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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

  • Rational design of sulfur-containing composites for high-performance lithium–sulfur batteries

    Sun, Jinhua; Ma, Junpeng; Fan, Jingbiao; Pyun, Jeffrey; Geng, Jianxin; Univ Arizona, Dept Chem & Biochem (AMER INST PHYSICS, 2019-02)
    Sulfur has received considerable attention as a cathode material for lithium-sulfur (Li-S) batteries due to its high theoretical energy density (2567 W h kg(-1)), high earth abundance, and environmental benignity. However, the insulating nature of sulfur and the shuttle effect of soluble lithium polysulfides result in serious technical issues, such as low utilization rate of sulfur, reduced columbic efficiency, and poor cycling stability, which compromise the high theoretical performance of Li-S batteries. In the past years, various attempts have been made to achieve high specific capacity and reliable cycling stability of Li-S batteries. Incorporation of sulfur into functional host materials has been demonstrated to be effective to improve the electrochemical performance of sulfur-based cathodes via enhancing the electron and Li ion conductivities, immobilizing sulfur/lithium polysulfides in cathodes, and accommodating the volume changes in sulfur-based cathodes. Therefore, the rational design of sulfur-containing composites needs to be emphasized as key strategies to develop high-performance cathodes for Li-S batteries. In this perspective, after reviewing the achievements obtained in the design of sulfur-containing composites as cathodes for Li-S batteries, we propose the new issues that should be overcome to facilitate the practical application of Li-S batteries. (C) 2019 Author(s).
  • Why Don’t People Lie? Negative Affect Intensity and Preferences for Honesty in Budgetary Reporting

    Blay, Allen; Douthit, Jeremy; Fulmer III, Bachman; Univ Arizona, Eller Coll Management (ELSEVIER SCIENCE BV, 2019-03)
    Budgets are instrumental in management control systems but are prone to gaming behavior that creates slack and limits the effectiveness of budgets. Research suggests, however, that subordinates have preferences for adhering to a social norm of honesty that limits slack in their budgetary reporting. As such, an increased understanding of subordinates’ preferences for honesty can improve participative budgeting systems. We develop and test theory that increases our understanding of the drivers of preferences for honesty. We test the theory that preferences for honesty originate from an individual’s desire to avoid negative affect from violating social norms. Further, individuals systematically differ in the intensity with which they experience their negative affective reactions. Those with higher levels of this intensity (negative affect intensity, NAI), experience more negative affect and disutility from violating a norm of honesty. Thus, NAI is predictive of subordinates’ preference for honesty. Experimental results support our theory. Budgetary slack is constrained by preferences for honesty and NAI increases preferences for honesty. As such, preferences for honesty are a stronger informal control for subordinates with higher NAI. We discuss the implications of our theory for contract design and job assignment.
  • How does Fetal Autopsy after Pregnancy Loss or Termination for Anomalies and other Complications Change Recurrence Risk?

    Cassidy, Arianna; Herrick, Claire; Norton, Mary E; Ursell, Philip C; Vargas, Juan; Kerns, Jennifer L; Univ Arizona, Dept Obstet & Gynecol (THIEME MEDICAL PUBL INC, 2019-01-01)
    Historically, fetal autopsy was common after terminations for anomalies. Previous studies report that fetal autopsy confirms ultrasound findings in the majority of cases. This study aims to examine correlation between prenatal and autopsy diagnoses at University of California, San Francisco (UCSF) and evaluate whether autopsy adds diagnostic information, specifically information that changes risk of recurrence for future pregnancies. We conducted a retrospective chart review of all fetal autopsies performed at UCSF between 1994 and 2009. Prenatal diagnosis was compared with autopsy diagnosis; for cases where there was a change in diagnosis, an MFM (maternal-fetal medicine specialist) reviewed the case to assign risk of recurrence before and after autopsy. Overall, there was concordance between prenatal diagnosis and autopsy diagnosis in greater than 91.7% of cases. Autopsy added information that resulted in a change in recurrence risk in 2.3% of cases ( n  = 9). For the vast majority of cases, there is agreement between prenatal and autopsy diagnosis after pregnancy loss or termination for fetal anomalies. Only a small percentage of autopsies change recurrence risk. This may be useful when counseling women about method of termination and when counseling couples about whether to have an autopsy.
  • Evolution and Competition of Block Copolymer Nanoparticles

    Glasner, Karl; Univ Arizona, Dept Math (SIAM PUBLICATIONS, 2019)
    Nanoparticle structures formed in a mixture of diblock copolymer and solvent are investigated using a three-phase density functional model and its sharp interface approximation. A wide variety of equilibria described by localized domain patterns are quantified both numerically and analytically. Competition among multiple particles is shown to occur through mass diffusion driven by differences in chemical potential, which may or may not lead to Ostwald ripening behavior. Late stage rigid body dynamics is shown to result from interaction through dipolar fields, leading to orientational alignment and long-range attraction.
  • Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate Colitis while Dysregulating the Inflammatory Response

    Maseda, Damian; Zackular, Joseph P; Trindade, Bruno; Kirk, Leslie; Roxas, Jennifer Lising; Rogers, Lisa M; Washington, Mary K; Du, Liping; Koyama, Tatsuki; Viswanathan, V K; Vedantam, Gayatri; Schloss, Patrick D; Crofford, Leslie J; Skaar, Eric P; Aronoff, David M; Univ Arizona, Sch Anim & Comparat Biomed Sci (AMER SOC MICROBIOLOGY, 2019-01-08)
    Clostridium difficile infection (CDI) is a major public health threat worldwide. The use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with enhanced susceptibility to and severity of CDI; however, the mechanisms driving this phenomenon have not been elucidated. NSAIDs alter prostaglandin (PG) metabolism by inhibiting cyclooxygenase (COX) enzymes. Here, we found that treatment with the NSAID indomethacin prior to infection altered the microbiota and dramatically increased mortality and the intestinal pathology associated with CDI in mice. We demonstrated that in C. difficile-infected animals, indomethacin treatment led to PG deregulation, an altered proinflammatory transcriptional and protein profile, and perturbed epithelial cell junctions. These effects were paralleled by increased recruitment of intestinal neutrophils and CD4+ cells and also by a perturbation of the gut microbiota. Together, these data implicate NSAIDs in the disruption of protective COX-mediated PG production during CDI, resulting in altered epithelial integrity and associated immune responses.IMPORTANCEClostridium difficile infection (CDI) is a spore-forming anaerobic bacterium and leading cause of antibiotic-associated colitis. Epidemiological data suggest that use of nonsteroidal anti-inflammatory drugs (NSAIDs) increases the risk for CDI in humans, a potentially important observation given the widespread use of NSAIDs. Prior studies in rodent models of CDI found that NSAID exposure following infection increases the severity of CDI, but mechanisms to explain this are lacking. Here we present new data from a mouse model of antibiotic-associated CDI suggesting that brief NSAID exposure prior to CDI increases the severity of the infectious colitis. These data shed new light on potential mechanisms linking NSAID use to worsened CDI, including drug-induced disturbances to the gut microbiome and colonic epithelial integrity. Studies were limited to a single NSAID (indomethacin), so future studies are needed to assess the generalizability of our findings and to establish a direct link to the human condition.
  • On the Probabilistic Shaping and Geometric Shaping in Optical Communication Systems

    Qu, Zhen; Djordjevic, Ivan B.; Univ Arizona, Dept Elect & Comp Engn (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2019)
    We introduce and compare typical shaping schemes suitable for optical communications. The geometrically shaped-quadrature amplitude modulation (GS-QAM) formats are characterized by the non-equidistant spacing of constellation points, transmitted uniformly, and applied to improve system capacity. On the other hand, the well-known constant composition distribution matcher (CCDM) is applied for the generation of probabilistically shaped QAM (PS-QAM) formats. Mutual information (MI) is used as a metric to analyze the performances of regular/GS/PS-MQAM formats. In a linear amplified spontaneous emission noise limited region, it can be proved by the numerical simulation that MI performances of the GS-8/16QAM are always better than regular 8/16QAM and PS-8/16QAM; the largest shaping gains can be separately reached by PS-32QAM and GS-32QAM. We continue with the experimental demonstration on the 16QAM-based transmission system, and find that GS-16QAM generally has the best MI performance. We also find that the modulation-dependent nonlinear noises of the GS-8/16/32QAM are comparable to that of the regular 8/16/32QAM and generally lower than PS-8/16/32QAM. By using the enhanced Gaussian noise model, we observe that the GS-8/16QAM formats have better performances than regular 8/16QAM and PS-8/16QAM over multi-span transmission. Meanwhile, PS-32QAM formats provide superior performance over a relatively long transmission distance.
  • Tsuji-Trost Cyclization of Disulfonamides: Synthesis of 12-Membered, 11-Membered, and Pyridine-Fused Macrocyclic Triamines

    Ali, Rameez; Anugu, Sreenivasa; Chawla, Reena; Demillo, Violeta G; Goulinet-Mateo, Florian; Gyawali, Sagar; Hamal, Sunil; Jones, Dylan E; Lamprecht, Katrin; Le, Truc; Lumangtad, Liezel A; Pflug, Nicholas C; Sama, Alekhya; Scarbrough, Emily D; Bell, Thomas W; Univ Arizona, BIO5 Inst (AMER CHEMICAL SOC, 2019-01-31)
    Macrocyclic triamine disulfonamides can be synthesized by double Tsuji-Trost N-allylation reaction of open-chain disulfonamides with 2-alkylidene-1,3-propanediyl bis(carbonates). The previously used Atkins-Richman macrocyclization method generally gives lower yields and requires more tedious purification of the product. Solvent, palladium source, ligand, and concentration have all been varied to optimize the yields of two key 12-membered ring bioactive compounds, CADA and VGD020. The new approach tolerates a wide range of functional groups and gives highest yields for symmetrical compounds in which the acidities of the two sulfonamide groups are matched, although the yields of unsymmetrical compounds are still generally good. The method has also been extended to the synthesis of 11-membered rings, pyridine-fused macrocycles, and products bearing an ester or aryl substituent on the exocyclic double bond.
  • Effects of cardiomyopathy-linked mutations K15N and R21H in tropomyosin on thin-filament regulation and pointed-end dynamics

    Ly, Thu; Pappas, Christopher T; Johnson, Dylan; Schlecht, William; Colpan, Mert; Galkin, Vitold E; Gregorio, Carol C; Dong, Wen-Ji; Kostyukova, Alla S; Univ Arizona, Dept Cellular & Mol Med; Univ Arizona, Sarver Mol Cardiovasc Res Program (AMER SOC CELL BIOLOGY, 2019-01-15)
    Missense mutations K15N and R21H in striated muscle tropomyosin are linked to dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), respectively. Tropomyosin, together with the troponin complex, regulates muscle contraction and, along with tropomodulin and leiomodin, controls the uniform thin-filament lengths crucial for normal sarcomere structure and function. We used Förster resonance energy transfer to study effects of the tropomyosin mutations on the structure and kinetics of the cardiac troponin core domain associated with the Ca2+-dependent regulation of cardiac thin filaments. We found that the K15N mutation desensitizes thin filaments to Ca2+ and slows the kinetics of structural changes in troponin induced by Ca2+ dissociation from troponin, while the R21H mutation has almost no effect on these parameters. Expression of the K15N mutant in cardiomyocytes decreases leiomodin's thin-filament pointed-end assembly but does not affect tropomodulin's assembly at the pointed end. Our in vitro assays show that the R21H mutation causes a twofold decrease in tropomyosin's affinity for F-actin and affects leiomodin's function. We suggest that the K15N mutation causes DCM by altering Ca2+-dependent thin-filament regulation and that one of the possible HCM-causing mechanisms by the R21H mutation is through alteration of leiomodin's function.
  • Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development

    Pearson, Talima; Caporaso, J Gregory; Yellowhair, Monica; Bokulich, Nicholas A; Padi, Megha; Roe, Denise J; Wertheim, Betsy C; Linhart, Mark; Martinez, Jessica A; Bilagody, Cherae; Hornstra, Heidie; Alberts, David S; Lance, Peter; Thompson, Patricia A; Univ Arizona, Ctr Canc; Univ Arizona, Dept Mol & Cellular Biol; Univ Arizona, Dept Nutr Sci (WILEY, 2019-02-01)
    It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal adenomatous polyps, we compared change in the microbiome composition after a 3-year intervention in a subset of participants randomized to oral UDCA at 8-10 mg/kg of body weight per day (n = 198) or placebo (n = 203). Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This reflected a UDCA-associated shift in microbial community composition (P < 0.001), independent of sex, with no evidence of a UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P > 0.05) in men or women. Separate analyses of microbial networks revealed an overrepresentation of Faecalibacterium prausnitzii in the post-UDCA arm and an inverse relationship between F prausnitzii and Ruminococcus gnavus. In men who received UDCA, the overrepresentation of F prausnitzii and underrepresentation of R gnavus were more prominent in those with no adenoma recurrence at follow-up compared to men with recurrence. This relationship was not observed in women. Daily UDCA use modestly influences the relative abundance of microbial species in stool and affects the microbial network composition with suggestive evidence for sex-specific effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.
  • Understanding the Intrinsic and Extrinsic Motivations Associated with Community Gardening to Improve Environmental Public Health Prevention and Intervention

    Ramirez-Andreotta, Monica D; Tapper, Abigail; Clough, Diamond; Carrera, Jennifer S; Sandhaus, Shana; Univ Arizona, Dept Soil Water & Environm Sci; Univ Arizona, Dept Community, Environm & Policy Dept, Mel & Enid Zuckerman Coll Publ Hlth (MDPI, 2019-02-11)
    Considering that community members continue to garden in and near environments impacted by pollutants known to negatively impact human health, this paper seeks to characterize the intrinsic and extrinsic motivations of a gardener and elucidate their perception of soil quality and environmental responsibility, awareness of past land use, and gardening behavior. Via semi-structured interviews with community gardeners in the Boston area (N = 17), multifactorial motivations associated with gardening as well as ongoing environmental health challenges were reported. Gardeners are knowledgeable about their garden's historical past and are concerned with soil quality, theft, trash maintenance, animal waste, and loss of produce from foraging animals. Study findings directly inform the field of environmental health exposure assessments by reporting gardening duration, activities that can lead to incidental soil ingestion, and consumption patterns of locally grown produce. This information combined with an understanding of a gardener's intrinsic and extrinsic motivations can be used to develop urban agricultural infrastructure and management strategies, educational programming, and place-based environmental public health interventions.
  • Neisseria gonorrhoeae evades autophagic killing by downregulating CD46-cyt1 and remodeling lysosomes

    Kim, Won J; Mai, Annette; Weyand, Nathan J; Rendón, Maria A; Van Doorslaer, Koenraad; So, Magdalene; Univ Arizona, BIO5 Inst; Univ Arizona, Dept Immunobiol; Univ Arizona, Sch Anim & Comparat Biomed Sci (PUBLIC LIBRARY SCIENCE, 2019-02-01)
    The Gram-negative human pathogen N. gonorrhoeae (Ngo) quickly attaches to epithelial cells, and large numbers of the bacteria remain on the cell surface for prolonged periods. Ngo invades cells but few viable intracellular bacteria are recovered until later stages of infection, leading to the assumption that Ngo is a weak invader. On the cell surface, Ngo quickly recruits CD46-cyt1 to the epithelial cell cortex directly beneath the bacteria and causes its cleavage by metalloproteinases and Presenilin/Secretease; how these interactions affect the Ngo lifecycle is unknown. Here, we show Ngo induces an autophagic response in the epithelial cell through CD46-cyt1/GOPC, and this response kills early invaders. Throughout infection, the pathogen slowly downregulates CD46-cyt1 and remodeling of lysosomes, another key autophagy component, and these activities ultimately promote intracellular survival. We present a model on the dynamics of Ngo infection and describe how this dual interference with the autophagic pathway allows late invaders to survive within the cell. Author summary Neisseria gonorrhoeae (Ngo), which causes the sexually transmitted disease of gonorrhea, primarily infects the uorgenital epithelium. It attaches to the epithelial surface for lengthy periods. It also invades epithelial cells, but few viable intracellular bacteria are recovered until later stages of infection. As Ngo is known to interfere with two key components in the autophagic pathway, we determined the influence of this host defense mechanism on the lifecycle of the pathogen. We report that Ngo induces autophagy in human primary cervical epithelial cells as well as endorvical cell lines ME180 and Hec1B. Autophagy is induced through the CD46-cyt1/GOPC pathway and this response kills Ngo invading cells early in infection. Throughout infection, Ngo mounts a counter-attack on the autophagic pathway by downregulating CD46-cyt1 and disturbing lysosome homeostasis. This interference allows late-invading Ngo to escape autophagic killing.
  • A Hierarchical Taxonomy of Psychopathology Can Transform Mental Health Research

    Conway, Christopher C; Forbes, Miriam K; Forbush, Kelsie T; Fried, Eiko I; Hallquist, Michael N; Kotov, Roman; Mullins-Sweatt, Stephanie N; Shackman, Alexander J; Skodol, Andrew E; South, Susan C; Sunderland, Matthew; Waszczuk, Monika A; Zald, David H; Afzali, Mohammad H; Bornovalova, Marina A; Carragher, Natacha; Docherty, Anna R; Jonas, Katherine G; Krueger, Robert F; Patalay, Praveetha; Pincus, Aaron L; Tackett, Jennifer L; Reininghaus, Ulrich; Waldman, Irwin D; Wright, Aidan G C; Zimmermann, Johannes; Bach, Bo; Bagby, R Michael; Chmielewski, Michael; Cicero, David C; Clark, Lee Anna; Dalgleish, Tim; DeYoung, Colin G; Hopwood, Christopher J; Ivanova, Masha Y; Latzman, Robert D; Patrick, Christopher J; Ruggero, Camilo J; Samuel, Douglas B; Watson, David; Eaton, Nicholas R; Univ Arizona, Dept Psychiat (SAGE PUBLICATIONS LTD, 2019-05-01)
    For more than a century, research on psychopathology has focused on categorical diagnoses. Although this work has produced major discoveries, growing evidence points to the superiority of a dimensional approach to the science of mental illness. Here we outline one such dimensional system-the Hierarchical Taxonomy of Psychopathology (HiTOP)-that is based on empirical patterns of co-occurrence among psychological symptoms. We highlight key ways in which this framework can advance mental-health research, and we provide some heuristics for using HiTOP to test theories of psychopathology. We then review emerging evidence that supports the value of a hierarchical, dimensional model of mental illness across diverse research areas in psychological science. These new data suggest that the HiTOP system has the potential to accelerate and improve research on mental-health problems as well as efforts to more effectively assess, prevent, and treat mental illness.
  • Comprehensive Lifestyle Improvement Program for Prostate Cancer (CLIPP): Protocol for a Feasibility and Exploratory Efficacy Study in Men on Androgen Deprivation Therapy

    Algotar, Amit; Hsu, Chiu-Hsieh; Sherry Chow, H H; Dougherty, Shona; Babiker, Hani M; Marrero, David; Abraham, Ivo; Kumar, Rachit; Ligibel, Jennifer; Courneya, Kerry S; Thomson, Cynthia; Univ Arizona (JMIR PUBLICATIONS, INC, 2019-02-05)
    Background: Androgen deprivation therapy (ADT) for prostate cancer is associated with adverse cardiometabolic effects such as reduced libido, hot flashes, metabolic syndrome, diabetes, myocardial infarction, and stroke. This reduces quality of life and potentially increases mortality. Several large clinical trials have demonstrated improvements in cardiometabolic risk with comprehensive multimodality lifestyle modification. However, there is a lack of data for such interventions in men on ADT for prostate cancer, and existing studies have used non-standardized interventions or lacked data on metabolic risk factors. Objective: The Comprehensive Lifestyle Improvement Project for Prostate Cancer (CLIPP) is designed to address these gaps by using an intervention modeled on the Diabetes Prevention Program, a standardized multicomponent intervention with demonstrated effectiveness in reducing cardiometabolic risk factors that has been successfully adapted for multiple disease types including breast cancer. Methods: A single-arm unblinded clinical trial will be conducted to determine the feasibility of conducting a 24-week comprehensive lifestyle modification intervention that targets weight loss and increased physical activity modeled on the Diabetes Prevention Program in 30 men on ADT for prostate cancer. Secondary aims are to determine the effect of the intervention on cardiometabolic markers and quality of life. The tertiary aim is to determine the effect of the intervention on markers of inflammation and angiogenesis, important mechanisms for prostate cancer progression. Participants will be recruited from the University of Arizona Cancer Center and the surrounding community. The intervention will be delivered weekly in person and over the phone for 16 weeks. For Weeks 16-24, participants receive weekly phone calls from the study health coach to motivate them to continue their lifestyle modification. Questionnaire and biological data are collected at baseline, 12 weeks, and 24 weeks. Body composition using dual-energy x-ray absorptiometry scans will be performed at baseline and end of study. Results: Based on a sample size of 30, the two-sided 95% confidence interval will not be wider than 0.373 standard deviations for the adherence rate and will not be wider than 0.374 for the retention rate. In addition, the study will have a power of 80% to detect a change of 0.47 standard deviations from baseline for each of the markers investigated in the secondary and tertiary aims assuming a within-subject correlation of 0.20 at a significance level of 5%. The recruitment period is from October 2018 to April 2019. Conclusions: The aim of CLIPP is to determine the feasibility of conducting a Diabetes Prevention Program-style comprehensive lifestyle modification intervention in men with ADT for prostate cancer and its effects on cardiometabolic adverse effects, quality of life, as well as markers of inflammation and angiogenesis. Results will inform the development of future clinical trials in this population.
  • UAV-Based High Resolution Thermal Imaging for Vegetation Monitoring, and Plant Phenotyping Using ICI 8640 P, FLIR Vue Pro R 640, and thermoMap Cameras

    Sagan, Vasit; Maimaitijiang, Maitiniyazi; Sidike, Paheding; Eblimit, Kevin; Peterson, Kyle; Hartling, Sean; Esposito, Flavio; Khanal, Kapil; Newcomb, Maria; Pauli, Duke; Ward, Rick; Fritschi, Felix; Shakoor, Nadia; Mockler, Todd; Univ Arizona, Sch Plant Sci (MDPI, 2019-02-01)
    The growing popularity of Unmanned Aerial Vehicles (UAVs) in recent years, along with decreased cost and greater accessibility of both UAVs and thermal imaging sensors, has led to the widespread use of this technology, especially for precision agriculture and plant phenotyping. There are several thermal camera systems in the market that are available at a low cost. However, their efficacy and accuracy in various applications has not been tested. In this study, three commercially available UAV thermal cameras, including ICI 8640 P-series (Infrared Cameras Inc., USA), FLIR Vue Pro R 640 (FLIR Systems, USA), and thermoMap (senseFly, Switzerland) have been tested and evaluated for their potential for forest monitoring, vegetation stress detection, and plant phenotyping. Mounted on multi-rotor or fixed wing systems, these cameras were simultaneously flown over different experimental sites located in St. Louis, Missouri (forest environment), Columbia, Missouri (plant stress detection and phenotyping), and Maricopa, Arizona (high throughput phenotyping). Thermal imagery was calibrated using procedures that utilize a blackbody, handheld thermal spot imager, ground thermal targets, emissivity and atmospheric correction. A suite of statistical analyses, including analysis of variance (ANOVA), correlation analysis between camera temperature and plant biophysical and biochemical traits, and heritability were utilized in order to examine the sensitivity and utility of the cameras against selected plant phenotypic traits and in the detection of plant water stress. In addition, in reference to quantitative assessment of image quality from different thermal cameras, a non-reference image quality evaluator, which primarily measures image focus that is based on the spatial relationship of pixels in different scales, was developed. Our results show that (1) UAV-based thermal imaging is a viable tool in precision agriculture and (2) the three examined cameras are comparable in terms of their efficacy for plant phenotyping. Overall, accuracy, when compared against field measured ground temperature and estimating power of plant biophysical and biochemical traits, the ICI 8640 P-series performed better than the other two cameras, followed by FLIR Vue Pro R 640 and thermoMap cameras. Our results demonstrated that all three UAV thermal cameras provide useful temperature data for precision agriculture and plant phenotying, with ICI 8640 P-series presenting the best results among the three systems. Cost wise, FLIR Vue Pro R 640 is more affordable than the other two cameras, providing a less expensive option for a wide range of applications.
  • Rescue of collapsed replication forks is dependent on NSMCE2 to prevent mitotic DNA damage

    Pond, Kelvin W; de Renty, Christelle; Yagle, Mary K; Ellis, Nathan A; Univ Arizona, Dept Cellular & Mol Med; Univ Arizona, Canc Ctr (PUBLIC LIBRARY SCIENCE, 2019-02-01)
    NSMCE2 is an E3 SUMO ligase and a subunit of the SMC5/6 complex that associates with the replication fork and protects against genomic instability. Here, we study the fate of collapsed replication forks generated by prolonged hydroxyurea treatment in human NSMCE2-deficient cells. Double strand breaks accumulate during rescue by converging forks in normal cells but not in NSMCE2-deficient cells. Un-rescued forks persist into mitosis, leading to increased mitotic DNA damage. Excess RAD51 accumulates and persists at collapsed forks in NSMCE2-deficient cells, possibly due to lack of BLM recruitment to stalled forks. Despite failure of BLM to accumulate at stalled forks, NSMCE2-deficient cells exhibit lower levels of hydroxyurea-induced sister chromatid exchange. In cells deficient in both NSMCE2 and BLM, hydroxyurea-induced double strand breaks and sister chromatid exchange resembled levels found in NSCME2-deficient cells. We conclude that the rescue of collapsed forks by converging forks is dependent on NSMCE2. Author summary DNA damage encountered by the replication fork causes fork stalling and is a major source of mutations when not adequately repaired. Fork stalling can lead to fork collapse, that is, a state of the fork in which normal DNA synthesis cannot be resumed at the site of stalling. Collapsed forks must be rescued by replication forks initiated nearby, but little is known about the rescue mechanism by which an active fork merges with a collapsed fork. We used an inhibitor of DNA replication to generate collapsed replication forks and then studied genetic control of collapsed-fork rescue. We found that NSMCE2, which is a gene product that is known to regulate repair responses to replication stress, is required for cells to effectively rescue collapsed replication forks in order to complete DNA synthesis. DNA double strand breaks that are associated with normal collapsed-fork rescue do not accumulate in cells that are deficient for NSMCE2, suggesting that DNA breakage is part of the rescue and repair mechanism. Failure to rescue collapsed forks leads to DNA damage in mitosis and DNA damage in the following cell cycle. Our work highlights a unique role for NSMCE2 in rescue of collapsed replication forks.
  • Development of a Plastic Surgery Supply Cart: Patient Outcomes and Quality of Care

    Fahrenkopf, Matthew P; Eichhorn, Mitchell G; Univ Arizona, Coll Med (LIPPINCOTT WILLIAMS & WILKINS, 2019-02-01)
    Background: Plastic surgeons experience unique quality issues related to the specialty nature of patient procedures. Lack of accessibility to specialty supplies is a rate-limiting variable that impacts treatment efficiency and hospital resources. This study had the following goals: (1) to develop a mobile plastic surgery cart and (2) to assess the impact of a plastic surgery cart on time to treatment of consults. Methods: Two plastic carts were developed using preexisting hospital supplies. Cart composition was designed and approved by hospital staff. A prospective study was conducted to assess overall time to treatment of patient consults throughout the hospital comparing a plastics cart versus a traditional hunt and gather methodology. One surgeon recorded time to treatment with and without the plastics cart for each consult during on-call duty hours over a 6-month period. Results: A total of 40 patients were treated for either head or neck (60%) or hand-related (40%) cases. The average time (minutes) to treatment across all procedures with the plastics cart was 3.7 +/- 1.9 versus 46.3 +/- 60.0 without the plastics cart. The maximum time to treatment was 9.5 minutes with the plastics cart and 3 hours without the plastics cart. Usage of the plastics cart resulted in a significant reduction in total time to treatment of 42.5 +/- 60.3 minutes (P < 0.0001). Conclusions: A specialty supplies cart has quality improvement implications for patients, physicians, and hospitals. Increased accessibility of specialty supplies may significantly reduce the time to treatment for plastic surgery patient consults throughout a hospital.
  • Solution Structure of a MYC Promoter G-Quadruplex with 1:6:1 Loop Length

    Dickerhoff, Jonathan; Onel, Buket; Chen, Luying; Chen, Yuwei; Yang, Danzhou; Univ Arizona, Coll Sci, Dept Chem & Biochem (AMER CHEMICAL SOC, 2019-02-28)
    The important MYC oncogene is deregulated in many cancer cells and comprises one of the most prominent G-quadruplex (G4) forming sequences in its promoter regions, the NHE III1 motif. Formation of G4s suppresses MYC transcription and can be modulated by drug binding, establishing these DNA structures as promising targets in cancer therapy. The NHE III1 motif can fold into more than one parallel G4s, including 1:2:1 and 1:6:1 loop length conformers, with the 1:2:1 conformer shown as the major species under physiological conditions in solution. However, additional factors such as protein interactions may affect the cellular folding equilibrium. Nucleolin, a protein shown to bind MYC G4 and repress MYC transcription, is reported herein to preferably bind to the 1:6:1 loop length conformer suggesting a physiological significance of this species. The high-resolution NMR solution structure of the 1:6:1 conformer is determined, which reveals a 5'-capping structure distinctive from the 1:2:1 form, with the 6 nt central loop playing an essential role for this specific capping structure. This suggests that each parallel G-quadruplex likely adopts unique capping and loop structures determined by the specific central loop and flanking sequences. The resulting structural information at the molecular level will help to understand protein recognition of different G4s, contribution of G4 polymorphism to gene regulation, and to rationally design small molecules selectively targeting the 1:6:1 MYC G4.
  • Circulating Microparticles Are Elevated in Treated HIV -1 Infection and Are Deleterious to Endothelial Cell Function

    Hijmans, Jamie G; Stockelman, Kelly A; Garcia, Vinicius; Levy, Ma'ayan V; Brewster, L Madden; Bammert, Tyler D; Greiner, Jared J; Stauffer, Brian L; Connick, Elizabeth; DeSouza, Christopher A; Univ Arizona, Div Infect Dis (WILEY, 2019-02-19)
    Background-Circulating microparticles have emerged as biomarkers and effectors of vascular disease. Elevated rates of cardiovascular disease are seen in HIV-1-seropositive individuals. The aims of this study were to determine: (1) if circulating microparticles are elevated in antiretroviral therapy-treated HIV-1-seropositive adults; and (2) the effects of microparticles isolated from antiretroviral therapy-treated HIV-1-seropositive adults on endothelial cell function, in vitro. Methods and Results-Circulating levels of endothelial-, platelet-, monocyte-, and leukocyte-derived microparticles were determined by flow cytometry in plasma from 15 healthy and 15 antiretroviral therapy-treated, virologically suppressed HIV-1-seropositive men. Human umbilical vein endothelial cells were treated with microparticles from individual subjects for 24 hours; thereafter, endothelial cell inflammation, oxidative stress, senescence, and apoptosis were assessed. Circulating concentrations of endothelial-, platelet-, monocyte-, and leukocyte-derived microparticles were significantly higher (approximate to 35%-225%) in the HIV-1-seropositive compared with healthy men. Microparticles from HIV-1-seropositive men induced significantly greater endothelial cell release of interleukin-6 and interleukin-8 (approximate to 20% and approximate to 35%, respectively) and nuclear factor-jB expression while suppressing anti-inflammatory microRNAs (miR-146a and miR-181b). Intracellular reactive oxygen species production and expression of reactive oxygen species-related heat shock protein 70 were both higher in cells treated with microparticles from the HIV-1-seropositive men. In addition, the percentage of senescent cells was significantly higher and sirtuin 1 expression lower in cells treated with HIV-1-related microparticles. Finally, caspase-3 was significantly elevated by microparticles from HIV-1-seropositive men. Conclusions-Circulating concentrations of endothelial-, platelet-, monocyte-, and leukocyte-derived microparticles were higher in antiretroviral therapy-treated HIV-1-seropositive men and adversely affect endothelial cells promoting cellular inflammation, oxidative stress, senescence, and apoptosis. Circulating microparticles may contribute to the vascular risk associated with HIV-1 infection.
  • Age-related variation in the oral microbiome of urban Cooper's hawks (Accipiter cooperii)

    Taylor, Michael J; Mannan, R William; U'Ren, Jana M; Garber, Nicholas P; Gallery, Rachel E; Arnold, A Elizabeth; Univ Arizona, Sch Nat Resources & Environm; Univ Arizona, Dept Biosyst Engn; Univ Arizona, Sch Plant Sci; Univ Arizona, Dept Ecol & Evolutionary Biol (BMC, 2019-02-21)
    Bird species worldwide are affected by trichomoniasis caused by the protist Trichomonas gallinae. In avivorous raptors such as Cooper's hawks (Accipiter cooperii), nestlings are more susceptible than fledglings and adults. Previous research suggested a link between oral pH and susceptibility: the oral pH of fledgling and adult hawks is more than seven times more acidic than that of nestlings. We speculated that this age-specific difference in pH would correspond to age-specific differences in the oral microbiota of Cooper's hawks. We examined the oral microbiomes of 31 healthy, wild Cooper's hawks in Tucson, Arizona (USA). Individuals represented three age classes (nestlings, fledglings, and adults). We designed our study with multiple controls, replicated sampling, mock communities, and stringent quality-controls to address challenges that can limit the inferential quality of microbiome data sets. Richness of bacterial communities in oral cavities of Cooper's hawks differed as a function of age but not as a function of sex, sampling date, or sampling location. Bacterial communities in oral cavities of nestlings differed from those of fledglings and adults, whereas communities in fledglings and adults did not differ from each other. Communities were similar in males and females and did not differ over the sampling season. Prevalence of acid-producing bacteria in fledgling and adults vs. nestlings is consistent with previous reports of age-specific variation in oral pH, but further research is needed to establish a causal link to pH levels or susceptibility to disease. Analyses of mock communities demonstrated high repeatability and showed that operon number and read abundance were highly correlated. The oral microbiota of wild Cooper's hawks differs between nestlings and older birds. Variation in the oral microbiome is consistent with differences in oral pH between nestlings and older individuals. Overall our study provides a first perspective on bacterial communities associated with oral cavities of a wild raptor.
  • Evaluating the utility of camera traps in field studies of predation

    Akcali, Christopher K; Adán Pérez-Mendoza, Hibraim; Salazar-Valenzuela, David; Kikuchi, David W; Guayasamin, Juan M; Pfennig, David W; Univ Arizona, Dept Ecol & Evolutionary Biol (PEERJ INC, 2019-02-25)
    Artificial prey techniques-wherein synthetic replicas of real organisms are placed in natural habitats-are widely used to study predation in the field. We investigated the extent to which videography could provide additional information to such studies. As a part of studies on aposematism and mimicry of coral snakes (Micrurus) and their mimics, observational data from 109 artificial snake prey were collected from video-recording camera traps in three locations in the Americas (terra firme forest, Tiputini Biodiversity Station, Ecuador; premontane wet forest, Nahá Reserve, Mexico; longleaf pine forest, Southeastern Coastal Plain, North Carolina, USA). During 1,536 camera days, a total of 268 observations of 20 putative snake predator species were recorded in the vicinity of artificial prey. Predators were observed to detect artificial prey 52 times, but only 21 attacks were recorded. Mammals were the most commonly recorded group of predators near replicas (243) and were responsible for most detections (48) and attacks (20). There was no difference between avian or mammalian predators in their probability of detecting replicas nor in their probability of attacking replicas after detecting them. Bite and beak marks left on clay replicas registered a higher ratio of avian:mammalian attacks than videos registered. Approximately 61.5% of artificial prey monitored with cameras remained undetected by predators throughout the duration of the experiments. Observational data collected from videos could provide more robust inferences on the relative fitness of different prey phenotypes, predator behavior, and the relative contribution of different predator species to selection on prey. However, we estimate that the level of predator activity necessary for the benefit of additional information that videos provide to be worth their financial costs is achieved in fewer than 20% of published artificial prey studies. Although we suggest future predation studies employing artificial prey to consider using videography as a tool to inspire new, more focused inquiry, the investment in camera traps is unlikely to be worth the expense for most artificial prey studies until the cost:benefit ratio decreases.

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