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Imaging and Computational Methods for Exploring Sub-cellular AnatomyMayerich, David 16 January 2010 (has links)
The ability to create large-scale high-resolution models of biological tissue provides an
excellent opportunity for expanding our understanding of tissue structure and function.
This is particularly important for brain tissue, where the majority of function occurs at the
cellular and sub-cellular level. However, reconstructing tissue at sub-cellular resolution is
a complex problem that requires new methods for imaging and data analysis.
In this dissertation, I describe a prototype microscopy technique that can image large
volumes of tissue at sub-cellular resolution. This method, known as Knife-Edge Scanning
Microscopy (KESM), has an extremely high data rate and can capture large tissue samples
in a reasonable time frame. We can therefore image complete systems of cells, such as
whole small animal organs, in a matter of days.
I then describe algorithms that I have developed to cope with large and complex data
sets. These include methods for improving image quality, tracing filament networks, and
constructing high-resolution anatomical models. These methods are highly parallel and designed
to allow users to segment and visualize structures that are unique to high-throughput
microscopy data. The resulting models of large-scale tissue structure provide much more
detail than those created using standard imaging and segmentation techniques.
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Pore-scale analysis of thermal remediation of NAPL-contaminated subsurface environmentsAhn, Min 15 May 2009 (has links)
The possible benefits of thermal remediation of NAPL-contaminated subsurface
were analyzed at pore-scale. Force balance analysis was performed to provide the insight
and information on the critical conditions for the blob mobilization. First, the critical
blob radius for blob mobilization was calculated in terms of blob radius, temperature,
and water velocity. Temperature increase enhanced the blob mobilization along with the
decrease of interfacial tension. Water velocity increase also enhanced the blob
mobilization. Critical water velocity provided the critical condition for the initiation of
blob mobilization to distinguish singlet and doublet in blob size.
Second, the terminal (or steady state) blob velocity at the steady state blob motion
was determined. Increases of temperature and water velocity raised the terminal blob
velocity. When the observation of blob mobilization moved from REV scale (macroscale)
to pore-scale, terminal blob velocity showed the different phenomena according to
the change of oil saturation. At macro-scale, the terminal blob velocity was smaller than water velocity by an order or two. However, the terminal blob velocity reached to water
velocity at pore-scale.
This investigation would provide the better understanding on the pore-scale analysis
of residual NAPL blob mobilization by thermal remediation. Additionally, the pore-scale
analysis developed in this study would be incorporated into a general conservation
equation in terms of the accumulation of multiple blobs. It would derive continuumaveraged
equations that accurately represent pore-level physics. In conclusion, the study
on the critical conditions for the initiation of blob mobilization as a single discrete blob
would have some contribution to the transport and fate of NAPL contaminant and the
desired subsurface remediation.
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Laboratory Study Investigating the Three-dimensional Turbulence and Kinematic Properties Associated with a Breaking Solitary WaveSwigler, David Townley 2009 August 1900 (has links)
A laboratory experiment was performed to investigate the three-dimensional turbulence and kinematic properties that develop due to a breaking solitary and an irregular shallow water bathymetry. A large basin equipped with a piston-type wavemaker was used to generate the wave, while the free surface elevations and fluid velocities were measured using wave gauges and three-dimensional acoustic-Doppler velocimeters (ADVs), respectively. From the free surface elevations, the evolution and runup of the wave was revealed; while from the ADVs, the velocity and turbulent energy was determined to identify specific turbulent events and coherent structures.
It was found that shoaling was confined to areas with gentler sloping bathymetry near the basin side walls and the runup shoreward of the still water shoreline was not uniform. The runup was characterized by a jetting mechanism caused by the convergence of water mass near the basin centerline as the wave refracted during breaking. The jetting mechanism caused the greatest cross-shore velocities to be located near the basin centerline. The greatest turbulent events were well correlated to borefronts, resembling hydraulic jumps, where the greatest shear and fluid accelerations occurred. Because of an abrupt change in the bathymetry, a coherent structure developed which was found to have a three-dimensional flow field. It was proposed that variations in the internal flow with depth were due to the orientation of multiple vortex rings.
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Effects of Winter Overseeding and Three-demensional Clipping Management on Warm-season TurfgrassesFontanier, Charles H. 2010 May 1900 (has links)
Perennial ryegrass (Lolium perenne L.) is commonly overseeded into hybrid
bermudagrass [Cynodon dactylon (L.) Pers. X C. transvaalensis Burtt Davy] turfs during autumn
in the southern United States. Overseeding can provide a green, actively-growing turf
throughout the winter dormancy period. Improved persistence of perennial ryegrass cultivars has
increased management inputs during the spring transition period. Lower input turf systems that
provide acceptable winter overseeding quality are preferred, and research aimed at evaluating
alternative overseeding species are warranted. Grooming reel attachments allowing for threedimensional
clipping management (3DCM) have become increasingly used by turf managers for
reducing grain and thatch, but scientific information on best management practices and canopy
effects of 3DCM-grooming are lacking. A field study was conducted at the Texas A&M
Turfgrass Field Laboratory in College Station, TX (30.6191 degrees N, 96.3576 degrees W), to investigate the
effects of overseeding using annual (Lolium multiflorum Lam.) and perennial ryegrasses on
3DCM-groomed and non-groomed fairway turfs of 'Tifway' hybrid bermudagrass, zoysiagrass
[Zoysia matrella (L.) Merr. 'Cavalier'], and seashore paspalum (Paspalum vaginatum Sw. 'Sea
Isle 1'). The study was arranged as a randomized complete block split-split-plot with three replications. Species whole main plots were split into three grooming intervals, which were
further split into four overseeding treatments. Data were collected assessing visual turf quality,
visual turf cover, leaf area index, clipping yield, shoot density, and biomass partitioning.
Results indicate annual ryegrass alone and an annual/perennial ryegrass overseeding mix
provided acceptable turf quality, but did not improve turf recovery over perennial ryegrass alone
in 'Tifway' or 'Sea Isle 1' turfs. In 'Cavalier' turfs, summer quality was affected by overseeding
treatment as follows: control > annual > annual/perennial > perennial. The overseeding
tolerance of the warm-season turfgrasses was as follows: 'Sea Isle 1' > 'Tifway' > 'Cavalier'.
Differences in canopy architecture of warm-season turfgrasses were related to the overseeding
tolerance of each species and used to explain plant competition during the spring transition
period. Grooming by 3DCM improved late-season turf quality and reduced scalping in 'Tifway'.
Overseeding establishment and canopy architecture were not affected by 3DCM.
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The Venetian Galley of Flanders: From Medieval (2-Dimensional) Treatises to 21st Century (3-Dimensional) ModelHiggins, Courtney Rosali 2012 May 1900 (has links)
Nautical archaeologists and scholars often try to recreate how ships were built and maneuvered. Due to the delicate nature of older wooden vessels, there is often little archaeological evidence remaining to aid in these studies, and researchers must supplement what little they have with other resources, such as texts. By using computer programs to synthesize and enhance the information in the texts, scholars can better understand the vessel and explore questions that even hull remains may not be able to address.
During the High to Late Middle Ages, Venice was a key city for trade and commerce. Its location on the Adriatic Sea connected merchants throughout mainland Europe and the Mediterranean Sea. Since its founding in the low Middle Ages, Venice has been connected to the sea, leading to a long history of seafaring and shipbuilding. By the end of the Middle Ages, Venice had established several trade routes throughout the Mediterranean and Black Seas, and one long sea route into the Atlantic, to Lisbon, Flanders, and London.
Although no archaeological evidence of these galleys have been found, several contemporary texts describe the merchant galleys of the 15th century. Two of these texts, dating to the first half of the 15th century discuss the dimensions the galley: The book of Michael of Rhodes and the book of Giorgio "Trombetta" da Modone. Perhaps complementary copies of the same original, these texts contain enough information to reconstruct a 3-dimensional model of the galley of Flanders's hull, in this case using off-the-shelf software ((Rhinoceros). From this computer model the vessel can then be analyzed for volumetric information in order to better understand the hull capacity and how the ship was laden.
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On Design of new Complementary CodesYang, Chih-yuan 02 September 2005 (has links)
In this thesis, we propose a new way to generate orthogonal code distinct from complete complementary (CC) code and Super CC code but it still have ideal auto-correlation and cross-correlation property. We also introduce the concept of correlation and propose six rules to determine if the code generated by different ways are the same.After that we use the rules on orthogonal matrix and find a new way to generate orthogonal matrix different from Hadamard marix. Then we will use this marix in 2-D orthogonal variable spreading factor (OVSF) code and generate similar codes.
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Generating Implicit Functions Model from Triangles Mesh Model by Using Genetic AlgorithmChen, Ya-yun 09 October 2005 (has links)
The implicit function model is nowadays generally applied to a lot of fields that need 3D, such as computer game, cartoon or for specially effect film. So far, most hardware are still to support the polygon-mesh model but not implicit function model, so polygon-mesh model is still the mainstream of computer graphics. However, translation between the two representation models becomes a new research topic.
This paper presents a new method to translate the triangles mesh model into the implicit functions model. The main concept is to use the binary space-partitioning tree to divide the points and patches in the triangle mesh model to create a hierarchical structure. For each leaf node in this hierarchical structure, we would generate a corresponding implicit function. These implicit functions are generated by the genetic algorithm. And the internal nodes in this hierarchical structure are blended by the blending operators. The blending operators make the surface become smooth and continual. The method we proposed reduces the data in a large amount because we only save the coefficients of the implicit surface. And the genetic algorithm can avoid the high computing complexity.
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Proteomic analysis of nitrile-induced proteins in Klebsiella oxytocaChou, Shu-min 06 September 2006 (has links)
The cyanide-degradation bacteria Klebsiella oxytoca SYSU-110 was isolated from the waste water of a metal-plating plant in southern Taiwan. K. oxytoca can utilize many nitrile compounds [including acetonitrile (100 mM), benzonitrile (1 mM), butyronitrile (100 mM), glutaronitrile (50 mM), methacrylnitrile (100 mM), phenylacetonitrile (1 mM), propionitrile (25 mM), succinonitrile (25 mM) and valeronitrile (50 mM)] as its sole nitrogen source. In this study, we found out that K. oxytoca was capable of degrading acetonitrile and propionitrile. Frome GC analysis, we recognized amide was an intermediate compound, while the carboxylic acid and ammonia were the final end-products. Therefore, we presume that K. oxytoca biodegraded nitrile compounds by two enzymes, the nitrile hydratase and amidase. We also analyzed the total cell proteins by 2-D polyacrylamide gel electrophoresis after the cells were cultured in medium containing 25mM succinonitrile. There were 23 proteins could be induced or overexpressed by nitrile and we had identified 11 by Mascot Peptide mass Fingerprint and Blast. Six proteins that can protect the cells from oxidative damage are: superoxide dismutase, glutathione s-transferase, dyp-type peroxidase, metal binding protein PsaA (that can transport metal ions into the cells), LraI, and FepA (used to transport inorganic ions into the cells). Three enzymes glutamine synthetase, methylenetetrahydrofolate reductase,¡@and dihydroxyacid dehydratase were used to synthesize amino acids. One protein was identified as ribosomal protein L9. The last identified protein is nucleoside triphosphates kinase which can convert nucleoside diphosphates to nucleoside triphosphates non-specifically. From the activity analysis, superoxide dismutase and glutathione S-transferase activities were escalated when the cells were cultured in 25mM succinonitrile, and the concentration of ROS has rise. These results suggested that succinonitrile could cause oxidative damage to the cells and induce some anti-oxidative damage proteins to protect them.
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Exotic Smooth Structures On Non-simply Connected 4-manifoldsTopkara, Mustafa 01 March 2010 (has links) (PDF)
In this thesis, we study exotic smooth structures on 4-manifolds with finite fundamental groups. For an arbitrary finite group G, we construct an infinite family of smooth 4-manifolds with fundamental group G, which are all homeomorphic but mutually non-diffeomorphic, using the small symplectic manifold with arbitrary fundamental group constructed by S. Baldridge and P. Kirk, together with the methods of A. Akhmedov, R.& / #221 / . Baykur and D. Park for constructing infinite families of exotic simply connected 4-manifolds. In the final chapter, pairs of small exotic 4-manifolds with a cyclic fundamental group of any odd order are constructed.
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ADVANCED NEW NEUROSURGICAL PROCEDURE USING INTEGRATED SYSTEM OF INTRAOPERATIVE MRI AND NEURONAVIGATION WITH MULTIMODAL NEURORADIOLOGICAL IMAGESWAKABAYASHI, TOSHIHIKO, FUJII, MASAZUMI, KAJITA, YASUKAZU, NATSUME, ATSUSHI, MAEZAWA, SATOSHI, YOSHIDA, JUN 09 1900 (has links)
No description available.
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