This open access archive contains publications from University of Arizona faculty, researchers and staff, primarily open-access versions of formally published journal articles. The collection includes published articles and final accepted manuscripts submitted by UA faculty under the UA Open Access Policy. The collection also includes books, book chapters, book reviews, presentations, data, and other scholarly materials submitters have chosen to make available in the repository.

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Recent Submissions

  • The impact of foreign fighters on civil conflict outcomes

    Chu, Tiffany S.; Braithwaite, Alex; Univ Arizona, Sch Govt & Publ Policy; School of Government & Public Policy, University of Arizona, USA; School of Government & Public Policy, University of Arizona, USA (SAGE PUBLICATIONS INC, 2017-08)
    There has been a great deal of discussion about the large volumes of foreign fighters involved in civil conflicts in Syria and Iraq over recent years. Yet, there remains little systematic evidence about the effect, if any, that foreign fighters have upon the conflicts they join. Existing literature distinguishes between the resources fighters bring to rebel groups and the liability they represent in regards to campaign cohesion. We seek to establish preliminary evidence as to whether or not foreign fighters contribute to the success of the campaigns they join. Our multinomial logistic and competing risks regression analyses of civil conflicts between 1946 and 2013 suggest that foreign fighters are associated with a decreased likelihood of government victory. Furthermore, we offer partial evidence to suggest that foreign fighters from non-contiguous countries are more likely to help rebels achieve a negotiated settlement or to continue their struggle against the government, but not to directly help them achieve victory.
  • Double-negative (CD27−IgD−) B cells are expanded in NSCLC and inversely correlate with affinity-matured B cell populations

    Centuori, Sara M.; Gomes, Cecil J.; Kim, Samuel S.; Putnam, Charles W.; Larsen, Brandon T.; Garland, Linda L.; Mount, David W.; Martinez, Jesse D.; Univ Arizona, Canc Ctr; Univ Arizona, Canc Biol Grad Interdisciplinary Program; Univ Arizona, Dept Surg; Univ Arizona, Dept Med, Div Hematol Oncol; Univ Arizona, Dept Mol & Cellular Biol; Univ Arizona, Cell & Mol Med (BIOMED CENTRAL LTD, 2018-02-15)
    Background: The presence of B cells in early stage non-small cell lung cancer (NSCLC) is associated with longer survival, however, the role these cells play in the generation and maintenance of anti-tumor immunity is unclear. B cells differentiate into a variety of subsets with differing characteristics and functions. To date, there is limited information on the specific B cell subsets found within NSCLC. To better understand the composition of the B cell populations found in NSCLC we have begun characterizing B cells in lung tumors and have detected a population of B cells that are CD79A(+)CD27(-)IgD(-). These CD27(-)IgD(-)(double-negative) B cells have previously been characterized as unconventional memory B cells and have been detected in some autoimmune diseases and in the elderly population but have not been detected previously in tumor tissue. Methods: A total of 15 fresh untreated NSCLC tumors and 15 matched adjacent lung control tissues were dissociated and analyzed by intracellular flow cytometry to detect the B cell-related markers CD79A, CD27 and IgD. All CD79A(+) B cells subsets were classified as either naive (CD27(-)IgD(+)), affinity-matured (CD27(+)IgD(-)), early memory/germinal center cells (CD27(+)IgD(+)) or double-negative B cells (CD27(-)IgD(-)). Association of double-negative B cells with clinical data including gender, age, smoking status, tumor diagnosis and pathologic differentiation status were also examined using the logistic regression analysis for age and student's t-test for all other variables. Associations with other B cell subpopulations were examined using Spearman's rank correlation. Results: We observed that double-negative B cells were frequently abundant in lung tumors compared to normal adjacent controls (13 out of 15 cases), and in some cases made up a substantial proportion of the total B cell compartment. The presence of double-negative cells was also found to be inversely related to the presence of affinity-matured B cells within the tumor, Spearman's coefficient of -0.76. Conclusions: This study is the first to observe the presence of CD27(-)IgD(-)double-negative B cells in human NSCLC and that this population is inversely correlated with traditional affinity-matured B cell populations.
  • Guidelines for responsible short-term global health activities: developing common principles

    Lasker, Judith N.; Aldrink, Myron; Balasubramaniam, Ramaswami; Caldron, Paul; Compton, Bruce; Evert, Jessica; Loh, Lawrence C.; Prasad, Shailendra; Siegel, Shira; Univ Arizona, Coll Med (BIOMED CENTRAL LTD, 2018-02-07)
    Background: Growing concerns about the value and effectiveness of short-term volunteer trips intending to improve health in underserved Global South communities has driven the development of guidelines by multiple organizations and individuals. These are intended to mitigate potential harms and maximize benefits associated with such efforts. Method: This paper analyzes 27 guidelines derived from a scoping review of the literature available in early 2017, describing their authorship, intended audiences, the aspects of short term medical missions (STMMs) they address, and their attention to guideline implementation. It further considers how these guidelines relate to the desires of host communities, as seen in studies of host country staff who work with volunteers. Results: Existing guidelines are almost entirely written by and addressed to educators and practitioners in the Global North. There is broad consensus on key principles for responsible, effective, and ethical programs-need for host partners, proper preparation and supervision of visitors, needs assessment and evaluation, sustainability, and adherence to pertinent legal and ethical standards. Host country staff studies suggest agreement with the main elements of this guideline consensus, but they add the importance of mutual learning and respect for hosts. Conclusions: Guidelines must be informed by research and policy directives from host countries that is now mostly absent. Also, a comprehensive strategy to support adherence to best practice guidelines is needed, given limited regulation and enforcement capacity in host country contexts and strong incentives for involved stakeholders to undertake or host STMMs that do not respect key principles.
  • Changes in Sensitivity to the Effects of Atrazine on the Luteinizing Hormone Surge in Female Sprague-Dawley Rats after Repeated Daily Doses: Correlation with Liver Enzyme Expression

    Breckenridge, Charles B.; Foradori, Chad D.; Sawhney Coder, Pragati; Simpkins, James W.; Sielken, Robert L.; Handa, Robert J.; Univ Arizona, Dept Basic Med Sci, Coll Med; Syngenta Crop Protection LLC; Greensboro North Carolina; Department of Basic Medical Sciences; University of Arizona College of Medicine; Phoenix Arizona; WIL Research; Ashland Ohio; Physiology and Pharmacology; West Virginia University; Morgantown West Virginia; Sielken & Associates Consulting, Inc.; College Station Texas; Department of Basic Medical Sciences; University of Arizona College of Medicine; Phoenix Arizona (WILEY, 2018-02-15)
    BackgroundAtrazine suppression of the LH surge slowly develops over time and peaks after 4 days; sensitivity to atrazine decreases after 8 or 14 days of dosing. Adaptation of the LH response was correlated with increased phase I and phase II liver enzyme activity/expression. MethodsThe effect of atrazine on the LH surge was evaluated in female Sprague-Dawley rats administered 100 mg/kg/day atrazine by gavage for 1, 2, 3, or 4 consecutive days or 6.5, 50, or 100 mg/kg/day atrazine for 4, 8, or 14 days. ResultsNo statistically significant effects of atrazine were seen on peak plasma LH or LH area under the curve (AUC) after one, two, or three doses of 100 mg/kg/day. Four daily doses of 50 or 100 mg/kg atrazine significantly reduced peak LH and LH AUCs, whereas 6.5 mg/kg/day had no effect. After 8 or 14 days of treatment, statistically significantly reduced peak LH and LH AUC were observed in the 100 mg/kg/day dose group, but not in the 6.5 or 50 mg/kg/day dose groups, although significantly reduced LH was observed in one sample 9 hr after lights-on in the 50 mg/kg/day dose group on day 14. The number of days of treatment required to achieve a significant suppression of the LH surge is consistent with the repeat-dose pharmacokinetics of the chlorotriazines. ConclusionThe apparent adaptation to the effect of atrazine on the LH surge after 8 or 14 days may be related to the induction of phase I or, more likely, phase II metabolism observed in this study after 8 days, or to a decreased sensitivity of the hypothalamic-pituitary-adrenal axis or an homeostatic adaption of the effect of atrazine on the LH surge mechanism. Birth Defects Research 110:246-258, 2018. (c) 2017 The Authors. Birth Defects Research Published by Wiley Periodicals, Inc.
  • Useful Bicistronic Reporter System for Studying Poly(A) Site-Defining cis Elements and Regulation of Alternative Polyadenylation

    Deng, Zhongyuan; Zhang, Shen; Gu, Shaohua; Ni, Xinzhi; Zeng, Wenxian; Li, Xianchun; Univ Arizona, Dept Entomol; Univ Arizona, Inst BIO5 (MDPI AG, 2018-01-17)
    The link between polyadenylation (pA) and various biological, behavioral, and pathological events of eukaryotes underlines the need to develop in vivo polyadenylation assay methods for characterization of the cis-acting elements, trans-acting factors and environmental stimuli that affect polyadenylation efficiency and/or relative usage of two alternative polyadenylation (APA) sites. The current protein-based CAT or luciferase reporter systems can measure the polyadenylation efficiency of a single pA site or candidate cis element but not the choice of two APA sites. To address this issue, we developed a set of four new bicistronic reporter vectors that harbor either two luciferase or fluorescence protein open reading frames connected with one Internal Ribosome Entry Site (IRES). Transfection of single or dual insertion constructs of these vectors into mammalian cells demonstrated that they could be utilized not only to quantify the strength of a single candidate pA site or cis element, but also to accurately measure the relative usage of two APA sites at both the mRNA (qRT-PCR) and protein levels. This represents the first reporter system that can study polyadenylation efficiency of a single pA site or element and regulation of two APA sites at both the mRNA and protein levels.
  • Spectrally controlled interferometry for measurements of flat and spherical optics

    Olszak, Artur G.; Salsbury, Chase; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-10-16)
    Conventional interferometry is widely used to measure spherical and flat surfaces with nanometer level precision but is plagued by back reflections. We describe a new method of isolating the measurement surface by controlling spectral properties of the source (Spectrally Controlled Interferometry - SCI). Using spectral modulation of the interferometer's source enables formation of localized fringes where the optical path difference is non-zero. As a consequence it becomes possible to form white-light like fringes in common path interferometers, such as the Fizeau. The proposed setup does not require mechanical phase shifting, resulting in simpler instruments and the ability to upgrade existing interferometers. Furthermore, it allows absolute measurement of distance, including radius of curvature of lenses in a single setup with possibility of improving the throughput and removing some modes of failure.
  • Challenges in coronagraph optical design

    Chipman, Russell A.; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-09-06)
    The point spread function (PSF) for astronomical telescopes and instruments depends not only on geometric aberrations and scalar wave diffraction, but also on the apodization and wavefront errors introduced by coatings on reflecting and transmitting surfaces within the optical system. Geometrical ray tracing provides incomplete image simulations for exoplanet coronagraphs with the goal of resolving planets with a brightness less than 10<^>-9 of their star located within 3 Airy disk radii. The Polaris-M polarization analysis program calculates uncorrected coating polarization aberrations couple around 10<^>-5 light into crossed polarized diffraction patterns about twice Airy disk size. These wavefronts not corrected by the deformable optics systems. Polarization aberrations expansions have shown how image defects scale with mirror coatings, fold mirror angles, and numerical aperture.
  • Volume holographic lens spectrum-splitting photovoltaic system for high energy yield with direct and diffuse solar illumination

    Chrysler, Benjamin D.; Wu, Yuechen; Kostuk, Raymond K.; Yu, Zhengshan; Univ Arizona, Elect & Comp Engn Dept; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-08-25)
    In this paper a prototype spectrum-splitting photovoltaic system based on volume holographic lenses (VHL) is designed, fabricated and tested. In spectrum-splitting systems, incident sunlight is divided in spectral bands for optimal conversion by a set of single-junction PV cells that are laterally separated. The VHL spectrum-splitting system in this paper has a form factor similar to conventional silicon PV modules but with higher efficiencies (>30%). Unlike many other spectrum-splitting systems that have been proposed in the past, the system in this work converts both direct and diffuse sunlight while using inexpensive 1-axis tracking systems. The VHL system uses holographic lenses that focus light at a transition wavelength to the boundary between two PV cells. Longer wavelength light is dispersed to the narrow bandgap cell and shorter wavelength light to the wide bandgap cell. A prototype system is designed with silicon and GaAs PV cells. The holographic lenses are fabricated in Covestro Bayfol HX photopolymer by 'stitching' together lens segments through sequential masked exposures. The PV cells and holographic lenses were characterized and the data was used in a raytrace simulation and predicts an improvement in total power output of 15.2% compared to a non-spectrum-splitting reference. A laboratory measurement yielded an improvement in power output of 8.5%.
  • Miniature camera lens design with a freeform surface

    Sasian, Jose; Yan, Yufeng; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    We present a miniature camera lens design method that uses a freeform surface based on the pedal curve to the ellipse in polynomial form. Two designs are presented and their benefits of optical performance and tolerance sensitivity are compared to designs with conventional aspheric surfaces. We also reverse a freeform design using even aspherical surfaces to show that the optimization solution of a freeform design cannot be reproduced by even aspherical surfaces.
  • Designing a freeform optic for oblique illumination

    Uthoff, Ross D.; Ulanch, Rachel N.; Williams, Kaitlyn E.; Ruiz Diaz, Liliana; King, Page; Koshel, R. John; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    The Functional Freeform Fitting (F4) method is utilized to design a freeform optic for oblique illumination of Mark Rothko's Green on Blue (1956). Shown are preliminary results from an iterative freeform design process; from problem definition and specification development to surface fit, ray tracing results, and optimization. This method is applicable to both point and extended sources of various geometries.
  • Optical transfer function expansion of quadratic pupils

    Schwiegerling, Jim; Univ Arizona (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    Quadratic pupils representing Gaussian apodization and defocus are expanded into Zernike polynomials. Combinations of the pupil expansion coefficients are used, in turn to expand the Optical Transfer Function into a novel set of basis functions.
  • Joseph Petzval lens design approach

    Sasián, José; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    We pose that there is enough information left to reconstruct Petzval lens design approach, and answer the question of how Joseph Petzval design his famous portrait objective.
  • A method for the design of unsymmetrical optical systems using freeform surfaces

    Reshidko, Dmitry; Sasian, Jose; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    A systematic method for the design of unsymmetrical optical systems is described. Freeform optical surfaces are constructed by superposition of a conic segment and a polynomial, and successfully applied to design relatively fast wide field-of-view optical systems.
  • 3D visualization of optical ray aberration and its broadcasting to smartphones by ray aberration generator

    Hellman, Brandon; Bosset, Erica; Ender, Luke; Jafari, Naveed; McCann, Phillip; Nguyen, Chris; Summitt, Chris; Wang, Sunglin; Takashima, Yuzuru; Univ Arizona (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    The ray formalism is critical to understanding light propagation, yet current pedagogy relies on inadequate 2D representations. We present a system in which real light rays are visualized through an optical system by using a collimated laser bundle of light and a fog chamber. Implementation for remote and immersive access is enabled by leveraging a commercially available 3D viewer and gesture-based remote controlling of the tool via bi-directional communication over the Internet.
  • Air lens vs aspheric surface: a lens design case study

    Gao, Weichuan; Sasian, Jose; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    We discuss the behavior of air lenses in lens design. The structural aberration coefficients of a thin air lens are derived and compared with their glass thin lens counterpart. Examples are provided for a telephoto lens and the Monochromatic Quartet where air lenses or aspheric surfaces are used.
  • Image formation in coronagraphs due to mirror polarization aberrations

    Chipman, Russell A.; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-11-27)
    The PSF for astronomical telescopes and instruments depends not only on geometric wavefront aberrations, but also on those polarization aberrations from the polarization properties of reflecting and transmitting surfaces. The image plane irradiance distribution is the linear superposition of four PSF images: one for each of the two orthogonal polarizations and one for each of two cross-coupled polarization terms.
  • Development of the LunaH-Map miniature neutron spectrometer

    Vogel, Samuel; Frank, Rebecca; Stoddard, Graham; Christian, James F.; Johnson, Erik B.; Hardgrove, Craig; Starr, Richard; West, Stephen; Univ Arizona, Sch Earth & Space Explorat (SPIE-INT SOC OPTICAL ENGINEERING, 2017-08-24)
    There is strong evidence that water-ice is relatively abundant within permanently shadowed lunar surface materials, particularly at the poles. Evidence for water-ice has been observed within the impact plume of the LCROSS mission and is supported by data gathered from the Lunar Exploration Neutron Detector (LEND) and the Lunar Prospector Neutron Spectrometer (LPNS). Albedo neutrons from the Moon are used for detection of hydrogen, where the epi-thermal neutron flux decreases as hydrogen content increases. The origin on the concentration of water within permanently shadowed regions is not completely understood, and the Lunar Polar Hydrogen Mapper (LunaH-Map) mission is designed to provide a high-resolution spatial distribution of the hydrogen content over the southern pole using a highly elliptical, low perilune orbit. The LunaH-Map spacecraft is a 6U cubesat consisting of the Miniature Neutron Spectrometer (Mini-NS). Mini-NS is not collimated, requiring a low altitude to achieve a higher spatial resolution compared to previous missions. To develop a compact neutron detector for epi-thermal neutrons, the Mini-NS comprises of 2-cm thick slabs of CLYC (Cs2LiYCl6), which provide a sensitivity similar to a 10-atm, 5.7-cm diameter He-3 tubes, as used in LPNS. The Mini-NS digital processing electronics can discriminate by shape and height to determine signal (albedo neutrons) from background (cosmic rays). The Mini-NS achieves a total active sensing area of 200 cm(2) and is covered with a cadmium sheet to shield against thermal neutrons. The research and development on the detector modules show a robust design ready for space flight.
  • Neutron detector development for microsatellites

    Bodnarik, Julia G.; Hamara, Dave; Groza, Michael; Stowe, Ashley C.; Burger, Arnold; Stassun, Keivan G.; Matei, Liviu; Egner, Joanna C.; Harris, Walter M.; Buliga, Vladimir; Univ Arizona, Lunar & Planetary Lab (SPIE-INT SOC OPTICAL ENGINEERING, 2017-08-29)
    We present a preliminary design for a novel neutron detection system that is compact, lightweight, and low power consuming, utilizing the CubeSat platform making it suitable for space-based applications. This is made possible using the scintillating crystal lithium indium diselenide ((LiInSe2)-Li-6), the first crystal to include Li-6 in the crystalline structure, and a silicon avalanche photodiode (Si-APD). The schematics of this instrument are presented as well as the response of the instrument to initial testing under alpha, gamma and neutron radiation. A principal aim of this work is to demonstrate the feasibility of such a neutron detection system within a CubeSat platform. The entire end-to-end system presented here is 10 cm x 10 cm x 15 cm, weighs 670 grams and requires 5 V direct current at 3 Watts.
  • General testing method for refractive surfaces based on reverse Hartmann test

    Wang, Daodang; Xu, Ping; Liang, Rongguang; Ming, Kong; Zhao, Jun; Gong, Zhidong; Mo, Linhai; Mo, Shuhui; Xie, Zhongmin; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-08-23)
    The testing technique with high dynamic range is required to meet the measurement of refractive wavefront with large distortion from test refractive surface. A general deflectometric method based on reverse Hartmann test is proposed to test refractive surfaces. Ray tracing of the modeled testing system is performed to reconstruct the refractive wavefront from test surface, in which computer-aided optimization of system geometry is performed to calibrate the geometrical error. For the refractive wavefront error with RMS 255 mu m, the testing precision better than 0.5 mu m is achieved.
  • Geometrical error calibration in reflective surface testing based on reverse Hartmann test

    Wang, Daodang; Gong, Zhidong; Xu, Ping; Liang, Rongguang; Kong, Ming; Zhao, Jun; Wang, Chao; Mo, Linhai; Mo, Shuhui; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2017-08-23)
    In the fringe-illumination deflectometry based on reverse-Hartmann-test configuration, ray tracing of the modeled testing system is performed to reconstruct the test surface error. Careful calibration of system geometry is required to achieve high testing accuracy. To realize the high-precision surface testing with reverse Hartmann test, a computer-aided geometrical error calibration method is proposed. The aberrations corresponding to various geometrical errors are studied. With the aberration weights for various geometrical errors, the computer-aided optimization of system geometry with iterative ray tracing is carried out to calibration the geometrical error, and the accuracy in the order of sub-nanometer is achieved.

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