Considerable evidence exists that the majority of low tension water flow through highly structured clayey soil occurs in a small fraction of total pore space and that the flow paths converge as depth increases. In structured clayey soils, water tends to flow in locations where macroporosity is high and roots tend to enjoy this condition as well. Water reduces the strength and mechanical impedance of the soil. Mechanical impedance of clayey soils tends to be extremely high when the soils are dry so one might expect that there would be a positive spatial correlation between the location of roots and the location of water flow paths in highly structured clayey soils. Understanding the relationship between the location of roots in soil relative to the location of water flow paths is important in understanding how plants obtain nutrients and water for growth, and it would also be of considerable importance in phytoremediation research and research into the prevention of groundwater contamination. This experiment was designed to map the locations of flow paths and roots and then measure the spatial association of the two. A pasture on Ship’s clay along the Brazos River was chosen as the research site. Three plots were irrigated with an Erioglaucine dye solution used to stain flow paths. After irrigation the soil was excavated to a depth of 25 cm. On the resulting horizontal plane the dye stain pattern was mapped using photography. The locations of roots were mapped on clear plastic sheets. During mapping the roots were categorized by size. The mapping procedure was repeated at depth of 45 cm and 75 cm for all plots. The root maps were overlaid on the photographic images and analyzed for a spatial association. There was no evidence the smallest (> 1 mm diameter) roots were not randomly distributed. The results did show that the larger roots were not randomly distributed, and evidence pointed to a clustering of roots in and around the dye stained flow paths. However, the data fell short of establishing a spatial association. The lack of more conclusive data was likely the result of inaccuracies in the mapping.

A low-clay version of fine translucent china was designed to have desired properties and acceptable behaviour during manufacture. Low-clay contents of 10 to ISw/o were employed to reduce the deterious effects of preferential clay particle alignment and its adverse effect on colour. For example, alignment of clay particles in cast wares causes anisotropic drying and firing shrinkages and these cause distortion. Replacing clay with a pre fired body with low Fe and Ti contents, as in the present case, allowed a very white material to be produced. The prefired body was made with calcium carbonate, aluminium trihydroxide, quartz and a small fluxing addition of an hydrated magnesIUm carbonate. Desification of a whiteware is enhanced by increasing volume fraction of the viscous liquid and reducing by its viscosity. Both of these also enhance sagging. Consequently, compositional change cannot on its own lead to the favourable combination of high density, required to give translucency, with little sagging, that will allow wares to be fired without significant distortion. It was found by trail and error that use of finer particles reduced the sagging occurring in the densification heat treatment and enhanced densification. This finding allowed the body to be designed so that it densified without sagging excessively. After establishing this important result, an iterative approach was employed to produce a ware that was very white, translucent, had the required thermal expansion coefficient for glaze fitting, shrank acceptably during the first firing and did not sag during the second firing that stimulated glost firing. The finding on sagging was applied to an anorthite/mullite porcelain body that was under development. This body was also made with a low-clay content and the same prefired body. This whitware has potential to replace bone china and hard porcelain for use in the servere service conditions of hotels and restaurants. It has a higher fracture toughness than hard porcelain but has the same scratch resistant glaze and is more resistant to thermal shock. The sagging of the anorthite/mullite porcelain was substantially reduced while the body was densified. This was achieved by using a combination of finer particles and a reduction in the liquid-phase content that developed during firing.

Genes are typically expressed in equal amounts from both parentally inherited chromosomes. However, recent studies have demonstrated that genes can be preferentially transcribed from a locus. Non-random preferential expression of alleles can occur in a parent-of-origin pattern, known as imprinting, where epigenetic factors regulate their transcription. Alternatively, it can occur in a haplotype-specific pattern, where cis-acting polymorphisms in regulatory regions are thought to underlie the phenomenon. Both forms of unequal allelic expression have been associated with human disease. Consequently, it is important to identify genes subject to unequal allelic expression and characterize mechanisms that regulate differential transcription. This thesis presents the results of a screen for unequal allelic expression where approximately 50 murine transcripts homologous to genes on human chromosome 7 were analyzed. Human chromosome 7 was selected due to its association with several human disorders that show parent-of-origin effects. The screen identified non-imprinted preferential allelic expression in numerous transcripts and demonstrated that such patterns can occur in tissue specific patterns. Paraoxonase-1 (Pon1), a gene implicated in arthrosclerosis, was identified as having a dynamic pattern of allelic expression which varies throughout embryonic development. This finding represents the first report of a developmentally regulated pattern of allelic variance. Carboxypeptidase-A4 (Cpa4) was identified as having a tissue-specific imprinted pattern of expression, where the maternal allele was preferentially expressed in all embryonic tissues, with the exception of the brain. The Krüppel-like factor 14 gene (Klf14), a novel imprinted transcript, was found to have ubiquitous maternal expression in all human and murine tissues analyzed. A differentially methylated region, generally associated with imprinted transcripts, was not found in the gene’s CpG island, nor was a differential pattern of histone modifications identified. However, it was determined that maternal methylation regulates the transcript. The data in this thesis contribute to our understanding of the numerous patterns of allelic expression that exist in nature and the diverse mechanisms that regulate them. Ultimately, quantitative analyses of allelic expression patterns and the identification of their underlying genomic DNA sequences will become standard protocol in all biomedical studies.

No description available.

Preferential attachment networks with power law degree sequence undergo a phase transition when the power law exponent τ changes. For τ > 3 typical distances in the network are logarithmic in the size of the network and for 2 < τ < 3 they are doubly logarithmic. In this thesis, we identify the correct scaling constant for τ ∈ (2, 3) and discover a surprising dichotomy between preferential attachment networks and networks without preferential attachment. This contradicts previous conjectures of universality. Moreover, using a model recently introduced by Dereich and Mörters, we study the critical behaviour at τ = 3, and establish novel results for the scale of the typical distances under lower order perturbations of the attachment function.

We present a statistical mechanical approach for quantifying thermodynamic properties of proteins in mixed solvents. This approach, based on molecular dynamics simulations which incorporate all atom models and the theory of preferential binding, allows us to compute transfer free energies with experimental accuracy and does not incorporate any adjustable parameters. Specifically, we applied our approach to the model proteins RNase A and T1, and the solvent components water, glycerol, and urea. We found that the observed differences in the binding of glycerol and urea to RNase T1 and A are predominantly a consequence of density differences in the first coordination shell of the protein with the cosolvents, but the second solvation shell also contributes to the overall binding coefficients. The success of this approach in modeling preferential binding indicates that it incorporates the important underlying physics of proteins in mixed solvent systems and that the difficulty in quantitative prediction to date can be surmounted by explicitly incorporating the complex protein-solvent and solvent-solvent interactions. / Singapore-MIT Alliance (SMA)

To predict the effectiveness of land reclamation, it is important to understand how water and solutes are transported within reconstructed landscapes. The objective of this study was to examine the influence of preferential flow on salt leaching in reclamation soil covers. The study site was a reconstructed landscape where saline-sodic minespoil from oil sands mining was capped with layers of glacial and peat mix soil. Preferential flow was investigated using laboratory column experiments and in situ adsorptive dye and conservative tracer experiments.<p> Results from column experiments and dye tracer experiments indicate that preferential flow is an important and prevalent mechanism of solute transport. Column experiments, which used time-domain reflectometry to monitor the transport of a chloride tracer through an undisturbed core of peat mix soil, determined immobile water fractions (èim/è) ranging from 80-99% and diffusive mass transfer rates (á) between 0.15 - 2.0 h-1. Breakthrough curves showed the early arrival of chloride and extended tailing. Dye tracer experiments, in which Brilliant Blue dye was applied in solution to the soil surface, were carried out at 6 hillslopes plots. Approximately 24 hours after dye application, a vertical soil face was excavated to reveal stained flow patterns. Preferential flow as macropore flow, fingering, and / or funneling was observed at each plot.<p> Results from the conservative tracer field study indicated soil solutes were flushed by a combination of vertical and lateral flow processes. A large pulse of bromide and chloride was applied across the lower slope of the 0.35-m cover. Soil sampling at approximately 1 and 2 years later determined vertical leaching, lateral translocation downslope, and upwards movement of soil solutes. Matrix flow during the spring melt, combined with matrix flow and / or preferential flow during summer and fall periods, was responsible for the vertical leaching of solutes. Subsurface flow generated in response to the spring melt or due to differences in soil hydraulic conductivity was responsible for the lateral transport of solutes. As a result of advective or diffusive processes, solutes were transported upwards into the overlying soil. These results suggested that despite the existence of preferential flow, there were other mechanisms of solute transport which served to leach and flush salts from the soil.

To predict the effectiveness of land reclamation, it is important to understand how water and solutes are transported within reconstructed landscapes. The objective of this study was to examine the influence of preferential flow on salt leaching in reclamation soil covers. The study site was a reconstructed landscape where saline-sodic minespoil from oil sands mining was capped with layers of glacial and peat mix soil. Preferential flow was investigated using laboratory column experiments and in situ adsorptive dye and conservative tracer experiments.<p> Results from column experiments and dye tracer experiments indicate that preferential flow is an important and prevalent mechanism of solute transport. Column experiments, which used time-domain reflectometry to monitor the transport of a chloride tracer through an undisturbed core of peat mix soil, determined immobile water fractions (èim/è) ranging from 80-99% and diffusive mass transfer rates (á) between 0.15 - 2.0 h-1. Breakthrough curves showed the early arrival of chloride and extended tailing. Dye tracer experiments, in which Brilliant Blue dye was applied in solution to the soil surface, were carried out at 6 hillslopes plots. Approximately 24 hours after dye application, a vertical soil face was excavated to reveal stained flow patterns. Preferential flow as macropore flow, fingering, and / or funneling was observed at each plot.<p> Results from the conservative tracer field study indicated soil solutes were flushed by a combination of vertical and lateral flow processes. A large pulse of bromide and chloride was applied across the lower slope of the 0.35-m cover. Soil sampling at approximately 1 and 2 years later determined vertical leaching, lateral translocation downslope, and upwards movement of soil solutes. Matrix flow during the spring melt, combined with matrix flow and / or preferential flow during summer and fall periods, was responsible for the vertical leaching of solutes. Subsurface flow generated in response to the spring melt or due to differences in soil hydraulic conductivity was responsible for the lateral transport of solutes. As a result of advective or diffusive processes, solutes were transported upwards into the overlying soil. These results suggested that despite the existence of preferential flow, there were other mechanisms of solute transport which served to leach and flush salts from the soil.

Genes are typically expressed in equal amounts from both parentally inherited chromosomes. However, recent studies have demonstrated that genes can be preferentially transcribed from a locus. Non-random preferential expression of alleles can occur in a parent-of-origin pattern, known as imprinting, where epigenetic factors regulate their transcription. Alternatively, it can occur in a haplotype-specific pattern, where cis-acting polymorphisms in regulatory regions are thought to underlie the phenomenon. Both forms of unequal allelic expression have been associated with human disease. Consequently, it is important to identify genes subject to unequal allelic expression and characterize mechanisms that regulate differential transcription. This thesis presents the results of a screen for unequal allelic expression where approximately 50 murine transcripts homologous to genes on human chromosome 7 were analyzed. Human chromosome 7 was selected due to its association with several human disorders that show parent-of-origin effects. The screen identified non-imprinted preferential allelic expression in numerous transcripts and demonstrated that such patterns can occur in tissue specific patterns. Paraoxonase-1 (Pon1), a gene implicated in arthrosclerosis, was identified as having a dynamic pattern of allelic expression which varies throughout embryonic development. This finding represents the first report of a developmentally regulated pattern of allelic variance. Carboxypeptidase-A4 (Cpa4) was identified as having a tissue-specific imprinted pattern of expression, where the maternal allele was preferentially expressed in all embryonic tissues, with the exception of the brain. The Krüppel-like factor 14 gene (Klf14), a novel imprinted transcript, was found to have ubiquitous maternal expression in all human and murine tissues analyzed. A differentially methylated region, generally associated with imprinted transcripts, was not found in the gene’s CpG island, nor was a differential pattern of histone modifications identified. However, it was determined that maternal methylation regulates the transcript. The data in this thesis contribute to our understanding of the numerous patterns of allelic expression that exist in nature and the diverse mechanisms that regulate them. Ultimately, quantitative analyses of allelic expression patterns and the identification of their underlying genomic DNA sequences will become standard protocol in all biomedical studies.

A superpattern is a string of characters of length n that contains as a subsequence, and in a sense that depends on the context, all the smaller strings of length k in a certain class. We prove structural and probabilistic results on superpatterns for preferential arrangements, including (i) a theorem that demonstrates that a string is a superpattern for all preferential arrangements if and only if it is a superpattern for all permutations; and (ii) a result that is reminiscent of a still unresolved conjecture of Alon on the smallest permutation on [n] that contains all k-permutations with high probability.