This thesis has investigated the chemical evolution of the inner regions (r ≤ 10 AU) of a modelled protoplanetary disk surrounding a low-mass T Tauri star; a phase our own solar system underwent some 4.5–4.6 billion years ago. A 1+1- dimensional physical model of a radially-accreting protoplanetary disk was combined with a chemical model consisting of gas-phase reactions extracted from the RATE95 UMIST database for Astrochemistry, and to this, a network of gas-grain interaction and deuterated reactions were added. Influenced by the knowledge that radionuclides may have been abnormally abundant in our early solar system compared with the interstellar medium, and that the energy expelled from their decay is sufficient to ionize molecules, a 1-dimensional simulation along the disk midplane was performed, comparing the chemistry with and without radionuclides, as a function of the radionuclide ionization rate. The molecules C4H2, HC3N, C3H, HCN, CH4, C2H2 and N2 were found to be particularly sensitive. Of these, HCN and C2H2 have already been detected in protoplanetary disks. Motivated by observations which suggest that T Tauri systems vary from faster to slower accretion rates, the chemical distributions of two disks with stellar accretion rates of 10−7 M⊙ yr−1 and 10−8 M⊙ yr−1 were compared. Allowing the mass accretion rate (and thus physical conditions) to vary in time, starting from 10−7 M⊙ yr−1, and evolving to a mass accretion rate of 10−8 M⊙ yr−1, the molecules CN, HCN, H2CO and NH3 were found to be particularly sensitive when compared to a standalone 10−8 M⊙ yr−1 simulation. With the use of a 1-D CASA LTE algorithm for ALMA, the sensitivities of HCN and H2CO were transcribed into integrated intensity differences, as a function of emissivity and optical depth. The largest differences were associated with the largest feasible transitions of HCN and H2CO; J = 8-7 and JK = 10010-909 respectively, but could not be converted into potentially observable integrated fluxes due to the restrictions of this model. Both molecules were found to trace different regions of the disk. Using the stellar accretion rate-to-age linear relation evaluated from observations, the calculation times for the 10−7 M⊙ yr−1 and 10−8 M⊙ yr−1 were re-evaluated, of which CN and NH3 emerged as the most sensitive molecules. Thus, CN and NH3 may be a possible tracer of calculation time, and disk age.

International Telemetering Conference Proceedings / October 17-20, 1994 / Town & Country Hotel and Conference Center, San Diego, California / In order to meet the high-speed and high-density recording requirements for today's development and testing environments, we are seeking to merge the cutting edge technologies of tiny, high-performance disk drives and field programmable gate arrays (FPGAs) to build a high-speed compact disk recorder (CHSDR). Specifically, we designed, built, and tested a multi-drive controller that handles the interleaving of data to eight inexpensive IDE drives. These drives and controller comprise a "cell" capable of transferring data at 2.45 MB/sec (4 to 5 times the rate of a single drive). Furthermore, these "cells" can be run in parallel (with a single controller interleaving data between the cells). This "tree" effect multiplies the data rate by the number of cells employed. For example, 8 cells (of 8 drives each) can reach nearly 20 MB/second (sustained) and can be built for less than $30,000. The drives we used are the size of match boxes (the Hewlett Packard KittyHawk). These tiny drives hold 42 megabytes each and can withstand 150 Gs while operating. The cell controller is a Xilinx 4005 FPGA. Furthermore, we've designed a 120 MB/sec RAM FIFO to buffer data entering the system (to account for unavoidable drive seek latencies). In short, the compact high-speed disk array is a small, relatively low cost recording solution for anyone requiring high data speed but modest data volume. Missile shots, nuclear tests, and other short-term experiments are good examples of such requirements.

published_or_final_version / abstract / Orthopaedics and Traumatology / Doctoral / Doctor of Philosophy

Thesis (Ph.D.) - University of Queensland, 2006. / Includes bibliography.

The pathogenesis of low back pain is complex but likely involves the intervertebral disc (Nachemson, 1976). Direct evidence for its importance is lacking because an accurate in vivo method of imaging the lumbar intervertebral disc has not been established. The objective of this research was to develop classifications of gross morphologic appearance and magnetic resonance image (MRI) of the disc that describe the changes associated with aging and degeneration, thereby permitting interpretation of the MRI in terms of gross morphology and allowing correlation of morphologic, chemical, mechanical, radiologic and epidemiologic data with a standard reference of disc aging and degeneration. The classifications were developed on the basis of literature review, detailed examination of 55 discs and expert advice. Two sets of three observers, one for the morphologic classification and one for the MRI classification evaluated 68 life size randomized duplicates of discs making detailed observations about overall category and 17 regional morphologic parameters and 11 regional MRI parameters. The data was tested to demonstrate the validity of the classifications using established criteria (Tugwell & Bombardier, 1982; Guyatt 4 Kirschner, 1985; Feinstein, 1985). The consistency with which the classifications could be applied was evaluated by calculating weighted kappa, a statistical test of agreement that corrects for agreement by chance; the ability of the classifications to distinguish stages in the process of ageing and degeneration by stepwise discriminant analysis; their conformity with other measures by comparisons within and between classifications and, comparisons with histologic and chemical data. The degree of agreement for all six intra-observer pairs was 'almost perfect' (weighted kappa > 0.80); for 5 interobserver pairs 'substantial' (weighted kappa > 0.60) and for one MRI interobserver pair 'moderate' (weighted kappa > 0.50). This represented a satisfactory level of agreement and indicated the classifications could be applied consistently (Feinstein, 1981). The linear regression model developed by stepwise discriminant analysis clearly demonstrated the ability of the classifications to distinguish distinct stages in disc aging and degeneration. Wilk's lambda, a likelihood ratio statistic reflecting discriminatory function, approached zero in both the morphologic (0.0408) and MRI (0.0H80) classifications. In both models, parameters pertaining to the nucleus pulposus of the disc accounted for the majority of the variance (morphologic partial R² 0.8598 and MRI partial R² 0.8811) suggesting nuclear parameters are the most important in distinguishing overall category. The correlation table generated by principal component analysis demonstrated that the categories assigned to regional parameters correlated significantly (p > 0.0001) with each other and with the overall category. From the linear combinations of parameters (principal components) generated the weighting of the nucleus pulposus behaved independently attesting to its importance. Comparisons of the morphologic and MRI classifications yielded high indices of trend (Pearson correlation coefficient of 0.81) and concordance (kappa of 0.62). Trends in the histologic and chemical data were consistent with the classifications but could not be evaluated statistically because only 15 specimens were studied. This research suggests that the classifications are valid and will form a basis for the interpretation of MRI. Preliminary evidence suggested MRI is sensitive to early changes in extracellular matrix composition not apparent in gross morphology. / Medicine, Faculty of / Graduate

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 94-97).

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

published_or_final_version / Orthopaedics and Traumatology / Doctoral / Doctor of Philosophy

Current treatments to intervertebral disc degeneration alter spine biomechanics and have complications. Tissue engineering offers an approach to regenerate a biological disc that provides flexibility and stability to, and integrates with the spine. To date, a scaffold that mimics the extracellular matrix composition and mechanical strength of a native disc is lacked. In this project, a biphasic scaffold was fabricated using glycosaminoglycan (GAG) and collagen, the prevalent ma-trix components in a native disc. It also adapted the structure of the disc, with la-mellae of collagen surrounding a collagen-GAG (CG) core. The first part of this project studied chemical modification of CG and evaluated the physiochemical and biological properties of modified CGs. As only loosely bound by GAG under physiological environment, collagen was modified by deamination, methylation and amination, and yielded Deaminated, Methylated and Aminated CGs upon co-precipitation with GAG. While GAG was mostly lost within 1 day in Untreated and Deaminated CGs, 20% and 40% GAG was retained after 6 days in Methylated and Aminated CGs respectively. In cell-seeded Aminated CG, over 60% GAG was retained after 8 days. Aminated CG, having the highest GAG/HYP of 4.5, best simulated the GAG-rich nucleus pulposus tissue. In ultrastructural analysis, Aminated CG consisted of abundant granular sub-stances that resembled the nucleus pulposus. Despite the differential initial number adhered to the CG scaffolds, human mesenchymal stem cells (hMSCs) had over 90% viability at all time points. Cell morphology was distinct, being round in Untreated and Methylated CGs but elongated in Deaminated and Aminated ones. The adhesion of hMSCs via collagen receptor, integrin alpha2beta1, was observed in all CG scaffolds, while adhesion via general matrix receptor, integrin alphaV, was extensive in all but Aminated CG. Based on improved GAG incor-poration and retention, which approximate the matrix composition of nucleus pulposus, Aminated CG was chosen as the core of the biphasic scaffold. The second part of this project studied lamination in biphasic disc scaffold and evaluated its mechanical properties in creep, recovery and dynamic loadings. A process was optimized to encapsulate a CG under physiological condition whilst producing an intact collagen gel, which allowed the CG to retain more GAGs and to be confined by the annulus structurally as was in the disc. This encasing approach was repeated for multiple lamellae, one lamella per day. Scaffolds with more lamellae had increased viscous compliance in creep and recovery, which was explained by the less laminated scaffolds being overloaded. Another lamination approach replaced most encasing lamellae with coiling ones. Despite low sample size, it was shown that this combined approach produced scaffolds with lower elastic and viscous compliances and longer equilibrating time in both creep and recovery, and higher complex modulus under dynamic loading. Full recovery was not achieved by any scaffold. This study demonstrated that a biphasic disc scaffold, made of GAG and collagen, contained similar matrix components to native disc, was almost mechanically comparable to the disc, and was cyto-compatible. It paved way towards tissue engineering of intervertebral disc and the intervertebral disc motion segment. / published_or_final_version / Mechanical Engineering / Doctoral / Doctor of Philosophy

Intervertebral disc(IVD) degeneration is associated with low back pain (LBP).Despite the endplates are located adjacent to the IVD, the phenotypes of endplate and vertebral bone marrow changes remain unclear. The objective of this study is to assess the prevalence and the associated determinants of these phenotypes of the lumbar spine. 2449 Southern Chinese subjects (aged 10 –88 years) undergone sagittal T2-weighted magnetic resonance imaging (MRI)examination to assess the presence of endplate and vertebral bone marrow changes including Schmorl’s nodes (SN) and Modic changes (MC),respectively, and scored for additional radiographic features over the lumbar spine. Subjects’ demographics, clinical profile, and functional status were assessed by means of standardized questionnaires. Anovel6-domain SN morphological classification based on MRI was developed to further analyze the characteristics of SN and its association with disc degeneration (DD). The prevalence of SN was 16.4%. Males, taller and heavier individuals had a significantly increased likelihood of SN. Overall presence of SN was age-independent, but was significantly associated with DD, and linearly correlated with increase in severity of DD. SN were particularly associated with severe DD at the upper two lumbar levels (L1/2 – L2/3). Based on the SN classification system, specific SN characteristics and endplate linkage patterns were found. Of these, two SN types were identified:“Typical SN” and “Atypical SN”. “Typical SN” were those smaller size SN with various shapes that were frequently located at caudal endplates of L1/2–L3/4disc levels. One variant of “Atypical SN” were those rectangular shape SN, which predominantly located at the posterior region of the rostral endplates of L1/2–L2/3disc levels. The other variant of “Atypical SN” was larger size SN with irregular shape that frequently presented at the L4/5endplates, they were also likely to be associated with marrow changes. Despite “Atypical SN” only entailed 8.3% of all identified SN, they were associated with increased severity of DD than “Typical SN”. Although the overall prevalence of MC among Southern Chinese was low (5.8%), after adjustments for other confounding factors, the presence of MC was associated with the presence and severity of LBP. Interestingly, the determinants of MC at upper (L1/2 – L3/4) and lower (L4/5 – L5/S1) lumbar showed distinct difference. The presence of MC at upper lumbar levels was only associated with the disc integrity only (i.e. the presence of disc displacement, and DD score), while the presence of MC at the lower levels, apart from the disc integrity, was also associated with increasing age, the presence of SN, smoking and obesity status. This study is the largest MRI study assessing the phenotypes of endplate and vertebral bone marrow changes in-vivo. The prevalence and distribution of SN and MC vary throughout the lumbar spine, and there are level and region-specific variations regarding these phenotypes. Determinants of SN and MC may be similar but do vary, suggesting distinct etiological factors. Findings of this study broaden the understanding of the various phenotypes of the lumbar spine and its association with DD. / published_or_final_version / Orthopaedics and Traumatology / Doctoral / Doctor of Philosophy