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These collections include publications and data from University of Arizona faculty, staff and researchers. The UA Faculty Publications collection consists primarily of open access versions of published journal articles, but also contains conference proceedings and other unique materials from faculty, staff and researchers. Organizational collections, such as the College of Agricultural and Life Sciences Publications, and Water Resources Research Center, contain additional faculty publications such as departmentally produced technical bulletins, technical reports, and working papers.


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Recent Submissions

  • Standoff 250 m Open-path Detection of Chemical Plumes Using a Broadband Swept-ECQCL

    Phillips, Mark C.; Bernacki, Bruce E.; Harilal, Sivanandan S.; Yeak, Jeremy; Jones, R. Jason; Univ Arizona, Coll Opt Sci (IEEE, 2019)
    We measure chemical plumes at a 250 m standoff distance by sweeping an external cavity quantum cascade laser over a broad spectral range of 920-1220 cm(-1) at a rate of 200 Hz. (C) 2019 The Author(s)
  • Time-Resolved Dual Frequency Comb Spectroscopy for Broadband Multi-Species Detection in Laser-Induced Plasmas

    Lecaplain, Caroline; Zhang, Yu; Weeks, Reagan R. D.; Yeak, Jeremy; Harilal, Sivanandan S.; Phillips, Mark C.; Jones, R. Jason; Univ Arizona, Coll Opt Sci; Univ Arizona, Dept Phys (IEEE, 2019)
    We present the first results using time-resolved broadband dual-comb spectroscopy in a laser-induced plasma. Preliminary results identifying multiple species in a Nd magnet will be shown. (c) 2019 The Author(s)
  • Time-Resolved Dual Frequency Comb Phase Spectroscopy of Laser-Induced Plasmas

    Weeks, Reagan R. D.; Zhang, Yu; Lecaplain, Caroline; Yeak, Jeremy; Harilal, Sivanandan S.; Phillips, Mark C.; Jones, R. Jason; Univ Arizona, Coll Opt Sci; Univ Arizona, Dept Phys (IEEE, 2019)
    We present the first results using time-resolved dual-comb phase spectroscopy in a laser-induced plasma. It can allow for simultaneous plasma characterization as well as multi-species detection and plasma characterization. (c) 2019 The Author(s)
  • Characterization of a Laser-Induced Plasma Using Time-Resolved Dual-Frequency-Comb Spectroscopy

    Zhang, Yu; Lecaplain, Caroline; Weeks, Reagan R. D.; Yeak, Jeremy; Harilal, Sivanandan S.; Phillips, Mark C.; Jones, R. Jason; Univ Arizona, Dept Phys; Univ Arizona, Coll Opt Sci (IEEE, 2019)
    We characterize the dynamics of laser-induced plasmas using time-resolved dual-frequency-comb spectroscopy. The temporal evolution of plasma's temperature, population number density are estimated for multiple Fe transitions. (C) 2019 The Author(s)
  • Dual-comb laser system for time-resolved studies of fireballs in the MIR

    Rhoades, Ryan T.; Lecaplain, Caroline; Schunemann, Peter G.; Jones, R. Jason; Univ Arizona, Coll Opt Sci (IEEE, 2019)
    We present a high power all-fiber dual-comb system suitable for time-resolved spectroscopy measurements in the mid-infrared to study explosion dynamics and detection of chemical species. (C) 2019 The Author(s)
  • Using a mechanistic framework to characterise chemistry students' reasoning in written explanations

    Moreira, Patricia; Marzabal, Ainoa; Talanquer, Vicente; Univ Arizona, Dept Chem & Biochem (ROYAL SOC CHEMISTRY, 2019-01-02)
    The central goal of this research study was to characterise the different types of reasoning manifested by high school chemistry students when building initial written explanations of a natural phenomenon. In particular, our study participants were asked to explain why a mixture of water and alcohol works as an antifreeze. Data collected in the form of written explanations were analysed using a mechanistic reasoning framework based on the characterisation of system components (e.g., entities, properties, activities, organisation) and paying attention to the causal models invoked by the participants in their explanations. Our analysis revealed that students at the same educational level construct a wide range of explanations for the same phenomenon that are indicative of different reasoning modes going from descriptive to relational to simple causal to emerging mechanistic. Although the explanations generated by students in our sample were not very sophisticated in terms of the causal models on which they relied, some participants were capable of generating mechanistic explanations using particulate models of matter. The framework for analysis introduced in this contribution can be of use to teachers and researchers in the characterisation of student reasoning.
  • Investigating the effect of teacher mediation on student expressed reasoning

    Moreira, Patricia; Marzabal, Ainoa; Talanquer, Vicente; Univ Arizona, Dept Chem & Biochem (ROYAL SOC CHEMISTRY, 2019-07-01)
    Understanding how chemistry teachers' interventions shape the reasoning that students express after a lesson is critical to support prospective and in-service teachers as they work with students' ideas in the classroom. In this qualitative research study, we analysed changes in the reasoning expressed by 10th grade students in a Chilean school in their written explanations about freezing point depression before and after a lesson on the topic. We also investigated how the teacher's interventions shaped the type of reasoning expressed by participating students. Our findings revealed significant shifts in the types of explanations generated after the lesson. A significant number of students transitioned from relational to simple causal reasoning in their pre- and post-lesson explanations. After the lesson most of the explanations were based on the activities of one or more of the system's entities. Analysis of teacher-student interactions during the observed lesson suggests that the teacher's mediation played a central role in the shift towards simple causal reasoning with centralized causality that was observed. The teacher in our study was more skilled at eliciting students' ideas than at helping students develop them with proper scaffolding. Thus, the observed classroom talk could not be considered as accountable talk, as most of the key ideas were introduced, selected, or reshaped by the teacher.
  • Ironic Consumption

    Warren, Caleb; Mohr, Gina S; Univ Arizona, Eller Coll Management (OXFORD UNIV PRESS INC, 2018-08-07)
    Ironic consumption refers to using a product (brand, style, behavior, etc.) with the intent of signaling a meaning (identity, message, belief, etc.) that reverses the conventional meaning of the product. We report five studies showing that people are more likely to think that a consumer is using a product ironically when the product is incongruent with the consumer's known identity or beliefs. The impression that ironic consumers make on an observer depends on the observer's relationship with the consumed product. When a consumer uses a product associated with the observer's in-group (e.g., wearing a "Powered by Kale" shirt in front of a vegan), observers have a less favorable impression if they believe the consumer is using the product ironically. Conversely, when a consumer uses a product that is not associated with the observer's in-group (e.g., wearing a "Powered by Kale" shirt in front of a meat-eater), observers have a more favorable impression if they believe the consumer is using the product ironically. Collectively, our studies suggest that consumers can use products ironically to selectively signal one meaning to an in-group (who is likely to detect irony), and another to out-groups (who are unlikely to detect irony).
  • Measurements of I-129 in the Pacific Ocean at Scripps Pier and Pacific Northwest sites: A search for effects from the 2011 Fukushima Daiichi Nuclear Power Plant accident and Hanford

    Chang, Ching-Chih; Burr, George S; Jull, A J Timothy; Russell, Joellen; Priyadarshi, Antra; Lin, Mang; Thiemens, Mark; Biddulph, Dana; Univ Arizona, AMS Lab; Univ Arizona, Dept Geosci (ELSEVIER, 2019-11-01)
    Radionuclides from the Fukushima Daiichi Nuclear Power Plant were released directly into the ocean as a result of the Great East Japan Earthquake on March 11, 2011. This material became entrained in surface ocean currents and subsequently transported for great distances. In June 2011, a few months after the disaster, we began a surface ocean 129I monitoring program, with samples from Scripps Pier, La Jolla, California, USA, with the expectation that surface currents originating off the east coast of Japan would eventually carry radionuclides to the La Jolla site. After 7 years of ocean transport, a distinct signal has not yet arrived at Scripps Pier. We have however, recorded an interesting systematic seasonal 129I time series record that stems from surface circulation variations along the California coast. To provide a more comprehensive picture of the 129I budget in coastal surface waters off the west coast of the U.S., we also include 129I data from the Columbia River, and offshore sites along the coast of Washington State. Anthropogenic nuclides are carried by the Columbia River into the Pacific Ocean from the vicinity of the decommissioned Hanford nuclear facility. We find highly elevated 129I/127I values in the Columbia River, downstream from the Hanford site, but this anthropogenic 129I becomes significantly diluted once it reaches the Pacific Ocean. Nonetheless, its imprint persists in surface seawater off the west coast of the U.S. that has significantly higher 129I/127I levels than other surface sites in the Pacific Ocean.
  • Simplified White Blood Cell Differential: An Inexpensive, Smartphone- and Paper-Based Blood Cell Count

    Bills, Matthew V.; Nguyen, Brandon T.; Yoon, Jeong-Yeol; Univ Arizona, Dept Biomed Engn (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2019-09-15)
    Sorting and measuring blood by cell type is extremely valuable clinically and provides physicians with key information for diagnosing many different disease states including: leukemia, autoimmune disorders, and bacterial infections. Despite the value, the present methods are unnecessarily costly and inhibitive particularly in resource poor settings, as they require multiple steps of reagent and/or dye additions and subsequent rinsing followed by manual counting using a hemocytometer, or they require a bulky, expensive equipment such as a flow cytometer. While direct on-paper imaging has been considered challenging, paper substrate offers a strong potential to simplify such reagent/dye addition and rinsing. In this paper, three-layer paper-based device is developed to automate such reagent/dye addition and rinsing via capillary action, and separating white blood cells (WBCs) from whole blood samples. Direct on-paper imaging is demonstrated using a commercial microscope attachment to a smartphone coupled with a blue LED and 500 nm long pass optical filter. Image analysis is accomplished using an original MATLAB code, to evaluate the total WBC count, and differential WBC count, i.e., granulocytes (primarily neutrophils) versus agranulocytes (primarily lymphocytes). Only a finger-prick of whole blood is required for this assay. The total assay time from finger-prick to data collection is under five minutes. Comparison with a hemocytometry-based manual counting corroborates the accuracy and effectiveness of the proposed method. This approach could he potentially used to help make blood cell counting technologies more readily available, especially in resource poor and point-of-care settings.
  • TWO RECONSTRUCTIONS OF AUGUST–JULY PRECIPITATION FOR CENTRAL NORTHERN ARIZONA FROM TREE RINGS

    Fletcher, Tamara; Touchan, Ramzi; Lepley, Kai; Rouini, Nesrine; Bloye, Robert; Tremarelli, Thomas S.; Peña, Kelly; Meko, David M.; Univ Arizona, Lab Tree Ring Res (TREE-RING SOC, 2019-08-07)
    This study reports two multi-century regional reconstructions of annual precipitation based on Pinus ponderosa and P. edulis from four sites in central northern Arizona. It compares standard regional and time-nested methods to generate reconstructions from 1581-2016 C.E. and 1529-2016 C.E., respectively. The strongest climate relationship is a positive correlation between total ring width and 12-month total precipitation ending in July of the growth year. The chronologies account for 50% of the variance of observed annual precipitation in the regional model and 59%, 60%, and 47% and 35% in the nested models. The two reconstructions are highly correlated (Pearson's correlation r > 0.97, p < 0.001) demonstrating that the reconstructions are highly similar over the period common to both reconstructions, with the nested-model's advantage of extending the range of the reconstruction. The precipitation reconstructions are significantly correlated (r = 0.66, p < 0.001) with the North American Drought Atlas (NADA).
  • PKCζ and JNK signaling regulate radiation-induced compensatory proliferation in parotid salivary glands

    Wong, Wen Yu; Allie, Sydney; Limesand, Kirsten H; Univ Arizona, Canc Biol Grad Interdisciplinary Program; Univ Arizona, Dept Nutr Sci (PUBLIC LIBRARY SCIENCE, 2019-07-09)
    Radiotherapy is a common treatment option for head and neck cancer patients; however, the surrounding healthy salivary glands are often incidentally irradiated during the process. As a result, patients often experience persistent xerostomia and hyposalivation, which deceases their quality of life. Clinically, there is currently no standard of care available to restore salivary function. Repair of epithelial wounds involves cellular proliferation and establishment of polarity in order to regenerate the tissue. This process is partially mediated by protein kinase C zeta (PKC zeta), an apical polarity regulator; however, its role following radiation damage is not completely understood. Using an in vivo radiation model, we show a significant decrease in active PKC zeta in irradiated murine parotid glands, which correlates with increased proliferation that is sustained through 30 days post-irradiation. Additionally, salivary glands in PKC zeta null mice show increased basal proliferation which radiation treatment did not further potentiate. Radiation damage also activates Jun N-terminal kinase (JNK), a proliferation-inducing mitogen-activated protein kinase normally inhibited by PKC zeta. In both a PKC zeta null mouse model and in primary salivary gland cell cultures treated with a PKC zeta inhibitor, there was increased JNK activity and production of downstream proliferative transcripts. Collectively, these findings provide a potential molecular link by which PKC zeta suppression following radiation damage promotes JNK activation and radiation-induced compensatory proliferation in the salivary gland.
  • Inverse scattering transform for two-level systems with nonzero background

    Biondini, Gino; Gabitov, Ildar; Kovačič, Gregor; Li, Sitai; Univ Arizona, Dept Math (AMER INST PHYSICS, 2019-07-24)
    We formulate the inverse scattering transform for the scalar Maxwell-Bloch system of equations describing the resonant interaction of light and active optical media in the case when the light intensity does not vanish at infinity. We show that pure background states in general do not exist with a nonzero background field. We then use the formalism to compute explicitly the soliton solutions of this system. We discuss the initial population of atoms and show that the pure soliton solutions do not correspond to a pure state initially. We obtain a representation for the soliton solutions in determinant form and explicitly write down the one-soliton solutions. We next derive periodic solutions and rational solutions from the one-soliton solutions. We then analyze the properties of these solutions, including discussion of the sharp-line and small-amplitude limits, and thereafter show that the two limits do not commute. Finally, we investigate the behavior of general solutions, showing that solutions are stable (i.e., the radiative parts of solutions decay) only when initially atoms in the ground state dominate, i.e., initial population inversion is negative. Published under license by AIP Publishing.
  • Online yoga in myeloproliferative neoplasm patients: results of a randomized pilot trial to inform future research

    Huberty, Jennifer; Eckert, Ryan; Dueck, Amylou; Kosiorek, Heidi; Larkey, Linda; Gowin, Krisstina; Mesa, Ruben; Univ Arizona (BMC, 2019-06-07)
    Background Myelo proliferative neoplasm (MPN) patients suffer from significant symptoms, inflammation and reduced quality of life. Yoga improves these outcomes in other cancers, but this hasn't been demonstrated in MPNs. The purpose of this study was to: (1) explore the limited efficacy (does the program show promise of success) of a 12-week online yoga intervention among MPN patients on symptom burden and quality of life and (2) determine feasibility (practicality: to what extent a measure can be carried out) of remotely collecting inflammatory biomarkers. Methods Patients were recruited nationally and randomized to online yoga (60min/week of yoga) or wait-list control (asked to maintain normal activity). Weekly yoga minutes were collected with Clicky (online web analytics tool) and self-report. Those in online yoga completed a blood draw at baseline and week 12 to assess inflammation (interleukin-6, tumor necrosis factor-alpha [TNF-]). All participants completed questionnaires assessing depression, anxiety, fatigue, pain, sleep disturbance, sexual function, total symptom burden, global health, and quality of life at baseline, week seven, 12, and 16. Change from baseline at each time point was computed by group and effect sizes were calculated. Pre-post intervention change in inflammation for the yoga group was compared by t-test. Results Sixty-two MPN patients enrolled and 48 completed the intervention (online yoga=27; control group=21). Yoga participation averaged 40.8min/week via Clicky and 56.1min/week via self-report. Small/moderate effect sizes were generated from the yoga intervention for sleep disturbance (d=-0.26 to -0.61), pain intensity (d=-0.34 to -0.51), anxiety (d=-0.27 to -0.37), and depression (d=-0.53 to -0.78). A total of 92.6 and 70.4% of online yoga participants completed the blood draw at baseline and week 12, respectively, and there was a decrease in TNF- from baseline to week 12 (-1.31.5pg/ml). Conclusions Online yoga demonstrated small effects on sleep, pain, and anxiety as well as a moderate effect on depression. Remote blood draw procedures are feasible and the effect size of the intervention on TNF- was large. Future fully powered randomized controlled trials are needed to test for efficacy. Trial registration This trial was retrospectively registered with clinicaltrials.gov (ID: NCT03503838) on 4/19/2018.
  • Material Provocations in the Archives

    Stuchel, Dani; Univ Arizona (Litwin Books, 2019-04-07)
    As a name, “Anthropocene” would seem to signal that this geologic epoch is both because of humans and about humans. The latter implication draws on pervasive cultural ideas about nature which underlie the Anthropocene and its climatic impacts, namely nature as an extractable, endlessly-renewable resource. While scholars in the environmental humanities, animal studies, and critical plant studies have been quick to both diagnose and propose new directions for our engagements with the material universe, scholarship on archival materiality has continued to focus on the archives as an institution for and about human intellectual endeavors. In other words, the archives continues to be an extractable resource. Within the archives animal, plant, and abiotic changes which work against projects of human history are seen as failures, infestations, or disasters – they can never be properly archival. This essay offers a potential corrective to anthropocentric archiving, by bringing together Jane Bennett’s new materialist project of “vibrant matter,” Michael Marder’s vegetal philosophy, and Caitlin DeSilvey’s curation of decay to suggest avenues of engaging archival materiality as meaningful and provocative. As an analytic schema, this focus on the ‘vibrant archives’ does not aim to save records from planetary changes but to begin the work of re-thinking archival materiality (and its destruction) within the context of the Anthropocene.
  • Conflict Kitchen and Enemy Kitchen: Socially Engaged Food Pedagogy

    Shin, Ryan; Bae, Jaehan; Univ Arizona (ROUTLEDGE JOURNALS, TAYLOR & FRANCIS LTD, 2019-08-19)
    In this article, we examine food-engaged art practice and its artistic and pedagogical possibilities. First, we describe the precedents of socially engaged food art practices and provide a detailed account of Conflict Kitchen and Enemy Kitchen, from which we envision new pedagogical possibilities to embrace food and cooking as socially engaged art. In the second part of the study, we discuss the two kitchens through Deleuzian concepts such as nomadism, agencement, and becoming-others, to explore and encourage a shift from the pedagogy of being to the pedagogy of becoming. We argue that art educators pay attention to the becoming pedagogy as a rhizomatic, transforming, and unresting status of socially engaged learning, challenging the being pedagogy of the structured, goals-oriented, and standard-based learning.
  • Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

    Harper, J; De Vega, J; Swain, S; Heavens, D; Gasior, D; Thomas, A; Evans, C; Lovatt, A; Lister, S; Thorogood, D; et al. (OXFORD UNIV PRESS, 2019-05-08)
    Background and Aims Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS). Methods BAC-based physical maps for L. perenne were constructed from similar to 212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map. Key Results Between similar to 3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with similar to 35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes. Conclusions Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.
  • ONE POSITIVE AND TWO NEGATIVE RESULTS FOR DERIVED CATEGORIES OF ALGEBRAIC STACKS

    Hall, Jack; Neeman, Amnon; Rydh, David; Univ Arizona, Dept Math (CAMBRIDGE UNIV PRESS, 2019-09)
    Let X be a quasi-compact and quasi-separated scheme. There are two fundamental and pervasive facts about the unbounded derived category of X: (1) D-qc(X) is compactly generated by perfect complexes and (2) if X is noetherian or has affine diagonal, then the functor : Psi(X): D(QCoh(X)) -> D-qc (X) is an equivalence. Our main results are that for algebraic stacks in positive characteristic, the assertions (1) and (2) are typically false.
  • Modeling Harmonic Generation in Polycrystalline ZnSe

    Hastings, Michael G.; Werner, Kevin; Schweinsberg, Aaron; Wilmer, Brian L.; Austin, Drake; Wolfe, Christopher M.; Ensley, Trenton R.; Vanderhoef, Laura; Valenzuela, Anthony; Chowdhury, Enam; et al. (IEEE, 2019)
    High harmonic generation in polycrystalline ZnSe is modeled as an effective medium. The non-perturbative behavior observed experimentally was recreated, showing that an effective model captures the underlying physics. (C) 2019 The Author(s)
  • DEVELOPING A GUIDED IMAGERY TELEPHONE-BASED TOBACCO CESSATION PROGRAM FOR A RANDOMIZED CONTROLLED TRIAL

    Armin, Julie; Nair, Uma; Giacobbi, Peter Jr; Povis, Gayle; Barraza, Yessenya; Gordon, Judith; Mel and Enid Zuckerman College of Public Health, Department of Health Promotion Sciences; College of Medicine, Department of Family & Community Medicine; College of Nursing; Collaboratory for Metabolic Disease Prevention and Treatment
    BACKGROUND/AIMS: Guided imagery is an evidence-based, multi-sensory, cognitive process that can be used to increase motivation and achieve a desired behavior. Quitlines are effective, standard care approaches for tobacco cessation; however, utilization of quitlines is low. Using guided imagery-based interventions for smoking cessation may appeal to smokers who do not utilize traditional quitline services. This paper reports the development of program materials for a randomized controlled feasibility trial of a guided imagery-based smoking cessation intervention. The objective of the formative work was to ensure that program materials are inclusive of groups that are less likely to use quitlines, including men and racial/ethnic minority smokers. METHODS: A three-phase process was used to complete formative assessment: 1) integration of evidence-based cessation practices into program development; 2) iterative small group interviews (N=46) to modify the program; and 3) user-testing the coaching protocol and study process among a small sample of smokers (N=5). RESULTS: The Community Advisory Board and project consultants offered input on program content and study recruitment based on their knowledge of minority communities with whom they conduct outreach. Small group interview participants included members of underserved quitline populations (52.37% non-white; 55.56% men). Only 28.26% of participants had prior experience with guided imagery, but others described the use of similar mindfulness and meditation practices. Participant feedback was incorporated into program materials and protocols. DISCUSSION: Iteratively collected feedback and user testing influenced program content and delivery and informed study processes for a randomized controlled feasibility trial of a telephone-delivered, guided imagery-based intervention.

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