This thesis presents experimental and theoretical studies of the characteristics of the head/disk interface at very low flying height. The study starts with a discussion of the tribological background of the head/disk interface and presents a review of the literature related to studies of the head/disk interface. Then, mechanical scaling laws for hard disk drives are discussed. Numerical results for failure inception of brittle and ductile hard disks due to high shock levels are presented. An experimental setup for measuring slider dynamics in five degrees-of-freedom (DOF) is presented. This is followed by experimental studies of slider vibrations due to slider/disk contacts. Thereafter, a study of slider vibrations due to write-head induced "thermal" pole-tip-protrusion is presented. Numerical simulations of slider vibrations are compared with experimental results. A method for measuring the magnetic spacing based on the read-back signal is presented. Finally, the results of this thesis are summarized and directions for future research are given

Objective

To examine African-American prostate cancer (PCa) survivors' involvement in treatment decision-making (TDM), and examine the association between TDM and quality of life (QOL), using secondary data.

Methods

African-American PCa survivors (181) were recruited from the North Carolina Central Cancer Registry. Participants completed a cross-sectional survey that asked about their chosen cancer treatment, TDM factors, and PCa-specific QOL (using the Expanded Prostate Cancer Index Composite--EPIC). Multivariate analysis of covariance was conducted to determine the association between TDM and QOL, controlling for confounders.

Results

Most men reported being active (44.2%) or collaborative (38.1%) in TDM, while 14.4% preferred a passive role. Adjusting for marital status, education and treatment, passive patients reported somewhat better QOL compared to active patients in the following QOL domains: urinary summary (p=0.04), urinary function (p=0.01), and urinary incontinence (p=0.03).

Conclusion

Most African-American PCa survivors preferred to be, and were, actively or collaboratively involved in TDM. However, those who preferred a passive role reported better PCa-specific QOL for the urinary domain compared to others.

Practice implications

It is important to assess patients' TDM preference. Patients' QOL may differ by their TDM role, such that active patients may be more bothered by treatment side effects than other patients.

Ultra-high areal density for hard disk drives requires a stable head disk interface at a flying height lower than 8 nm. At such a low flying height, small flying height variations may cause slider/disk contacts. Slider/disk contacts can also occur when a write-current is applied to the write coil since the flying height between slider and disk can be affected by the thermal expansion of the pole tip. In this paper, we investigate the vibration characteristics of sliders during thermally induced contacts using laser Doppler vibrometry. We perform a parametric study of contact events using disks with different surface roughness and lubricant thicknesses, and analyze the slider motion statistically. For a given write current, we observe that the slider vibrations increase with disk roughness and lubricant thickness.

Some extant organisms reassign the amber stop codon to a sense codon through evolution, and suppression of the amber codon with engineered tRNAs has been exploited to expand the genetic code for incorporating non-canonical amino acids (ncAAs) in live systems. However, it is unclear how the host cells respond and adapt to such amber suppression. Herein we suppressed the amber codon in Escherichia coli with an orthogonal tRNA/synthetase pair and cultured the cells under such a pressure for about 500 generations. We discovered that E. coli quickly counteracted the suppression with transposon insertion to inactivate the orthogonal synthetase. Persistent amber suppression evading transposon inactivation led to global proteomic changes with a notable up-regulation of a previously uncharacterized protein (YdiI) for which we identified an unexpected function of expelling plasmids. These results should be valuable for understanding codon reassignment in genetic code evolution and for improving the efficiency of ncAA incorporation.

Optical simulation of the detector module level is highly desired for Position Emission Tomography (PET) system design. Commonly used simulation toolkits such as GATE are not efficient in the optical simulation of detector modules with complicated light-sharing configurations, where a vast amount of photons need to be tracked. We present a fast approach based on a simplified specular reflectance model and a structured light-tracking algorithm to speed up the photon tracking in detector modules constructed with polished finish and specular reflector materials. We simulated conventional block detector designs with different slotted light guide patterns using the new approach and compared the outcomes with those from GATE simulations. While the two approaches generated comparable flood maps, the new approach was more than 200-600 times faster. The new approach has also been validated by constructing a prototype detector and comparing the simulated flood map with the experimental flood map. The experimental flood map has nearly uniformly distributed spots similar to those in the simulated flood map. In conclusion, the new approach provides a fast and reliable simulation tool for assisting in the development of light-sharing-based detector modules with a polished surface finish and using specular reflector materials.

The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direct effects of their interaction on gene expression remain elusive. Here, we quantify the concurrence of DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying 'methylation concurrence' by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation concurrence is strongly correlated with gene expression. Notably, elevated methylation concurrence in tumors is associated with the repression of 40~60% of tumor suppressor genes, which cannot be explained by promoter hypermethylation alone. Furthermore, methylation concurrence can be used to stratify large undermethylated regions with negligible differences in average methylation into two subgroups with distinct chromatin accessibility and gene regulation patterns. Together, methylation concurrence represents a unique methylation metric important for transcription regulation and is distinct from conventional metrics, such as average methylation and methylation variation.

Immune cells, including natural killer (NK) cells, recognize transformed cells and eliminate them in a process termed immunosurveillance. It is thought that tumor cells evade immunosurveillance by shedding membrane ligands that bind to the NKG2D-activating receptor on NK cells and/or T cells, and desensitize these cells. In contrast, we show that in mice, a shed form of MULT1, a high-affinity NKG2D ligand, causes NK cell activation and tumor rejection. Recombinant soluble MULT1 stimulated tumor rejection in mice. Soluble MULT1 functions, at least in part, by competitively reversing a global desensitization of NK cells imposed by engagement of membrane NKG2D ligands on tumor-associated cells, such as myeloid cells. The results overturn conventional wisdom that soluble ligands are always inhibitory and suggest a new approach for cancer immunotherapy.

Promoter DNA methylation is a well-established mechanism of transcription repression, though its global correlation with gene expression is weak. This weak correlation can be attributed to the failure of current methylation quantification methods to consider the heterogeneity among sequenced bulk cells. Here, we introduce Cell Heterogeneity-Adjusted cLonal Methylation (CHALM) as a methylation quantification method. CHALM improves understanding of the functional consequences of DNA methylation, including its correlations with gene expression and H3K4me3. When applied to different methylation datasets, the CHALM method enables detection of differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.

Stop codons have been exploited for genetic incorporation of unnatural amino acids (Uaas) in live cells, but their low incorporation efficiency, which is possibly due to competition from release factors, limits the power and scope of this technology. Here we show that the reportedly essential release factor 1 (RF1) can be knocked out from Escherichia coli by 'fixing' release factor 2 (RF2). The resultant strain JX33 is stable and independent, and it allows UAG to be reassigned from a stop signal to an amino acid when a UAG-decoding tRNA-synthetase pair is introduced. Uaas were efficiently incorporated at multiple UAG sites in the same gene without translational termination in JX33. We also found that amino acid incorporation at endogenous UAG codons is dependent on RF1 and mRNA context, which explains why E. coli tolerates apparent global suppression of UAG. JX33 affords a unique autonomous host for synthesizing and evolving new protein functions by enabling Uaa incorporation at multiple sites.

Macrophage-mediated inflammation is a major contributor to obesity-associated insulin resistance. The corepressor NCoR interacts with inflammatory pathway genes in macrophages, suggesting that its removal would result in increased activity of inflammatory responses. Surprisingly, we find that macrophage-specific deletion of NCoR instead results in an anti-inflammatory phenotype along with robust systemic insulin sensitization in obese mice. We present evidence that derepression of LXRs contributes to this paradoxical anti-inflammatory phenotype by causing increased expression of genes that direct biosynthesis of palmitoleic acid and ω3 fatty acids. Remarkably, the increased ω3 fatty acid levels primarily inhibit NF-κB-dependent inflammatory responses by uncoupling NF-κB binding and enhancer/promoter histone acetylation from subsequent steps required for proinflammatory gene activation. This provides a mechanism for the in vivo anti-inflammatory insulin-sensitive phenotype observed in mice with macrophage-specific deletion of NCoR. Therapeutic methods to harness this mechanism could lead to a new approach to insulin-sensitizing therapies.