellet release intervals of each individual female. Potential sources/causes of variability in the sizes and rates of copepods in the ocean are evaluated.
Date: December 1, 1995
Creator: Paffenhoefer, G.A.; Lewis, K.D.; Bundy, M.H. & Metz, C.
Partner: UNT Libraries Government Documents Department

Recent developments in ecological theory: hierarchy and scale

Description: Over the past decade, hierarchy and scale have been adopted as an ecological paradigm. Beyond this new awareness, however, a number of studies have attempted to test the underlying hierarchy theory and developed new analytical applications. The purpose of the present paper is to review these recent developments. Tests of the theory have focused on the prediction that ecological systems should not be uniformly distributed across scale, but grouped or lumped into discrete levels. The predicted breaks in spatial distribution have been found in vegetation transects. Vertebrate weight distributions are also distinctly aggregated, corresponding to the spatial scale at which each species operates. An important development of hierarchy theory has considered extrapolating information upscale. Simply stated, the dynamics of the higher level cannot be represented by the same functional form as its components. One cannot insert the mean parameter value for the components and predict higher level effects. Analytical methods, derived from hierarchy theory, have been developed deal with the problem.
Date: December 31, 1995
Creator: O`Neill, R.V.
Partner: UNT Libraries Government Documents Department

Cycle pattern of a R allelic variation. Progress report, 1 November 1978-31 January 1980

Description: Two R alleles vary in cycle fashion. The original, intensely pigmenting forms change to weakly acting ones which revert in turn to the original. Neither direction of change is correlated with recombination of flanking markers. The reversion frequencies do not differ from the respective frequencies of change in the forward direction. The changes are restricted in the life cycle to about the time of meiosis. Modifying tthe incidence of crossing over in the R region altered the frequency of reversion proportionately. These features of instability could result from switching by intrachromosomal recombination between alternative arrangements of an R segment associated with an inverted duplication.
Date: January 1, 1980
Creator: Kermicle, J.L.
Partner: UNT Libraries Government Documents Department

Visualization of monoamine oxidase in human brain

Description: Monoamine oxidase is a flavin enzyme which exists in two subtypes, MAO A and MAO B. In human brain MAO B predominates and is largely compartmentalized in cell bodies of serotonergic neurons and glia. Regional distribution of MAO B was determined by positron computed tomography with volunteers after the administration of deuterium substituted [11C]L-deprenyl. The basal ganglia and thalamus exhibited the greatest concentrations of MAO B with intermediate levels in the frontal cortex and cingulate gyrus while lowest levels were observed in the parietal and temporal cortices and cerebellum. We observed that brain MAO B increases with are in health normal subjects, however the increases were generally smaller than those revealed with post-mortem studies.
Date: December 31, 1996
Creator: Fowler, J.S.; Volkow, N.D.; Wang, G.J.; Pappas, N.; Shea, C.; MacGregor, R.R. et al.
Partner: UNT Libraries Government Documents Department

Addendum to the 1996 Gunnison Monitoring Report for the Gunnison, Colorado Wetlands Mitigation Plan

Description: This document is an addendum to the 1996 Gunnison Monitoring Report for the Gunnison, Colorado, Wetlands Mitigation Report, dated July 1997. The purpose of this addendum is to: (1) modify how information on plant height and plant species criteria are presented; and (2) provide more detailed information regarding the evaluation of the bare ground criteria at the Camp Ketle site. The information in this addendum is provided at the request of the Bureau of Land Management to aid in future monitoring and evaluation of the wetland mitigation sites.
Date: October 1, 1997
Partner: UNT Libraries Government Documents Department

Report on the biological monitoring program for Bear Creek at the Oak Ridge Y-12 Plant, Oak Ridge, Tennessee, 1989-1994

Description: The Bear Creek Valley watershed drains the area surrounding several closed Oak Ridge Y-12 Plant waste disposal facilities. Past waste disposal practices in the Bear Creek Valley resulted in the contamination of Bear Creek and consequent ecological damage. Ecological monitoring by the Biological Monitoring and Abatement Program (BMAP) was initiated in the Bear Creek watershed in May 1984 and continues at present. Studies conducted during the first year provided a detailed characterization of the benthic invertebrate and fish communities in Bear Creek. The initial characterization was followed by a biological monitoring phase in which studies were conducted at reduced intensities.
Date: April 1, 1996
Creator: Hinzman, R.L.; Beauchamp, J.J.; Cada, G.F. & Peterson, M.J.
Partner: UNT Libraries Government Documents Department

Biochemical and biophysical characterization of the major outer surface protein, OSP-A from North American and European isolates of Borrelia burgdorferi

Description: Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne disease in North America and Western Europe. As the major delayed immune response in humans, a better understanding of the major outer surface lipoproteins OspA and OspB are of much interest. These proteins have been shown to exhibit three distinct phylogenetic genotypes based on their DNA sequences. This paper describes the cloning of genomic DNA for each variant and amplification of PCR. DNA sequence data was used to derive computer driven phylogenetic analysis and deduced amino acid sequences. Overproduction of variant OspAs was carried out in E. coli using a T7-based expression system. Circular dichroism and fluorescence studies was carried out on the recombinant B31 PspA yielding evidence supporting a B31 protein containing 11% alpha-helix, 34% antiparallel beta-sheet, 12% parallel beta sheet.
Date: December 31, 1995
Creator: McGrath, B.C.; Dunn, J.J.; France, L.L.; Jaing, W.; Polin, D.; Gorgone, G. et al.
Partner: UNT Libraries Government Documents Department

Uncertainties in Organ Burdens Estimated from PAS

Description: To calculate committed effective dose equivalent, one needs to know the quantity of the radionuclide in all significantly irradiated organs (the organ burden) as a function of time following the intake. There are two major sources of uncertainty in an organ burden estimated from personal air sampling (PAS) data: (1) The uncertainty in going from the exposure measured with the PAS to the quantity of aerosol inhaled by the individual, and (2) The uncertainty in going from the intake to the organ burdens at any given time, taking into consideration the biological variability of the biokinetic models from person to person (interperson variability) and in one person over time (intra-person variability). We have been using biokinetic modeling methods developed by researchers at the University of Florida to explore the impact of inter-person variability on the uncertainty of organ burdens estimated from PAS data. These initial studies suggest that the uncertainties are so large that PAS might be considered to be a qualitative (rather than quantitative) technique. These results indicate that more studies should be performed to properly classify the reliability and usefulness of using PAS monitoring data to estimate organ burdens, organ dose, and ultimately CEDE.
Date: February 2, 2004
Creator: La Bone, T.R.
Partner: UNT Libraries Government Documents Department

Study of mathematical models of mutation and selection in multi-locus systems. Annual progress report, October 1, 1980-September 30, 1981

Description: During the past year, research has been devoted to two related studies of two-locus systems under natural selection and one on selection in haplo-diploid organisms. The principal results are: (1) Numerical studies were made of 2 locus selection models with asymmetric fitnesses. These were created by perturbing the fitness matrices of symmetric models whose results are known analytically. A complete classification of solved models has been made and all perturbations of these have been undertaken. The result is that all models lead to three classes of equilibrium structure. All are characterized by multiple equilbria with small linkage disequilibria under loose linkage and high complementarity equilibria under tight linkage. In some cases there is gene fixation at intermediate linkage. (2) It has been shown that selection may favor more recombination, contrary to the usual expectation, if multiple locus polymorphisms are maintained by a mechanism other than marginal overdominance. This may be the result of mutation-selection balance or frequency-dependent selection. (3) In a haplo-diploid system in which diploid males are lethal (as in bees and braconid wasps) the number of sex alleles that can be maintained depends both on breeding size and the number of colonies. Simulations show that the steady number is sensitive to the number of colonies but insensitive to the number of matings. Thirty-five to fifty colonies are sufficient to maintain very large numbers of sex alleles.
Date: January 1, 1981
Creator: Lewontin, R C
Partner: UNT Libraries Government Documents Department

Analyses of inter- and intra-patient variation in the V3 loop of the HIV-1 envelope protein

Description: The third hypervariable domain of the HIV-1 gp120 envelope protein (V3) has been the focus of intensive sequencing efforts. To date, nearly one thousand V3 loop sequences have been stored in the HIV sequence database. Studies have revealed that the V3 loop elicits potent type-specific immune responses, and that it plays a significant role in cell tropism and fusion . The immunogenic tip of the loop can serve as a type-specific neutralizing antibody epitope, as well as a cytotoxic T-cell epitope. A helper T-cell epitope that lies within the amino terminal half of the V3 loop has also been characterized. Despite the richness of the immunologic response to this region, its potential for variation makes it an elusive target for vaccine design. Analyses of sibling sequence sets (sets of viral sequences derived from one person) show that multiple forms of the immunogenic tip of the loop are found within most HIV-1 infected individuals. Viral V3 sequences obtained from epidemiologically unlinked individuals from North America and Europe show extensive variation. However, some amino acid positions distributed throughout the V3 loop are highly conserved, and there is also conservation of the charge class of amino acid able to occupy certain positions relative to the tip of the loop. By contrast, the sequences obtained from many countries throughout the African continent reveal that V3 is a remarkably fluid region with few absolute constraints on the nature of the amino acids that can occupy most positions in the loop. The high degree of heterogeneity in this region is particularly striking in view of its contribution to biologically important viral functions.
Date: September 17, 1991
Creator: Korber, B.; Myers, G. & Wolinsky, S.
Partner: UNT Libraries Government Documents Department

Enzymatic studies of radiation damage

Description: Progress is reported on studies related to molecular mechanisms for radiation damage to cells. Mung bean nuclease was shown to excise the A + T rich regions from different species of DNA exposed to premelting temperatures. This suggests an additional application of mung bean nuclease as a means of detection of slightly damaged reglons of DNA. A new sensitive method for the determination of nucleoside monophosphates and nucleoside 3', 5'-diphosphates was developed. The method was applied to the determination of the frequency of nucleosides appearing in the terminal position of an oligonucleotide. An argument serves biological unity of all nucaeases is presented. (auth)
Date: January 1, 1974
Creator: Laskowski, M Sr
Partner: UNT Libraries Government Documents Department

Direct effects of cold shock: bioassays with three Columbia River organisms

Description: Results of studies of the direct effects of cold shock on the pumpkinseed sunfish (representing a warmwater fish), the rainbow trout (representing a coldwater fish), and the common crayfish showed that resistance to cold shock varies between species, is dependent on acclimation temperature, and resistance to temperature declines is dependent on the decline rate. Severe cold shock at a sublethal level is accompanied by disorientation, loss of equilibrium, and immobilization. Pumpkinseed, the warm water species, are most susceptible. Rainbow, the cold water species, are less susceptible; at an acclimation 10$sup 0$C, rainbow survive abrupt shock to levels slightly above freezing. Crayfish, the decapod crustacean, are most resistant; at an acclimation of 15$sup 0$C, crayfish survive abrupt shock to the point just above freezing. (CH)
Date: January 1, 1975
Creator: Becker, C.D. & Schneider, M.J.
Partner: UNT Libraries Government Documents Department

International workshop of chromosome 19

Description: This document summarizes the workshop on physical and genetic mapping of chromosome 19. The first session discussed the major disease loci found on the chromosome. The second session concentrated on reference families, markers and linkage maps. The third session concentrated on radiation hybrid mapping, somatic cell hybrid panels, macro restriction maps and YACs, followed by cDNA and long range physical maps. The fourth session concentrated on compiling consensus genetic and physical maps as well as discussing regions of conflict. The final session dealt with the LLNL cosmid contig database and comparative mapping of homologous regions of the human and mouse genomes, and ended with a discussion of resource sharing. 18 refs., 2 figs. (MHB)
Date: September 16, 1991
Creator: Pericak-Vance, M.A. (Duke Univ. Medical Center, Durham, NC (United States). Div. of Neurology) & Carrano, A.J. (Lawrence Livermore National Lab., CA (United States))
Partner: UNT Libraries Government Documents Department

Relationships between histone phosphorylation and cell proliferation

Description: From studies with various Peromyscus cell lines, correlations were made which led to the proposal that H2A phosphorylation is most active in constitutive heterochromatin. Recent studies on the two H2A variants found in these cells have revealed that the high level of H2A phosphorylation associated with heterochromatin is not the result of an increase in H2A phosphorylation rate or an increase in the number of phosphorylation sites, but rather, is due to an increase in the proportion of one of the H2A variants which is more highly phosphorylated than the other. If H2A phosphorylation is necessary for the constitutive heterochromatin state, it is reasonable that the cell would accomplish the generation of this structure by permanently installing a more highly phosphorylated H2A in the heterochromatin nucleosome rather than by trying to modulate the phosphorylation rate in such a condensed structure. The proposal that histone phosphorylation is involved with the condensed structures of chromatin is based primarily on correlations between histone phosphorylation measurements and cellular phenomena. One proof that this concept is correct ultimately rests in the ability to demonstrate these correlations in isolated chromosomes and chromatin fractions. This demonstration is presently limited by the excessive dephosphorylation of histones which occurs during the isolation of chromosomes and chromatin fractions. Thus, the demonstration of an effective inhibitor of histone dephosphorylation which is compatible with the isolation of nuclear structures and chromatin fractions having native morphologies is essential for future studies on the biological function of histone phosphorylation. (ERB)
Date: January 1, 1980
Creator: Gurley, L.R.; D'Anna, J.A.; Halleck, M.S.; Barham, S.S.; Walters, R.A.; Jett, J.H. et al.
Partner: UNT Libraries Government Documents Department

HIV envelope drift

Description: The consensus sequences for (HIV) the Human Immunodeficiency Virus,envelope proteins can also be examined with regard to what might be called differential drift. Conserved and hypervariable regions, or domains, of the envelope were defined in 1986, when the extent of conspicuous HIV variation began to be noticed. Although a large fraction of the envelope residues are subject to drift, once substition at some particular site begins, constraints will most likely naturally arise in relation to which residues will admit of substitution thereafater. Thus, we should not expect that the type 1 and type 2 HIVs will manifest identical patterns of conservation and hypervariability. They already reveal significant differences in the number of cysteine residues, for example; although it is far less obvious, there is some indication that with the sequences analyzed thus far that the Zairean and North American HIVs may be differentially drifting as a direct consequence of their high rates of diversification. What makes this case of drift so extraordinary is the rapid pace which appears to be characteristic of the HIV speciation, stemming from not merely the high mutation rate, but also from proliferation in what might be for these viruses a relatively new ecological niche. 3 figs.
Date: January 1, 1988
Creator: Myers, G.
Partner: UNT Libraries Government Documents Department

HIV-1 sequence variation between isolates from mother-infant transmission pairs

Description: To examine the sequence diversity of human immunodeficiency virus type 1 (HIV-1) between known transmission sets, sequences from the V3 and V4-V5 region of the env gene from 4 mother-infant pairs were analyzed. The mean interpatient sequence variation between isolates from linked mother-infant pairs was comparable to the sequence diversity found between isolates from other close contacts. The mean intrapatient variation was significantly less in the infants' isolates then the isolates from both their mothers and other characterized intrapatient sequence sets. In addition, a distinct and characteristic difference in the glycosylation pattern preceding the V3 loop was found between each linked transmission pair. These findings indicate that selection of specific genotypic variants, which may play a role in some direct transmission sets, and the duration of infection are important factors in the degree of diversity seen between the sequence sets.
Date: January 1, 1991
Creator: Wike, C.M.; Daniels, M.R.; Furtado, M.; Wolinsky, M.; Korber, B.; Hutto, C. et al.
Partner: UNT Libraries Government Documents Department

Analyses of inter- and intra-patient variation in the V3 loop of the HIV-1 envelope protein

Description: The third hypervariable domain of the HIV-1 gp120 envelope protein (V3) has been the focus of intensive sequencing efforts. To date, nearly one thousand V3 loop sequences have been stored in the HIV sequence database. Studies have revealed that the V3 loop elicits potent type-specific immune responses, and that it plays a significant role in cell tropism and fusion . The immunogenic tip of the loop can serve as a type-specific neutralizing antibody epitope, as well as a cytotoxic T-cell epitope. A helper T-cell epitope that lies within the amino terminal half of the V3 loop has also been characterized. Despite the richness of the immunologic response to this region, its potential for variation makes it an elusive target for vaccine design. Analyses of sibling sequence sets (sets of viral sequences derived from one person) show that multiple forms of the immunogenic tip of the loop are found within most HIV-1 infected individuals. Viral V3 sequences obtained from epidemiologically unlinked individuals from North America and Europe show extensive variation. However, some amino acid positions distributed throughout the V3 loop are highly conserved, and there is also conservation of the charge class of amino acid able to occupy certain positions relative to the tip of the loop. By contrast, the sequences obtained from many countries throughout the African continent reveal that V3 is a remarkably fluid region with few absolute constraints on the nature of the amino acids that can occupy most positions in the loop. The high degree of heterogeneity in this region is particularly striking in view of its contribution to biologically important viral functions.
Date: September 17, 1991
Creator: Korber, B.; Myers, G. (Los Alamos National Lab., NM (United States)) & Wolinsky, S. (Northwestern Univ., Chicago, IL (United States). Medical School)
Partner: UNT Libraries Government Documents Department