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


    Massaro, Toni M.; Norton, Helen; Univ Arizona, James E Rogers Coll Law; Univ Arizona, James E Rogers Coll Law, Constitut Law (NORTHWESTERN UNIV, 2016)
    Computers with communicative artificial intelligence (AI) are pushing First Amendment theory and doctrine in profound and novel ways. They are becoming increasingly self-directed and corporal in ways that may one day make it difficult to call the communication ours versus theirs. This, in turn, invites questions about whether the First Amendment ever will (or ever should) cover AI speech or speakers even absent a locatable and accountable human creator. In this Article, we explain why current free speech theory and doctrine pose surprisingly few barriers to this counterintuitive result; their elasticity suggests that speaker humanness no longer may be a logically essential part of the First Amendment calculus. We further observe, however, that free speech theory and doctrine provide a basis for regulating, as well as protecting, the speech of nonhuman speakers to serve the interests of their human listeners should strong AI ever evolve to this point. Finally, we note that the futurist implications we describe are possible, but not inevitable. Moreover, contemplating these outcomes for AI speech may inspire rethinking of the free speech theory and doctrine that make them plausible.
  • A Theorem at the Core of Colliding Bias

    Shahar, Doron J.; Shahar, Eyal; Univ Arizona, Dept Math; Univ Arizona, Dept Epidemiol & Biostat, Mel & Enid Zuckerman Coll Publ Hlth (WALTER DE GRUYTER GMBH, 2017-05)
    Conditioning on a shared outcome of two variables can alter the association between these variables, possibly adding a bias component when estimating effects. In particular, if two causes are marginally independent, they might be dependent in strata of their common effect. Explanations of the phenomenon, however, do not explicitly state when dependence will be created and have been largely informal. We prove that two, marginally independent, causes will be dependent in a particular stratum of their shared outcome if and only if they modify each other's effects, on a probability ratio scale, on that value of the outcome variable. Using our result, we also qualify the claim that such causes will "almost certainly" be dependent in at least one stratum of the outcome: dependence must be created in one stratum of a binary outcome, and independence can be maintained in every stratum of a trinary outcome.
  • Gle1 Regulates RNA Binding of the DEAD-Box Helicase Ded1 in Its Complex Role in Translation Initiation

    Aryanpur, Peyman P.; Regan, Chelsea A.; Collins, John M.; Mittelmeier, Telsa M.; Renner, David M.; Vergara, Ashley M.; Brown, Nicolette P.; Bolger, Timothy A.; Univ Arizona, Dept Mol & Cellular Biol (AMER SOC MICROBIOLOGY, 2017-11)
    DEAD-box proteins (DBPs) are required in gene expression to facilitate changes to ribonucleoprotein complexes, but the cellular mechanisms and regulation of DBPs are not fully defined. Gle1 is a multifunctional regulator of DBPs with roles in mRNA export and translation. In translation, Gle1 modulates Ded1, a DBP required for initiation. However, DED1 overexpression causes defects, suggesting that Ded1 can promote or repress translation in different contexts. Here we show that GLE1 expression suppresses the repressive effects of DED1 in vivo and Gle1 counteracts Ded1 in translation assays in vitro. Furthermore, both Ded1 and Gle1 affect the assembly of preinitiation complexes. Through mutation analysis and binding assays, we show that Gle1 inhibits Ded1 by reducing its affinity for RNA. Our results are consistent with a model wherein active Ded1 promotes translation but inactive or excess Ded1 leads to translation repression. Gle1 can inhibit either role of Ded1, positioning it as a gatekeeper to optimize Ded1 activity to the appropriate level for translation. This study suggests a paradigm for finely controlling the activity of DEAD-box proteins to optimize their function in RNA-based processes. It also positions the versatile regulator Gle1 as a potential node for the coordination of different steps of gene expression.
  • Search for diboson resonances in hadronic final states in 139 fb(-1) of pp collisions at root s=13 TeV with the ATLAS detector

    Berlendis, S.; Cheu, E.; Johns, K.A.; Jones, S.; Lampl, W.; LeBlanc, M.; Leone, R.; Loch, P.; Nayyar, R.; Varnes, E.W.; et al. (SPRINGER, 2019-09-12)
    Narrow resonances decaying into WW, WZ or ZZ boson pairs are searched for in 139 fb(-1) of proton-proton collision data at a centre-of-mass energy of root s = 13TeV recorded with the ATLAS detector at the Large Hadron Collider from 2015 to 2018. The diboson system is reconstructed using pairs of high transverse momentum, large-radius jets. These jets are built from a combination of calorimeter- and tracker-inputs compatible with the hadronic decay of a boosted W or Z boson, using jet mass and substructure properties. The search is performed for diboson resonances with masses greater than 1.3TeV. No significant deviations from the background expectations are observed. Exclusion limits at the 95% confidence level are set on the production cross-section times branching ratio into dibosons for resonances in a range of theories beyond the Standard Model, with the highest excluded mass of a new gauge boson at 3.8TeV in the context of mass-degenerate resonances that couple predominantly to gauge bosons.
  • What's New in Musculoskeletal Infection: Update Across Orthopaedic Subspecialties

    Chen, Antonia F.; Nana, Arvind D.; Nelson, Sandra B.; McLaren, Alex; Univ Arizona, Coll Med Phoenix (LIPPINCOTT WILLIAMS & WILKINS, 2017-07-19)
  • Shear-Wave Elastography: Basic Physics and Musculoskeletal Applications

    Taljanovic, Mihra S; Gimber, Lana H; Becker, Giles W; Latt, L Daniel; Klauser, Andrea S; Melville, David M; Gao, Liang; Witte, Russell S; Univ Arizona, Coll Med, Dept Med Imaging; Univ Arizona, Coll Med, Dept Orthopaed Surg; et al. (RADIOLOGICAL SOC NORTH AMERICA, 2017)
    In the past 2 decades, sonoelastography has been progressively used as a tool to help evaluate soft-tissue elasticity and add to information obtained with conventional gray-scale and Doppler ultrasonographic techniques. Recently introduced on clinical scanners, shear-wave elastography (SWE) is considered to be more objective, quantitative, and reproducible than compression sonoelastography with increasing applications to the musculoskeletal system. SWE uses an acoustic radiation force pulse sequence to generate shear waves, which propagate perpendicular to the ultrasound beam, causing transient displacements. The distribution of shear-wave velocities at each pixel is directly related to the shear modulus, an absolute measure of the tissue's elastic properties. Shear-wave images are automatically coregistered with standard B-mode images to provide quantitative color elastograms with anatomic specificity. Shear waves propagate faster through stiffer contracted tissue, as well as along the long axis of tendon and muscle. SWE has a promising role in determining the severity of disease and treatment follow-up of various musculoskeletal tissues including tendons, muscles, nerves, and ligaments. This article describes the basic ultrasound physics of SWE and its applications in the evaluation of various traumatic and pathologic conditions of the musculoskeletal system.
  • Search for excited electrons singly produced in proton-proton collisions at root s=13 TeV with the ATLAS experiment at the LHC

    Berlendis, S.; Cheu, E.; Delitzsch, C.M.; Johns, K.A.; Jones, S.; Lampl, W.; LeBlanc, M.; Leone, R.; Loch, P.; Rutherfoord, J.P.; et al. (SPRINGER, 2019-09)
    A search for excited electrons produced in pp collisions at root s = 13 TeV via a contact interaction q (q) over bar -> ee* is presented. The search uses 36.1 fb(-1) of data collected in 2015 and 2016 by the ATLAS experiment at the Large Hadron Collider. Decays of the excited electron into an electron and a pair of quarks (eq (q) over bar) are targeted in final states with two electrons and two hadronic jets, and decays via a gauge interaction into a neutrino and a W boson (nu W) are probed in final states with an electron, missing transverse momentum, and a large-radius jet consistent with a hadronically decaying W boson. No significant excess is observed over the expected backgrounds. Upper limits are calculated for the pp -> ee* -> eeq (q) over bar and pp -> ee* -> e nu W production cross sections as a function of the excited electron mass m(e)* at 95% confidence level. The limits are translated into lower bounds on the compositeness scale parameter Lambda of the model as a function of m(e)*. For m(e)* < 0.5 TeV, the lower bound for Lambda is 11 TeV. In the special case of m(e)* = Lambda, the values of m(e)* < 4.8 TeV are excluded. The presented limits on Lambda are more stringent than those obtained in previous searches.
  • Measurement of the inclusive cross-section for the production of jets in association with a Z boson in proton-proton collisions at 8 TeV using the ATLAS detector

    Berlendis, S.; Cheu, E.; Delitzsch, C.M.; Johns, K.A.; Jones, S.; Lampl, W.; LeBlanc, M.; Leone, R.; Loch, P.; Rutherfoord, J.P.; et al. (SPRINGER, 2019-10)
    The inclusive cross-section for jet production in association with a Z boson decaying into an electronpositron pair is measured as a function of the transverse momentum and the absolute rapidity of jets using 19.9 fb(-1) of root s = 8 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. The measured Z + jets cross-section is unfolded to the particle level. The cross-section is compared with state-of-the-art Standard Model calculations, including the next-to-leading-order and next-to-next-to-leading-order perturbative QCD calculations corrected for non-perturbative and QED radiation effects. The results of the measurements cover final-state jets with transverse momenta up to 1 TeV and show good agreement with fixed-order calculations.
  • Identification of boosted Higgs bosons decaying into b-quark pairs with the ATLAS detector at 13 TeV

    Berlendis, S.; Cheu, E.; Delitzsch, C.M.; Johns, K.A.; Jones, S.; Lampl, W.; LeBlanc, M.; Leone, R.; Loch, P.; Rutherfoord, J.P.; et al. (SPRINGER, 2019-10)
    This paper describes a study of techniques for identifying Higgs bosons at high transverse momenta decaying into bottom-quark pairs, H -> b (b) over bar, for proton-proton collision data collected by the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy root s = 13 TeV. These decays are reconstructed from calorimeter jets found with the anti-k(t) R = 1.0 jet algorithm. To tag Higgs bosons, a combination of requirements is used: b-tagging of R = 0.2 track-jets matched to the large-R calorimeter jet, and requirements on the jet mass and other jet substructure variables. The Higgs boson tagging efficiency and corresponding multijet and hadronic top-quark background rejections are evaluated using Monte Carlo simulation. Several benchmark tagging selections are defined for different signal efficiency targets. The modelling of the relevant input distributions used to tag Higgs bosons is studied in 36 fb(-1) of data collected in 2015 and 2016 using g -> b (b) over bar and Z(-> b (b) over bar)gamma event selections in data. Both processes are found to be well modelled within the statistical and systematic uncertainties.
  • An Attempt to Probe the Radio Jet Collimation Regions in NGC 4278, NGC 4374 (M84), and NGC 6166

    Ly, C.; Walker, R. C.; Wrobel, J. M.; Univ Arizona, Steward Observ (IOP Publishing, 2004-01)
    NRAO Very Long Baseline Array (VLBA) observations of NGC 4278, NGC 4374 (M84), NGC 6166, and M87 (NGC 4486) have been made at 43 GHz in an effort to image the jet collimation region. This is the first attempt to image the first three sources at 43 GHz using very long baseline interferometry (VLBI) techniques. These three sources were chosen because their estimated black hole mass and distance implied a Schwarzschild radius with large angular size, giving hope that the jet collimation regions could be studied. Phase referencing was utilized for the three sources because of their expected low flux densities. M87 was chosen as the calibrator for NGC 4374 because it satisfied the phase-referencing requirements: near the source and sufficiently strong. Having observed M87 for a long integration time, we have detected its subparsec jet, allowing us to confirm previous high-resolution observations made by Junor, Biretta, & Livio, who have indicated that a wide opening angle was seen near the base of the jet. Phase referencing successfully improved our image sensitivity, yielding detections and providing accurate positions for NGC 4278, NGC 4374, and NGC 6166. These sources are point dominated but show suggestions of extended structure in the direction of the large-scale jets. However, higher sensitivity will be required to study their subparsec jet structure.
  • Uncommon BRAF Mutations Associated with Durable Response to Immunotherapy in Patients with Metastatic Melanoma

    Swofford, Brenen P.; Homsi, Jade; Univ Arizona, Coll Med Phoenix (HINDAWI LTD, 2017)
    Melanoma is a disease process which has been increasing in incidence over the past three decades and metastatic melanoma carries a poor prognosis. Through genetic studies of this disease, it has been determined that the BRAF V600 mutation plays a major role in the pathophysiology of the disease and this has led to the utilization of targeted therapy (BRAF and MEK inhibitors) in its treatment. Other BRAF mutations (non-V600 mutations) are rare in melanoma and targeted therapy is not indicated for patients with these mutations due to reduced response rates. An emerging option for metastatic melanoma with uncommon BRAF mutations is immunotherapy using checkpoint inhibitors such as PD-1 inhibitors or CTLA-4 inhibitors. Currently, it is unknown how patients with BRAF non-V600 mutations respond to immunotherapy. This report will examine the effect of immunotherapy on two distinct metastatic melanoma patients, each with uncommon BRAF mutations, occurring outside the V600 locus (E586K and G469E). These patients were noted to have a durable, complete response when treated with immunotherapy and continue to exhibit a response 9 and 15 months after discontinuing therapy. Further research and clinical trials are needed to study patients with uncommon BRAF mutations and the potential therapeutic benefit of immunotherapy.
  • Major Health Law and Policy Positions Among 2020 Democratic Presidential Candidates

    Hodge, James G; Barraza, Leila; Castagne, Michelle; Fleming, Hannah-Kaye; White, Erica N; Univ Arizona, Zuckerman Coll Publ Hlth (SAGE PUBLICATIONS INC, 2019-09-01)
  • What about aging? Perspectives from high school teachers and students on integrating aging into the high school curriculum

    Davis, Tracy E K; Sokan, Amanda E; Univ Arizona, Div Publ Hlth & Translat Res, Mel & Enid Zuckerman Coll Publ Hlth (ROUTLEDGE JOURNALS, TAYLOR & FRANCIS LTD, 2019-10-02)
    Most educational programs on aging target college students in disciplines which might provide services or work with older adults, such as medicine or social work, to the exclusion of students in high school. The purpose of this study is to better understand high school students and teacher?s attitudes and perceptions regarding aging. Focus groups were conducted to collect data for this study. A total of 35 teachers and 55 students participated in the study. Findings indicate that attitudes about aging are both positive and negative, however, there is a consensus among both teachers and students that incorporating aging into the high school curriculum would be beneficial. Teachers are in need of strategies to incorporate aging education into the high school curriculum, as there are many barriers. Results from this study can be used to aid in the development of educational modules designed to incorporate aging content into the curriculum.
  • Antiretroviral therapy and vaginally administered contraceptive hormones: a three-arm, pharmacokinetic study

    Scarsi, Kimberly K; Cramer, Yoninah S; Rosenkranz, Susan L; Aweeka, Francesca; Berzins, Baiba; Coombs, Robert W; Coughlin, Kristine; Moran, Laura E; Zorrilla, Carmen D; Akelo, Victor; et al. (ELSEVIER INC, 2019-09-01)
    We did a parallel, three-group, pharmacokinetic evaluation at HIV clinics in Asia (two sites), South America (five), sub-Saharan Africa (three), and the USA (11) between Dec 30, 2014, and Sept 12, 2016. We enrolled women with HIV who were either ART-naive (control group; n=25), receiving efavirenz-based ART (n=25), or receiving atazanavir-ritonavir-based ART (n=24). Women receiving ART were required to be on the same regimen for at least 30 days, with 400 copies or less per mL of plasma HIV-1 RNA; women not receiving ART had CD4 counts of 350 cells per μL or less. We excluded participants who had a bilateral oophorectomy or conditions that were contraindicated in the intravaginal ring product labelling. An intravaginal ring releasing etonogestrel and ethinylestradiol was inserted at entry (day 0). Single plasma samples for hormone concentrations were collected on days 7, 14, and 21 after intravaginal ring insertion. The primary outcome was the plasma concentration of etonogestrel and ethinylestradiol on day 21. Etonogestrel and ethinylestradiol concentrations were compared between each ART group and the control group by geometric mean ratio (GMR) with 90% CIs and Wilcoxon rank-sum test. As secondary outcomes, efavirenz or ritonavir-boosted atazanavir concentrations were assessed by 8-h intensive pharmacokinetic sampling at entry before intravaginal ring insertion and before intravaginal ring removal on day 21. Antiretroviral areas under the concentration-time curve (AUC0-8 h) were compared before and after intravaginal ring insertion by GMR (90% CI) and Wilcoxon signed-rank test. This study is registered with ClinicalTrials.gov, number NCT01903031.
  • Travel Nurse Onboarding: Current Trends and Identified Needs

    Bethel, Claire; Olson, Susan; Bay, Curt; Uyeda, Tami; Johnson, Karen; Univ Arizona, Coll Nursing (LIPPINCOTT WILLIAMS & WILKINS, 2019-09-01)
    OBJECTIVE The purpose of this study was to describe current practices for onboarding travel nurses (TRNs) and identify TRNs' specific onboarding needs. BACKGROUND Onboarding must be streamlined and organized for TRNs to provide safe patient care. METHODS Cross-sectional descriptive survey was used with 306 TRNs throughout United States who were recruited electronically from a closed social media group page. RESULTS The TRNs identified critical information, including unit patient ratios, onboarding schedule 7 to 14 days before travel assignment start, and login IDs/accesses on day 1. Travel nurse onboarding and competency assessment checklists should be specific to the unit/facility where they will work. CONCLUSION Findings from this study have the potential to support hospitals in the development of streamlined and tailored TRN onboarding to support regulatory compliance and patient safety as well as realize significant cost savings for TRN onboarding.
  • Rectangular domain curl polynomial set for optical vector data processing and analysis

    Aftab, Maham; Graves, Logan R.; Burge, James H.; Smith, Greg A.; Oh, Chang-Jin; Kim, Dae Wook; Univ Arizona, Steward Observ; Univ Arizona, Large Opt Fabricat & Testing Grp (SPIE-SOC PHOTO-OPTICAL INSTRUMENTATION ENGINEERS, 2019-09-24)
    Rectangular pupils are employed in many optical applications such as lasers and anamorphic optics, as well as for detection and metrology systems such as some Shack−Hartmann wavefront sensors and deflectometry systems. For optical fabrication, testing, and analysis in the rectangular domain, it is important to have a well-defined set of polynomials that are orthonormal over a rectangular pupil. Since we often measure the gradient of a wavefront or surface, it is necessary to have a polynomial set that is orthogonal over a rectangular pupil in the vector domain as well. We derive curl (called C) polynomials based on two-dimensional (2-D) versions of Chebyshev polynomials of the first kind. Previous work derived a set of polynomials (called G polynomials) that are obtained from the gradients of the 2-D Chebyshev polynomials. We show how the two sets together can be used as a complete representation of any vector data in the rectangular domain. The curl polynomials themselves or the complete set of G and C polynomials has many interesting applications. Two of those applications shown are systematic error analysis and correction in deflectometry systems and mapping imaging distortion.
  • Defects in THO/TREX-2 function cause accumulation of novel cytoplasmic mRNP granules that can be cleared by autophagy

    Eshleman, Nichole; Liu, Guangbo; McGrath, Kaitlyn; Parker, Roy; Buchan, J Ross; Univ Arizona, Dept Mol & Cellular Biol (COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2016-06-01)
    The nuclear THO and TREX-2 complexes are implicated in several steps of nuclear mRNP biogenesis, including transcription, 3′ end processing and export. In a recent genomic microscopy screen in Saccharomyces cerevisiae for mutants with constitutive stress granules, we identified that absence of THO and TREX-2 complex subunits leads to the accumulation of Pab1-GFP in cytoplasmic foci. We now show that these THO/TREX-2 mutant induced foci (“TT foci”) are not stress granules but instead are a mRNP granule containing poly(A)+ mRNA, some mRNP components also found in stress granules, as well several proteins involved in mRNA 3′ end processing and export not normally seen in stress granules. In addition, TT foci are resistant to cycloheximide-induced disassembly, suggesting the presence of mRNPs impaired for entry into translation. THO mutants also exhibit defects in normal stress granule assembly. Finally, our data also suggest that TT foci are targeted by autophagy. These observations argue that defects in nuclear THO and TREX-2 complexes can affect cytoplasmic mRNP function by producing aberrant mRNPs that are exported to cytosol, where they accumulate in TT foci and ultimately can be cleared by autophagy. This identifies a novel mechanism of quality control for aberrant mRNPs assembled in the nucleus.
  • Tobacco Use Behaviors and Perceptions of Parental Smokers in the Emergency Department Setting

    Mahabee-Gittens, E Melinda; Merianos, Ashley L; Stone, Lara; Tabangin, Meredith E; Khoury, Jane C; Gordon, Judith S (SAGE PUBLICATIONS LTD, 2019-06-19)
    Parents were 56.1% non-Hispanic black; 87.5% women; mean (SD) number of cigarettes smoked/day was 10.5(6.8). A higher proportion of parents with younger children <3 years old reported smoking bans compared with parents with older children ⩾3 to <18 years old (41.3% vs 19.7%, P < .0001). Subsequent analyses revealed this pattern for both black and white parents. A total of 212 (51%) of children had biochemical assessment of TSE; 89.6% had detectable TSE. Younger children had significantly higher cotinine levels than older children independent of their race (P < .001).
  • Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex

    Hall, Branwen M; Roberts, Sue A; Cordes, Matthew H J; Univ Arizona, Dept Chem & Biochem (OXFORD UNIV PRESS, 2019-07-26)
    The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein–DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.
  • Constraining the Early History of Mercury and Its Core Dynamo by Studying the Crustal Magnetic Field

    Oliveira, Joana S.; Hood, Lon L.; Langlais, Benoit; Univ Arizona, Lunar & Planetary Lab (AMER GEOPHYSICAL UNION, 2019-09-09)
    Low‐altitude magnetic field data acquired by MESSENGER (MErcury Surface, Space ENvironment, GEochemistry, and Ranging) over a small portion of Mercury's surface revealed weak crustal magnetic field signatures. Here we study the crustal magnetic anomalies associated with impact craters on Mercury. We assume that the sources of these anomalies consist of impact melt, enriched in impactor iron. We assume that the subsurfaces of Mercury's impact craters have cooled in the presence of a constant global magnetic field, thus becoming thermoremanently magnetized. We invert for the crustal magnetization direction within five craters using a unidirectional magnetization model which assumes that the melt impact rocks recorded the constant core magnetic field present when the crater was formed and that the crater's magnetization has not been altered since its formation. From the best fitting magnetization direction we then obtain the corresponding north magnetic paleopole position assuming a centered core dipolar field. Results show that all five magnetic paleopoles lie in the southern hemisphere but are not required to be located near the present‐day magnetic pole, which lies near the south geographic pole. Accounting for the uncertainties, we show that our results all agree in a common small region that excludes the current magnetic pole. This strongly suggests that the dynamo has evolved with time. Our results represent valuable information for understanding the evolution of Mercury and emphasize the importance of including more anomaly analyses to complete and refine our conclusions.

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