Method optimization and gene expression analysis for interferon Kappa mRNA in HPV-associated cervical disease / by Correne A. Decarlo.

Interferons (IFNs) are a common biological treatment option for many cancers as well as for human papillomavirus (HPV)-associated diseases, but current IFN treatments have not been optimized as disease progression subsists and treatment-limiting side effects still exist. IFN kappa (IFN-), a novel type I IFN, principally expressed in keratinocytes, may offer improvements in current IFN treatment regimes. The goal of the current study was to characterize the IFN-, IFN- and IFN- mRNA levels in normal, dysplastic and cervical carcinoma tissue, as well as microdissected cervical epithelium and stroma, to determine the effects of HPV on IFN- gene expression in relation to other common IFNs. Optimal sample handling techniques for tissue preparation and storage, RNA extraction and quantification, and target gene detection are crucial for reliable gene expression analysis. Methods for measuring mRNA levels of low-expressing genes, such as IFNs, in human cervical samples are not described in the scientific literature. Thus, we obtained normal and dysplastic frozen and formalin-fixed cervical biopsies from colposcopy. Histopathological diagnoses were performed by one pathologist. Cervical keratinocytes and stroma were isolated using laser capture microdissection. Immortalized keratinocytes transduced with or devoid of an HPV oncogene were used for initial method development. Human keratinocytes, cervical cancer-derived cell lines as well as patient-derived peripheral blood lymphocytes were used for supportive experiments. Here we report optimal methods for gene expression analysis of IFNs in cervical tissue as well as the comprehensive analysis of whole tissue and cell-specific IFN-y, -B and -K gene expression in HPV-associated cervical disease. IFN-K gene expression increased with disease progression, while IFN-B gene expression decreased with disease progression. IFN-y levels remained unchanged despite HPV infection. Furthermore, IFN-K expression in cervical stroma cells was induced upon HPV infection, implicating the involvement of cervical stroma cells in the HPV-associated increase in IFN-k expression. The described optimized methods could lead to improvements in immunological profiling and disease diagnosis, techniques without which IFN-k would remain undetectable in cervical samples. Further, characterization of the IFN immune profile in patients with different stages of HPV-associated cervical disease, with emphasis on the novel IFN-k, could help develop patient-tailored IFN treatment regimes that lead to the promotion of viral regression in women suffering from cervical disease

Investigation of flow fields within large scale hypersonic inlet models

Analytical and experimental investigations were conducted to determine the internal flow characteristics in model passages representative of hypersonic inlets for use at Mach numbers to about 12. The passages were large enough to permit measurements to be made in both the core flow and boundary layers. The analytical techniques for designing the internal contours and predicting the internal flow-field development accounted for coupling between the boundary layers and inviscid flow fields by means of a displacement-thickness correction. Three large-scale inlet models, each having a different internal compression ratio, were designed to provide high internal performance with an approximately uniform static-pressure distribution at the throat station. The models were tested in the Ames 3.5-Foot Hypersonic Wind Tunnel at a nominal free-stream Mach number of 7.4 and a unit free-stream Reynolds number of 8.86 X one million per meter

Factors affecting B/Ca ratios in synthetic aragonite

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Chemical Geology 437 (2016): 67-76, doi:10.1016/j.chemgeo.2016.05.007.Measurements of B/Ca ratios in marine carbonates have been suggested to record seawater carbonate chemistry, however experimental calibration of such proxies based on inorganic partitioning remains limited. Here we conducted a series of synthetic aragonite precipitation experiments to evaluate the factors influencing the partitioning of B/Ca between aragonite and seawater. Our results indicate that the B/Ca ratio of synthetic aragonites depends primarily on the relative concentrations of borate and carbonate ions in the solution from which the aragonite precipitates; not on bicarbonate concentration as has been previously suggested. The influence of temperature was not significant over the range investigated (20 – 40°C), however, partitioning may be influenced by saturation state (and/or growth rate). Based on our experimental results, we suggest that aragonite B/Ca ratios can be utilized as a proxy of [CO32-]. Boron isotopic composition (δ11B) is an established pH proxy, thus B/Ca and δ11B together allow the full carbonate chemistry of the solution from which the aragonite precipitated to be calculated. To the extent that aragonite precipitation by marine organisms is affected by seawater chemistry, B/Ca may also prove useful in reconstructing seawater chemistry. A simplified boron purification protocol based on amberlite resin and the organic buffer TRIS is also described.This work was supported by the Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies. Research conducted at WHOI was supported by NSF grant OCE-1338320. M.H. was supported by an ARC Super Science Fellowship and an NSF International Postdoctoral Fellowship. T.D. was supported by a NSF Graduate Research Fellowship. M.M. was supported by a Western Australian Premiers Fellowship and an ARC Laureate Fellowship

Fault Detection in Surface PMSM with Applications to Heavy Hybrid Vehicles

This report explores detecting inter-turn short circuit (ITSC) faults in surface permanent magnet synchronous machines (SPMSM). ITSC faults are caused by electrical insulation failures in the stator windings and can lead to shorts to ground and even fires. This report proposes methods for detecting these faults using a moving horizon observer (MHO) to reduce the chance of electrical shocks and fires. Specifically, this report constructs a MHO for ITSC fault detection in SPMSM. ITSC fault tolerant control is investigated for a 2004 Toyota Prius hybrid vehicle having a traction SPMSM. Once the supervisory-level powertrain power flow control becomes aware of the presence of a fault and its degree from the MHO, the control (i) reduces the maximum possible vehicle speed to ensure SPMSM thermal constraints are not violated and (ii) switches to a traction motor input-output power efficiency appropriate for the degree of fault. These steps are taken during a fault rather than shutting down the traction motor to provide a “limp home” capability. The traction motor cannot simply be turned off because its rotation is not independent of drive wheel rotation. The control is demonstrated by simulating the Prius over a 40 s drive velocity profile with faults levels of 0.5%, 1%, 2%, and 5% detected at the midpoint of the profile. For comparison, the Prius is also simulated without a traction motor fault. Results show that the control reduced vehicle velocity upon detection of a fault to appropriate safe values. Further, the challenges of ITSC fault tolerant control for heavy hybrid vehicles are examined. This work is partially supported by the Department of Energy, Award No. DE-EE0005568. The authors would like to acknowledge the support of Greg Shaver and the Hoosier Heavy Hybrid Center of Excellence. S. Johnson, R. DeCarlo, and S. Pekarek are with the Department of Electrical and Computer Engineering at Purdue University, 610 Purdue Mall, West Lafayette, IN 47907 (email: [email protected], [email protected], [email protected]). R. Meyer is with the Department of Mechanical and Aerospace Engineering at Western Michigan University, 1903 West Michigan Avenue, Kalamazoo, MI 49008 (email: [email protected])

Comparison and contrast in perceptual categorization

People categorized pairs of perceptual stimuli that varied in both category membership and pairwise similarity. Experiments 1 and 2 showed categorization of 1 color of a pair to be reliably contrasted from that of the other. This similarity-based contrast effect occurred only when the context stimulus was relevant for the categorization of the target (Experiment 3). The effect was not simply owing to perceptual color contrast (Experiment 4), and it extended to pictures from common semantic categories (Experiment 5). Results were consistent with a sign-and-magnitude version of N. Stewart and G. D. A. Brown's (2005) similarity-dissimilarity generalized context model, in which categorization is affected by both similarity to and difference from target categories. The data are also modeled with criterion setting theory (M. Treisman & T. C. Williams, 1984), in which the decision criterion is systematically shifted toward the mean of the current stimuli

Coral reef drag coefficients – water depth dependence

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1061-1075, doi:10.1175/JPO-D-16-0248.1.A major challenge in modeling the circulation over coral reefs is uncertainty in the drag coefficient because existing estimates span two orders of magnitude. Current and pressure measurements from five coral reefs are used to estimate drag coefficients based on depth-average flow, assuming a balance between the cross-reef pressure gradient and the bottom stress. At two sites wind stress is a significant term in the cross-reef momentum balance and is included in estimating the drag coefficient. For the five coral reef sites and a previous laboratory study, estimated drag coefficients increase as the water depth decreases consistent with open channel flow theory. For example, for a typical coral reef hydrodynamic roughness of 5 cm, observational estimates, and the theory indicate that the drag coefficient decreases from 0.4 in 20 cm of water to 0.005 in 10 m of water. Synthesis of results from the new field observations with estimates from previous field and laboratory studies indicate that coral reef drag coefficients range from 0.2 to 0.005 and hydrodynamic roughnesses generally range from 2 to 8 cm. While coral reef drag coefficients depend on factors such as physical roughness and surface waves, a substantial fraction of the scatter in estimates of coral reef drag coefficients is due to variations in water depth.The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST to S. Lentz and J. Churchill. The Palau field program was funded by NSF Award OCE-1220529

Relationship between water and aragonite barium concentrations in aquaria reared juvenile corals

This paper is not subject to U.S. copyright. The definitive version was published in Geochimica et Cosmochimica Acta 209 (2017): 123-134, doi:10.1016/j.gca.2017.04.006.Coral barium to calcium (Ba/Ca) ratios have been used to reconstruct records of upwelling, river and groundwater discharge, and sediment and dust input to the coastal ocean. However, this proxy has not yet been explicitly tested to determine if Ba inclusion in the coral skeleton is directly proportional to seawater Ba concentration and to further determine how additional factors such as temperature and calcification rate control coral Ba/Ca ratios. We measured the inclusion of Ba within aquaria reared juvenile corals (Favia fragum) at three temperatures (∼27.7, 24.6 and 22.5 °C) and three seawater Ba concentrations (73, 230 and 450 nmol kg−1). Coral polyps were settled on tiles conditioned with encrusting coralline algae, which complicated chemical analysis of the coral skeletal material grown during the aquaria experiments. We utilized Sr/Ca ratios of encrusting coralline algae (as low as 3.4 mmol mol−1) to correct coral Ba/Ca for this contamination, which was determined to be 26 ± 11% using a two end member mixing model. Notably, there was a large range in Ba/Ca across all treatments, however, we found that Ba inclusion was linear across the full concentration range. The temperature sensitivity of the distribution coefficient is within the range of previously reported values. Finally, calcification rate, which displayed large variability, was not correlated to the distribution coefficient. The observed temperature dependence predicts a change in coral Ba/Ca ratios of 1.1 μmol mol−1 from 20 to 28 °C for typical coastal ocean Ba concentrations of 50 nmol kg−1. Given the linear uptake of Ba by corals observed in this study, coral proxy records that demonstrate peaks of 10–25 μmol mol−1 would require coastal seawater Ba of between 60 and 145 nmol kg−1. Further validation of the coral Ba/Ca proxy requires evaluation of changes in seawater chemistry associated with the environmental perturbation recorded by the coral as well as verification of these results for Porites species, which are widely used in paleo reconstructions.M.E.G. was supported by a NDSEG graduate fellowship. Funding for this research came from the NSF Chemical Oceanography program (OCE-0751525) and the Coastal Ocean Institute, the Ocean and Climate Change Institute and the Ocean Ventures Fund at Woods Hole Oceanographic Institution