The Female Cervicovaginal Mucosa Is a Unique Site for the Production of Autoantibodies Associated with Rheumatoid Arthritis

Purpose/Background: Women have a 3-fold higher incidence of rheumatoid arthritis (RA) and a lower likelihood of remission compared to men suggesting a gender disparity in the etiology of RA. In order to devise female specific prevention and treatment strategies, it is critical to understand the mechanism initiating the production of RA autoantibodies termed anti-citrullinated protein antibodies (ACPA). ACPA target proteins that are posttranslationally modified by a family of enzymes termed peptidylarginine deiminases (PADs), which convert arginine into citrulline. Research suggests that ACPA are generated at a mucosal site years before becoming systemic and causing clinical joint disease. Mucosal sites such as the lung, gut, and gingiva have been explored as sites of ACPA production, yet none of these account for the higher incidence of RA in women. We hypothesize that the cervicovaginal mucosa is a novel, sex-specific site for APCA production in women. Materials & Methods: To begin to test this hypothesis, healthy control (HC) women, women at risk for RA (AR), and those with clinical RA self-collected cervicovaginal fluid (CVF) at three time points during the menstrual cycle. CVF samples were examined for PAD activity, total citrulline concentration, and cyclic citrullinated peptides (CCP) as a marker for ACAP levels. Results: In naturally cycling HC women, CCP peak in early follicular phase (d5), dropped substantially by ovulation (d14), and remained low at the end of the luteal phase (d26). PAD enzymatic activity and total citrulline concentration also peak in CVF at d5 of the menstrual cycle, suggesting that changes in citrullinated proteins may drive local ACPA production. We next examined if CCP, PAD activity, and total citrulline concentration are increased in CVF from women at-risk (AR) for developing RA and women with RA. Although PAD activity and total citrulline concentration does not increase in these groups compared to health controls, CCP levels are significantly increased between the HC and RA CVF samples at d25. At issue is the identity of the citrullinated proteins in HC, AR and RA CVF, and if their abundance changes across the cycle and with disease progression. To address this, we performed mass spectrometry on CVF samples which identified a number of citrullinated proteins present in HC, AR, and RA women. Discussion/Conclusion: Our work suggests that citrullinated proteins and ACPA are produced in the cervicovaginal mucosa and may help explain why women have increased risk of developing RA

Human-Machine Cooperative Decision Making

The research reported in this thesis focuses on the decision making aspect of human-machine cooperation and reveals new insights from theoretical modeling to experimental evaluations: Two mathematical behavior models of two emancipated cooperation partners in a cooperative decision making process are introduced. The model-based automation designs are experimentally evaluated and thereby demonstrate their benefits compared to state-of-the-art approaches

An Investigation of Energy Migration in Rare Earth Oxyorthosilicate Scintillation Materials

In most scintillator applications, the energy resolution is an important scintillation property and is related to other scintillator properties. In order to observe how these properties relate to the energy resolution, a simulation was created to quantify most of these characteristics for a LSO:Ce scintillator. These results were validated with good agreement to experimental results. From the separable components of the simulation, an understanding of the contributions to the energy resolution broadening was developed. A thought to improve the energy resolution by improving the energy migration was tested by observing and modifying the scintillation kinetics of YSO:Ce. The scintillation kinetics in YSO:Ce are quite different from LSO:Ce even though the materials are similar in crystal lattice structure and the cerium activator dopant. The scintillation kinetics differences are observed when measuring the scintillation decay time with the results varying in decay times and different mathematical decay models. Using thermoluminescence, it was observed that YSO:Ce has more shallow traps with trap lifetimes at ~300K on the same order as the Ce3+ excited state lifetime. Using these same data, it was calculated that these shallow traps have lifetimes ~years when the sample is cooled to 40K. Re-measuring the decay time at 40K yields a decay time of 32ns and shows that the shallow traps in YSO:Ce are the cause of impeded energy migration to the luminescence centers. By using calcium co-doping during crystal growth, most of the trap structure was significantly suppressed. With these YSO:Ce:Ca samples, the scintillation decay times were decreased nearly to the cerium excited lifetimes. In order to measure any improvement in the non-proportional response, a new measurement technique was developed. The new method used angular based measurements using a PET scanner to calculate the energy of a Compton electron deposited in the sample. The results agreed with published data for NaI:Tl and LSO:Ce scintillators. Finally, it was demonstrated that the non-proportional response of YSO samples were the same with improvement in energy resolution without a large increase in light output. The conclusion was that the homogeneity of our YSO:Ce:Ca samples led to a 3% improvement in energy resolution

Characterization of Protein Folding Pathways and Structural Stability

Proteins are large, flexible molecules with an extremely large number of potential conformations. Proteins expressed in cells traverse available conformations to reach a consistent, thermodynamically stable, biologically active structure through a process known as protein folding. The atomic composition of the protein, defined by a sequence of amino acid residues encoded in DNA as a gene, determines the protein folding pathway and ultimate native structure of the protein molecule. Understanding the relationship between the sequence of amino acids and the resulting protein structure has been a central challenge in protein research for decades. To fill this knowledge gap, we test the hypothesis that the distribution of conformers observed for a short protein sequence across all known protein structures reflects that sequence\u27s intrinsic structural properties. Qualitative and quantitative predictions based on our model are tested against experimental data for protein stability and folding pathways. Replica-exchange Monte Carlo simulations, data mining of the Worldwide Protein Data Bank (wwPDB), analysis of published protein stability data, thermodynamic and kinetic folding experiments, and Xray crystallography were used to characterize the structural properties of amino acid sequences. The role of turn sequences in guiding the protein folding process was extensively characterized by the combined methods. Turn composition, structural preferences, and cooperation with neighboring residues determined whether a turn had an active, passive, or counter-active role in a protein\u27s folding process. Proline-rich turns, NPSNP and KPSDP, from the two-helix bundles found in bacterial type III secretion system needle proteins form native-like structure early in the folding process. Each of these turns are flanked by sequences with very high helix propensity that, when oriented by the turn, can actively nucleate the hydrophobic core of the protein. The hydrophobic turn, MGYE, from the three-helix bundle UBA(1) also forms native-like structure early in the folding process. This turn structure places the Met (M) and Tyr (Y) residues together, nucleating the hydrophobic core of UBA(1). These two residues can then stabilize the adjacent helices to form a Helix- Turn-Helix structure. The second, proline-containing turn in UBA(1), ASYNNP, forms non-native structure early in the folding process. This turn restructures late in the folding process when the third helix docks to the previous Helix-Turn-Helix structure. Each of the active turns characterized (NPSNP, KPSDP, and MGYE) direct the folding process by nucleating the protein\u27s hydrophobic core. A general purpose computational method to model the local structural properties of protein sequences was developed from data mined from the wwPDB. Turn mechanisms can be rapidly characterized using the tool, EmCAST, in conjunction with a PDB structure of the protein of interest. The impact of surface mutations on protein stability can also be scored by EmCAST. Models and calculations were extensively validated against experimental data for multiple protein and peptide systems. Calculations for stabilizing mutations at well-structured positions in UBA(1) produced a near perfect correlation with experimental measurements (R2 = 0.97). A user-friendly web interface to the software was developed to share the method with other protein researchers. Our model provides key insights into the protein sequence/structure relationship that can be used to characterize protein surface stability, identify regions with dynamic structure, and predict protein folding intermediates

Human-Machine Cooperative Decision Making

The research reported in this thesis focuses on the decision making aspect of human-machine cooperation and reveals new insights from theoretical modeling to experimental evaluations: Two mathematical behavior models of two emancipated cooperation partners in a cooperative decision making process are introduced. The model-based automation designs are experimentally evaluated and thereby demonstrate their benefits compared to state-of-the-art approaches

How Basic Course Directors Evaluate Teaching Assistants: Social Constructionism in BasicCourseLand

This essay examines the ways basic course directors assess their teaching staff. In particular, the study describes ways course directors from a variety of disciplines use language to evaluate teaching competence and to differentiate among staff members with regard to job performance. As would be expected, most course directors in this sample used evaluation terms such as good/bad or effective/ineffective. Only a few used other types of differentiation schemes, such as those based on maturity of the teaching assistant or attitudes toward teaching