• Distribution of active ingredients of a commercial aflatoxin biocontrol product in naturally occurring fungal communities across Kenya

      Islam, M.-S.; Callicott, K.A.; Mutegi, C.; Bandyopadhyay, R.; Cotty, P.J.; School of Plant Sciences, USDA-ARS, The University of Arizona (John Wiley and Sons Ltd, 2020)
      Human populations in Kenya are repeatedly exposed to dangerous aflatoxin levels through consumption of contaminated crops. Biocontrol with atoxigenic Aspergillus flavus is an effective method for preventing aflatoxin in crops. Although four atoxigenic A. flavus isolates (C6E, E63I, R7H and R7K) recovered from maize produced in Kenya are registered as active ingredients for a biocontrol product (Aflasafe KE01) directed at preventing contamination, natural distributions of these four genotypes prior to initiation of commercial use have not been reported. Distributions of the active ingredients of KE01 based on haplotypes at 17 SSR loci are reported. Incidences of the active ingredients and closely related haplotypes were determined in soil collected from 629 maize fields in consecutive long and short rains seasons of 2012. The four KE01 haplotypes were among the top ten most frequent. Haplotype H-1467 of active ingredient R7K was the most frequent and widespread haplotype in both seasons and was detected in the most soils (3.8%). The four KE01 haplotypes each belonged to large clonal groups containing 27–46 unique haplotypes distributed across multiple areas and in 21% of soils. Each of the KE01 haplotypes belonged to a distinct vegetative compatibility group (VCG), and all A. flavus with haplotypes matching a KE01 active ingredient belonged to the same VCG as the matching active ingredient as did all A. flavus haplotypes differing at only one SSR locus. Persistence of the KE01 active ingredients in Kenyan agroecosystems is demonstrated by detection of identical SSR haplotypes six years after initial isolation. The data provide baselines for assessing long-term influences of biocontrol applications in highly vulnerable production areas of Kenya. © 2020 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
    • Effects of HIV infection on metastatic cervical cancer and age at diagnosis among patients in Lusaka, Zambia

      Trejo, Mario Jesus; Soliman, Amr S; Chen, Yuli; Kalima, Mulele; Chuba, Alick; Chama, Eslone; Mwaba, Catherine K; Banda, Lewis; Lishimpi, Kennedy; Department of Epidemiology and Biostatistics, Mel & Enid Zuckerman College of Public Health, The University of Arizona (John Wiley and Sons Ltd, 2021-06-14)
      Objective: To examine the association between the duration of HIV infection and the stage of cervical cancer in Lusaka, Zambia. Methods: This retrospective case-case study included 1583 cervical cancer patients from the Cancer Diseases Hospital in Lusaka, Zambia. A sub-population of HIV-positive patients with additional clinical HIV information was identified following linkage of cancer and HIV databases. Logistic regression models examined the relationship between HIV status and early-onset cervical cancer diagnosis, and between HIV infection duration and initial diagnosis of metastatic cervical cancer. Results: The study population had an average age of 49 years and 40.9% had an initial diagnosis of metastatic cancer. HIV-positive women were more than twice as likely to be diagnosed at early-onset cervical cancer compared with HIV-negative women. Among the sub-population of HIV-positive patients, a longer duration of HIV infection was associated with 20% lowered odds of initial metastatic cancer diagnosis. Conclusion: The availability, accessibility, and impact of the cervical screening program in this population should be further examined to elucidate the relationship between cervical screening, age, and duration of HIV infection and the the stage of diagnosis of cervical cancer. © 2021 International Federation of Gynecology and Obstetrics.
    • Hydraulic redistribution buffers climate variability and regulates grass‐tree interactions in a semiarid riparian savanna

      Barron‐Gafford, Greg A.; Knowles, John F.; Sanchez‐Cañete, Enrique P.; Minor, Rebecca L.; Lee, Esther; Sutter, Leland; Tran, Newton; Murphy, Patrick; Hamerlynck, Erik P.; Kumar, Praveen; et al. (John Wiley and Sons Ltd, 2020-12-13)
      Anticipating the ability of ecosystems to maintain functional integrity across predicted altered precipitation regimes remains a grand ecohydrological challenge. Overstory trees and understory grasses within semiarid savannas vary in their structure and sensitivity to environmental pressures, underscoring the need to examine the ecohydrological implications of this climatic variability. Whereas precipitation has long been recognized as a key driver of landscape ecohydrology, understanding a site's hydraulic redistribution regime (the balance in downward and upward movement of water and the seasonality of these bidirectional flows) may be equally important to understanding moisture availability to vegetation in these dryland ecosystems. As a result, we linked measures of ecosystem-scale carbon exchange, overstory tree sap flux and leaf-level gas exchange to understory whole-plot and leaf-level carbon and water exchange within intact and trenched plots (isolating trees from grasses) in a riparian savanna ecosystem. We maintained measurements across 2 years with distinct precipitation regimes. We found that interannual precipitation variability yielded a categorical shift in the directionality and magnitude of the hydraulic redistribution regime—even within this single site. Additionally, we found that connectivity between overstory trees and understory grasses through hydraulic redistribution created a short period of competition within an average rain year but that facilitation of understory function by overstory trees was much greater and lasted longer during drier years. Together, these findings suggest that hydraulic redistribution can serve as a hydrologic buffer against interannual precipitation variability. Given current climate projections of more variable precipitation within and across years, understanding how hydraulic redistribution regimes vary through time will greatly enhance our capacity to anticipate future ecohydrological function. © 2021 John Wiley & Sons, Ltd.
    • Long‐term research catchments to investigate shrub encroachment in the Sonoran and Chihuahuan deserts: Santa Rita and Jornada experimental ranges

      Vivoni, Enrique R.; Pérez‐Ruiz, Eli R.; Keller, Zachary T.; Escoto, Eric A.; Templeton, Ryan C.; Templeton, Nolie P.; Anderson, Cody A.; Schreiner‐McGraw, Adam P.; Méndez‐Barroso, Luis A.; Robles‐Morua, Agustin; et al. (John Wiley and Sons Ltd, 2021-01-02)
      Woody plant encroachment is a global phenomenon whereby shrubs or trees replace grasses. The hydrological consequences of this ecological shift are of broad interest in ecohydrology, yet little is known of how plant and intercanopy patch dynamics, distributions, and connectivity influence catchment-scale responses. To address this gap, we established research catchments in the Sonoran and Chihuahuan Deserts (near Green Valley, Arizona and near Las Cruces, New Mexico, respectively) that represent shrub encroachment in contrasting arid climates. Our main goals in the coordinated observations were to: (a) independently measure the components of the catchment water balance, (b) deploy sensors to quantify the spatial patterns of ecohydrological processes, (c) use novel methods for characterizing catchment properties, and (d) assess shrub encroachment impacts on ecohydrological processes through modelling studies. Datasets on meteorological variables; energy, radiation, and CO2 fluxes; evapotranspiration; soil moisture and temperature; and runoff at various scales now extend to nearly 10 years of observations at each site, including both wet and dry periods. Here, we provide a brief overview of data collection efforts and offer suggestions for how the coordinated datasets can be exploited for ecohydrological inferences and modelling studies. Given the representative nature of the catchments, the available databases can be used to generalize findings to other catchments in desert landscapes. © 2021 John Wiley & Sons Ltd
    • Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii

      Goldberg, J.K.; Sternlieb, S.R.; Pintel, G.; Delph, L.F.; Department of Ecology and Evolutionary Biology, University of Arizona (John Wiley and Sons Ltd, 2021)
      Associational effects—in which the vulnerability of a plant to herbivores is influenced by its neighbors—have been widely implicated in mediating plant–herbivore interactions. Studies of associational effects typically focus on interspecific interactions or pest–crop dynamics. However, associational effects may also be important for species with intraspecific variation in defensive traits. In this study, we observed hundreds of Datura wrightii—which exhibits dimorphism in its trichome phenotype—from over 30 dimorphic populations across California. Our aim was to determine whether a relationship existed between the trichome phenotype of neighboring conspecifics and the likelihood of being damaged by four species of herbivorous insects. We visited plants at three timepoints to assess how these effects vary both within and between growing seasons. We hypothesized that the pattern of associational effects would provide rare morphs (i.e., focal plants that are a different morph than their neighbors) with an advantage in the form of reduced herbivory, thereby contributing to the negative frequency-dependent selection previously documented in this system. We found the best predictor of herbivory/herbivore presence on focal plants was the phenotype of the focal plant. However, we also found some important neighborhood effects. The total number of plants near a focal individual predicted the likelihood and/or magnitude of herbivory by Tupiochoris notatus, Lema daturaphila, and Manduca sexta. We also found that velvety focal plants with primarily sticky neighbors are more susceptible to infestation by Tupiochoris notatus and Lema daturaphila. This does not align with the hypothesis that associational effects at the near-neighbor scale contribute to a rare-morph advantage in this system. Overall, the results of our study show that the number and trichome-morph composition of neighboring conspecifics impact interactions between D. wrightii and insect herbivores. © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
    • Radiation dosimetry of a clinical prototype dedicated cone‐beam breast CT system with offset detector

      Tseng, Hsin Wu; Karellas, Andrew; Vedantham, Srinivasan; Department of Medical Imaging, The University of Arizona; Department of Biomedical Engineering, The University of Arizona (John Wiley and Sons Ltd, 2021-01-26)
      Purpose: A clinical-prototype, dedicated, cone-beam breast computed tomography (CBBCT) system with offset detector is undergoing clinical evaluation at our institution. This study is to estimate the normalized glandular dose coefficients ((Formula presented.)) that provide air kerma-to-mean glandular dose conversion factors using Monte Carlo simulations. Materials and methods: The clinical prototype CBBCT system uses 49 kV x-ray spectrum with 1.39 mm 1st half-value layer thickness. Monte Carlo simulations (GATE, version 8) were performed with semi-ellipsoidal, homogeneous breasts of various fibroglandular weight fractions ((Formula presented.), chest wall diameters ((Formula presented.) cm), and chest wall to nipple length ((Formula presented.)), aligned with the axis of rotation (AOR) located at 65 cm from the focal spot to determine the (Formula presented.). Three geometries were considered – (Formula presented.) -cm detector with no offset that served as reference and corresponds to a clinical CBBCT system, (Formula presented.) -cm detector with 5 cm offset, and a (Formula presented.) -cm detector with 10 cm offset. Results: For 5 cm lateral offset, the (Formula presented.) ranged (Formula presented.) mGy/mGy and reduction in (Formula presented.) with respect to reference geometry was observed only for 18 cm ((Formula presented.)) and 20 cm ((Formula presented.)) diameter breasts. For the 10 cm lateral offset, the (Formula presented.) ranged (Formula presented.) mGy/mGy and reduction in (Formula presented.) was observed for all breast diameters. The reduction in (Formula presented.) was (Formula presented.), (Formula presented.), (Formula presented.), (Formula presented.), and (Formula presented.) for 8, 10, 14, 18, and 20 cm diameter breasts, respectively. For a given breast diameter, the reduction in (Formula presented.) with offset-detector geometries was not dependent on (Formula presented.). Numerical fits of (Formula presented.) were generated for each geometry. Conclusion: The (Formula presented.) and the numerical fit, (Formula presented.) would be of benefit for current CBBCT systems using the reference geometry and for future generations using offset-detector geometry. There exists a potential for radiation dose reduction with offset-detector geometry, provided the same technique factors as the reference geometry are used, and the image quality is clinically acceptable. © 2021 American Association of Physicists in Medicine
    • Using convolutional neural networks to discriminate between cysts and masses in Monte Carlo-simulated dual-energy mammography

      Makeev, Andrey; Toner, Brian; Qian, Marian; Badal, Andreu; Glick, Stephen J; Program in Applied Mathematics, University of Arizona (John Wiley and Sons Ltd, 2021-05-29)
      Purpose: A substantial percentage of recalls (up to 20%) in screening mammography is attributed to extended round lesions. Benign fluid-filled breast cysts often appear similar to solid tumors in conventional mammograms. Spectral imaging (dual-energy or photon-counting mammography) has been shown to discriminate between cysts and solid masses with clinically acceptable accuracy. This work explores the feasibility of using convolutional neural networks (CNNs) for this task. Methods: A series of Monte Carlo experiments was conducted with digital breast phantoms and embedded synthetic lesions to produce realistic dual-energy images of both lesion types. We considered such factors as nonuniform anthropomorphic background, size of the mass, breast compression thickness, and variability in lesion x-ray attenuation. These data then were used to train a deep neural network (ResNet-18) to learn the differences in x-ray attenuation of cysts and masses. Results: Our simulation results showed that the CNN-based classifier could reliably discriminate between cystic and solid mass round lesions in dual-energy images with an area under the receiver operating characteristic curve (ROC AUC) of 0.98 or greater. Conclusions: The proposed approach showed promising performance and ease of implementation, and could be applied to novel photon-counting detector-based spectral mammography systems. © 2021 American Association of Physicists in Medicine. This article has been contributed to by US Government employees and their work is in the public domain in the USA.