Now showing items 6454-6473 of 12955


      Kamenetzky, J. R.; Rangwala, N.; Glenn, J.; Maloney, P. R.; Conley, A.; Univ Arizona, Steward Observ (IOP PUBLISHING LTD, 2016-09-26)
      We present a catalog of all CO (J = 4-3 through J = 13-12), [ C I], and [ N II] lines available from extragalactic spectra from the Herschel SPIRE Fourier Transform Spectrometer (FTS) archive combined with observations of the low-J CO lines from the literature and from the Arizona Radio Observatory. This work examines the relationships between L-FIR, L'(CO), and L-CO/L-CO,L-1-0. We also present a new method for estimating probability distribution functions from marginal signal-to-noise ratio Herschel FTS spectra, which takes into account the instrumental "ringing" and the resulting highly correlated nature of the spectra. The slopes of log(L-FIR) versus log (L'(CO)) are linear for all mid- to high-J CO lines and slightly sublinear if restricted to (ultra) luminous infrared galaxies ((U) LIRGs). The mid-to high-J CO luminosity relative to CO J - 1-0 increases with increasing L-FIR, indicating higher excitement of the molecular gas, although these ratios do not exceed similar to 180. For a given bin in L-FIR, the luminosities relative to CO J = 1-0 remain relatively flat from J = 6-5 through J = 13-12, across three orders of magnitude of L-FIR. A single component theoretical photodissociation region (PDR) model cannot match these flat SLED shapes, although combinations of PDR models with mechanical heating added qualitatively match the shapes, indicating the need for further comprehensive modeling of the excitation processes of warm molecular gas in nearby galaxies.

      Stone, Jordan M.; Eisner, Josh A.; Skemer, Andrew J.; Morzinski, Katie M.; Close, Laird M.; Males, Jared R.; Rodigas, Timothy J.; Hinz, Phil; Puglisi, Alfio; Univ Arizona, Steward Observ (IOP PUBLISHING LTD, 2016-09-21)
      L-band spectroscopy is a powerful probe of cool low-gravity atmospheres: the P, Q, and R branch fundamental transitions of methane near 3.3 mu m provide a sensitive probe of carbon chemistry; cloud thickness modifies the spectral slope across the band; and H-3(+) opacity can be used to detect aurorae. Many directly imaged gas-giant companions to nearby young stars exhibit L-band fluxes distinct from the field population of brown dwarfs at the same effective temperature. Here we describe commissioning the L-band spectroscopic mode of Clio2, the 1-5 mu m instrument behind the Magellan adaptive-optics system. We use this system to measure L-band spectra of directly imaged companions. Our spectra are generally consistent with the parameters derived from previous near-infrared spectra for these late M to early L type objects. Therefore, deviations from the field sequence are constrained to occur below 1500 K. This range includes the L-T transition for field objects and suggests that observed discrepancies are due to differences in cloud structure and CO/CH4 chemistry.
    • La Vida Buena (The Good Life) evaluation: a quasi experimental intervention of a community health worker-led family-based childhood obesity program for Latino children 5-8 years of age on the US-Mexico border

      Tucker, Kathryn M; Ingram, Maia; Doubleday, Kevin; Piper, Rosie; Carvajal, Scott C; Univ Arizona, Prevent Res Ctr (BMC, 2019-06-14)
      Background: Due to multiple and interacting factors, Latino children are disproportionately at risk for overweight and obesity in the United States. Childhood obesity increases the risk for adverse physical and psychosocial outcomes throughout the lifespan. Intensive behavioral interventions recommended in primary care settings may not conform to current practices, and the most vulnerable populations are often unable to access these services. Community Health Workers (CHWs) offer a promising approach to bridging the gap between vulnerable communities and culturally competent services. La Vida Buena (The Good Life) is an 8-week family-focused intervention for Latino children 5-8years old and their parents or caregivers who are patients at a Federally-Qualified Community Health Center (FQHC). It is a culturally and linguistically appropriate curriculum, facilitated by CHWs, that targets family behaviors to foster a healthy lifestyle in order to prevent and mitigate childhood overweight and obesity. Methods: The primary objective is to test the effectiveness of the La Vida Buena (LVB) childhood obesity program among Latino children 5-8years old and their families as compared with a single educational session. This study uses a parallel two-arm quasi-experimental design. The intervention group receives the 8-week La Vida Buena intervention and the comparison group receives a single educational session. The primary outcome is the change in the child's BMI z-score from baseline to 6 months. Discussion: The implementation and evaluation of La Vida Buena may inform research and practice for linking Latino patients in FQHCs to culturally responsive community-based childhood obesity interventions. It will also contribute to the literature about CHWs as facilitators of behavior change for families underserved by health services and preventive programs. La Vida Buena can serve as a culturally and linguistically appropriate early intervention curriculum that will foster a healthy home environment for childhood obesity mitigation and prevention. Trial registration: The trial was retrospectively registered on December 18, 2018. The Identifier is NCT03781856.
    • LA-ICPMS U-Pb geochronology of detrital zircon grains from the Coconino, Moenkopi, and Chinle formations in the Petrified Forest National Park (Arizona)

      Gehrels, G.; Giesler, D.; Olsen, P.; Kent, D.; Marsh, A.; Parker, W.; Rasmussen, C.; Mundil, R.; Irmis, R.; Geissman, J.; et al. (Copernicus GmbH, 2020)
      Uranium-lead (U-Pb) geochronology was conducted by laser ablation - inductively coupled plasma mass spectrometry (LA-ICPMS) on 7175 detrital zircon grains from 29 samples from the Coconino Sandstone, Moenkopi Formation, and Chinle Formation. These samples were recovered from ∼520 m of drill core that was acquired during the Colorado Plateau Coring Project (CPCP), located in Petrified Forest National Park (Arizona). A sample from the lower Permian Coconino Sandstone yields a broad distribution of Proterozoic and Paleozoic ages that are consistent with derivation from the Appalachian and Ouachita orogens, with little input from local basement or Ancestral Rocky Mountain sources. Four samples from the Holbrook Member of the Moenkopi Formation yield a different set of Precambrian and Paleozoic age groups, indicating derivation from the Ouachita orogen, the East Mexico arc, and the Permo-Triassic arc built along the Cordilleran margin. A total of 23 samples from the Chinle Formation contain variable proportions of Proterozoic and Paleozoic zircon grains but are dominated by Late Triassic grains. LA-ICPMS ages of these grains belong to five main groups that correspond to the Mesa Redondo Member, Blue Mesa Member and lower part of the Sonsela Member, upper part of the Sonsela Member, middle part of the Petrified Forest Member, and upper part of the Petrified Forest Member. The ages of pre-Triassic grains also correspond to these chronostratigraphic units and are interpreted to reflect varying contributions from the Appalachian orogen to the east, Ouachita orogen to the southeast, Precambrian basement exposed in the ancestral Mogollon Highlands to the south, East Mexico arc, and Permian-Triassic arc built along the southern Cordilleran margin. Triassic grains in each chronostratigraphic unit also have distinct U and thorium (Th) concentrations, which are interpreted to reflect temporal changes in the chemistry of arc magmatism. Comparison of our LA-ICPMS ages with available chemical abrasion thermal ionization mass spectrometry (CA-TIMS) ages and new magnetostratigraphic data provides new insights into the depositional history of the Chinle Formation, as well as methods utilized to determine depositional ages of fluvial strata. For parts of the Chinle Formation that are dominated by fine-grained clastic strata (e.g., mudstone and siltstone), such as the Blue Mesa Member and Petrified Forest Member, all three chronometers agree (to within ∼ 1 Myr), and robust depositional chronologies have been determined. In contrast, for stratigraphic intervals dominated by coarse-grained clastic strata (e.g., sandstone), such as most of the Sonsela Member, the three chronologic records disagree due to recycling of older zircon grains and variable dilution of syn-depositional-age grains. This results in LA-ICPMS ages that significantly predate deposition and CA-TIMS ages that range between the other two chronometers. These complications challenge attempts to establish a well-defined chronostratigraphic age model for the Chinle Formation. © 2020 George Gehrels et al.
    • Label-free Mie Scattering Identification of Tumor Tissue Using an Angular Photodiode Array

      Bills, Matthew V; Yoon, Jeong-Yeol; Univ Arizona, Dept Biomed Engn (IEEE, 2020)
      Tumors differ from normal tissues in several meaningful ways, including cellular size, morphology, and protein expression, which will accordingly change the refractive index and the size/morphology of cells. There are also important differences in the tissue organization and unique tissue-specific cell densities. Instead of the time-consuming and labor-intensive histology involving the use of a benchtop microscope, a plot of Mie scattering intensities at a fixed wavelength against the scattering angle, which we referred to as “Mie spectrum,” is suggested as an alternative to identify a tumor from normal tissues. An angular photodiode array is developed to measure this Mie spectrum with three different light-emitting diodes (blue, green, and red) as light sources. The resulting Mie spectra show the characteristic peaks for the rat colonic tissues, and substantial differences can be found between the tumor and normal tissues. Two peaks were identified at 120° and 150° scattering angles, potentially representing the capillaries and colon cells, respectively. Contributions from crypts and goblet cells, represented by the scattering at 140°, were minimal. Substantial differences between the tumor and normal tissues were found with 45°–70° light irradiation angles.
    • A labor day warning

      Robbins, Richard A.; The University of Arizona College of Medicine - Phoenix (Arizona Thoracic Society, 2018-09-03)
    • Laboratory characterization of FIRSTv2 photonic chip for the study of substellar companions

      Barjot, K.; Huby, E.; Vievard, S.; Cvetojevic, N.; Lacour, S.; Martin, G.; Deo, V.; Lapeyrere, V.; Rouan, D.; Guyon, O.; et al. (SPIE, 2020)
      FIRST (Fibered Imager foR a Single Telescope instrument) is a post-AO instrument that enables high contrast imaging and spectroscopy at spatial scales below the diffraction limit. FIRST achieves sensitivity and accuracy by a unique combination of sparse aperture masking, spatial filtering by single-mode fibers and cross-dispersion in the visible. The telescope pupil is divided into sub-pupils by an array of microlenses, coupling the light into single-mode fibers. The output of the fibers are rearranged in a non redundant configuration, allowing the measurement of the complex visibility for every baseline over the 600-900 nm spectral range. A first version of this instrument is currently integrated to the Subaru Extreme AO bench (SCExAO). This paper focuses on the on-going instrument upgrades and testings, which aim at increasing the instrument's stability and sensitivity, thus improving the dynamic range. FIRSTv2's interferometric scheme is based on a photonic chip beam combiner. We report on the laboratory characterization of two different types of 5-input beam combiner with enhanced throughput. The interferometric recombination of each pair of sub-pupils is encoded on a single output. Thus, to sample the fringes we implemented a temporal phase modulation by pistoning the segmented mirrors of a Micro-ElectroMechanical System (MEMS). By coupling high angular resolution and spectral resolution in the visible, FIRST offers unique capabilities in the context of the detection and spectral characterization of close companions, especially on 30m-class telescopes. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.
    • Laboratory testing and calibration of the upgraded MMT adaptive secondary mirror

      Vaz, Amali; Morzinski, Katie M.; Montoya, Manny; Fellows, Chuck; Ford, John; Gardner, Andrew; Durney, Olivier; West, Grant; Harrison, Lori; Gacon, Frank; et al. (SPIE, 2020-12-13)
      The MMT Adaptive optics exoPlanet characterization System (MAPS) is a broad overhaul and upgrade of AO instrumentation at the 6.5-m MMT observatory, from deformable secondary mirror, through pyramid wavefront sensors in both the visible and near-infrared, to improved science cameras. MAPS is an NSF MSIP-funded program whose ultimate goal is a facility optimized for exoplanet characterization. Here we describe the laboratory testing and calibration of one MAPS component: the refurbished MMT adaptive secondary mirror (ASM). The new ASM includes a complete redesign of electronics and actuators, including simplified hub-level electronics and digital electronics incorporated into the actuators themselves. The redesign reduces total power to ?300W, from the original system's 1800W, which in turn allows us to eliminate liquid cooling at the hub with no loss of performance. We present testing strategies, results, and lessons learned from laboratory experience with the MAPS ASM. We discuss calibrations first on the level of individual actuators, including capacitive position sensing, force response function, and individual closed-loop position control with an improved control law. We then describe investigations into the full ASM system-hub, actuators, thin shell, and human-to understand how to optimize interactions between components for dynamical shape control using a feedforward matrix. Finally, we present our results in the form of feedforward matrix and control law parameters that successfully produce a desired mirror surface within 1ms settling time. © 2020 SPIE.
    • Labyrinth patterns in Magadi (Kenya) cherts: Evidence for early formation from siliceous gels

      Leet, Kennie; Lowenstein, Tim K.; Renaut, Robin W.; Owen, R. Bernhart; Cohen, Andrew; Department of Geosciences, University of Arizona (Geological Society of America, 2021-06-03)
      Sedimentary cherts, with well-preserved microfossils, are known from the Archean to the present, yet their origins remain poorly understood. Lake Magadi, Kenya, has been used as a modern analog system for understanding the origins of nonbiogenic chert. We present evidence for synsedimentary formation of Magadi cherts directly from siliceous gels. Petrographic thin-section analysis and field-emission scanning electron microscopy of cherts from cores drilled in Lake Magadi during the Hominin Sites and Paleolakes Drilling Project in 2014 led to the discovery of two-dimensional branching “labyrinth patterns” in chert, which are a type of fractal “squeeze” pattern formed at air-liquid interfaces. Labyrinth patterns preserved in chert from Lake Magadi cores indicate invasion of air along planes in dewatering gels. These patterns support the precipitation of silica gels in the saline-alkaline Lake Magadi system and syndepositional drying of gels in contact with air as part of chert formation. Recognizing cherts as syndepositional has been critical for our use of them for U-Th dating. Identification of labyrinth patterns in ancient cherts can provide a better understanding of paleoenvironmental and geochemical conditions in the past © 2021 Geological Society of America.
    • Lack of aggression and apparent altruism towards intruders in a primitive termite

      Cooney, Feargus; Vitikainen, Emma I. K.; Marshall, Harry H.; van Rooyen, Wilmie; Smith, Robert L.; Cant, Michael A.; Goodey, Nicole; Univ Arizona, Dept Entomol (ROYAL SOC, 2016-11-09)
      In eusocial insects, the ability to discriminate nest-mates from non-nest-mates is widespread and ensures that altruistic actions are directed towards kin and agonistic actions are directed towards non-relatives. Most tests of nest-mate recognition have focused on hymenopterans, and suggest that cooperation typically evolves in tandem with strong antagonism towards non-nest-mates. Here, we present evidence from a phylogenetically and behaviourally basal termite species that workers discriminate members of foreign colonies. However, contrary to our expectations, foreign intruders were the recipients of more rather than less cooperative behaviour and were not subjected to elevated aggression. We suggest that relationships between groups may be much more peaceable in basal termites compared with eusocial hymenoptera, owing to energetic and temporal constraints on colony growth, and the reduced incentive that totipotent workers (who may inherit breeding status) have to contribute to self-sacrificial intergroup conflict.
    • Lagged response of tropical tropospheric temperature to solar ultraviolet variations on intraseasonal time scales

      Hood, L. L.; Univ Arizona, Lunar & Planetary Lab (AMER GEOPHYSICAL UNION, 2016-04-28)
      Correlative and regression analyses of daily ERA-Interim reanalysis data for three separate solar maximum periods confirm the existence of a temperature response to short-term (mainly similar to 27 day) solar ultraviolet variations at tropical latitudes in both the lower stratosphere and troposphere. The response, which occurs at a phase lag of 6-10 days after the solar forcing peak, consists of a warming in the lower stratosphere, consistent with relative downwelling and a slowing of the mean meridional (Brewer-Dobson) circulation, and a cooling in the troposphere. The midtropospheric cooling response is most significant in the tropical Pacific, especially under positive El Nino-Southern Oscillation conditions and may be related to a reduction in the number of Madden-Julian oscillation events that propagate eastward into the central Pacific following peaks in short-term solar forcing.
    • Lagged response of tropical tropospheric temperature to solar ultraviolet variations on intraseasonal time scales

      Hood, L. L.; Univ Arizona, Lunar & Planetary Lab; Lunar and Planetary Laboratory; University of Arizona; Tucson Arizona USA (AMER GEOPHYSICAL UNION, 2016-04-28)
      Correlative and regression analyses of daily ERA-Interim reanalysis data for three separate solarmaximum periods confirm the existence of a temperature response to short-term (mainly ∼27 day) solarultraviolet variations at tropical latitudes in both the lower stratosphere and troposphere. The response,which occurs at a phase lag of 6–10 days after the solar forcing peak, consists of a warming in the lowerstratosphere, consistent with relative downwelling and a slowing of the mean meridional (Brewer-Dobson)circulation, and a cooling in the troposphere. The midtropospheric cooling response is most significant inthe tropical Pacific, especially under positive El Niño–Southern Oscillation conditions and may be relatedto a reduction in the number of Madden-Julian oscillation events that propagate eastward into the centralPacific following peaks in short-term solar forcing.
    • Lambda(c) -> Lambda l(+)nu(l) Form Factors and Decay Rates from Lattice QCD with Physical Quark Masses

      Meinel, Stefan; Univ Arizona, Dept Phys (AMER PHYSICAL SOC, 2017-02-21)
      The first lattice QCD calculation of the form factors governing Lambda(c) -> Lambda l(+)nu(l) decays is reported. The calculation was performed with two different lattice spacings and includes one ensemble with a pion mass of 139(2) MeV. The resulting predictions for the Lambda(c) -> Lambda e(+)nu(e) and Lambda(c) -> Lambda mu(+)nu(mu) decay rates divided by vertical bar V-cs vertical bar(2) are 0.2007(71)(74) and 0.1945(69)(72) p(s-1), respectively, where the two uncertainties are statistical and systematic. Taking the Cabibbo-Kobayashi-Maskawa (CKM) matrix element vertical bar V-cs vertical bar from a global fit and the Lambda(c) lifetime from experiments, this translates to branching fractions of B(Lambda(c) -> Lambda e(e)(+nu)) = 0.0380(19)(LQCD)(11)(tau Lambda c) and B(Lambda(c) -> Lambda mu(+)nu(mu)) 0.0369(19)(LQCD)(11)(tau Lambda c). These results are consistent with, and two times more precise than, the measurements performed recently by the BESIII Collaboration. Using instead the measured branching fractions together with the lattice calculation to determine the CKM matrix element gives vertical bar V-cs vertical bar = 0.949(24)(LQCD)(14)(tau)Lambda c (49)(B).
    • Laminin 521 maintains differentiation potential of mouse and human satellite cell-derived myoblasts during long-term culture expansion

      Penton, Christopher M.; Badarinarayana, Vasudeo; Prisco, Joy; Powers, Elaine; Pincus, Mark; Allen, Ronald E.; August, Paul R.; Univ Arizona, Sch Anim & Comparat Biomed Sci (BIOMED CENTRAL LTD, 2016-12-13)
      Background: Large-scale expansion of myogenic progenitors is necessary to support the development of high-throughput cellular assays in vitro and to advance genetic engineering approaches necessary to develop cellular therapies for rare muscle diseases. However, optimization has not been performed in order to maintain the differentiation capacity of myogenic cells undergoing long-term cell culture. Multiple extracellular matrices have been utilized for myogenic cell studies, but it remains unclear how different matrices influence long-term myogenic activity in culture. To address this challenge, we have evaluated multiple extracellular matrices in myogenic studies over long-term expansion. Methods: We evaluated the consequence of propagating mouse and human myogenic stem cell progenitors on various extracellular matrices to determine if they could enhance long-term myogenic potential. For the first time reported, we comprehensively examine the effect of physiologically relevant laminins, laminin 211 and laminin 521, compared to traditionally utilized ECMs (e.g., laminin 111, gelatin, and Matrigel) to assess their capacity to preserve myogenic differentiation potential. Results: Laminin 521 supported increased proliferation in early phases of expansion and was the only substrate facilitating high-level fusion following eight passages in mouse myoblast cell cultures. In human myoblast cell cultures, laminin 521 supported increased proliferation during expansion and superior differentiation with myotube hypertrophy. Counterintuitively however, laminin 211, the native laminin isoform in resting skeletal muscle, resulted in low proliferation and poor differentiation in mouse and human cultures. Matrigel performed excellent in short-term mouse studies but showed high amounts of variability following long-term expansion. Conclusions: These results demonstrate laminin 521 is a superior substrate for both short-term and long-term myogenic cell culture applications compared to other commonly utilized substrates. Since Matrigel cannot be used for clinical applications, we propose that laminin 521 could possibly be employed in the future to provide myoblasts for cellular therapy directed clinical studies.
    • Laminin-332 alters connexin profile, dye coupling and intercellular Ca2+ waves in ciliated tracheal epithelial cells

      Isakson, Brant; Olsen, Colin; Boitano, Scott; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia Charlottesville, Virginia 22908, USA; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA; Arizona Respiratory Center, Arizona Health Sciences Center, University of Arizona, Tucson, Arizona 85724, USA; Department of Physiology, Arizona Health Sciences Center, University of Arizona, Tucson, Arizona 85724, USA (BioMed Central, 2006)
      BACKGROUND:Tracheal epithelial cells are anchored to a dynamic basement membrane that contains a variety of extracellular matrix proteins including collagens and laminins. During development, wound repair and disease of the airway epithelium, significant changes in extracellular matrix proteins may directly affect cell migration, differentiation and events mediated by intercellular communication. We hypothesized that alterations in cell matrix, specifically type I collagen and laminin alpha3beta3gamma2 (LM-332) proteins within the matrix, directly affect intercellular communication in ciliated rabbit tracheal epithelial cells (RTEC).METHODS:Functional coupling of RTEC was monitored by microinjection of the negatively charged fluorescent dyes, Lucifer Yellow and Alexa 350, into ciliated RTEC grown on either a LM-332/collagen or collagen matrix. Coupling of physiologically significant molecules was evaluated by the mechanism and extent of propagated intercellular Ca2+ waves. Expression of connexin (Cx) mRNA and proteins were assayed by reverse transcriptase - polymerase chain reaction and immunocytochemistry, respectively.RESULTS:When compared to RTEC grown on collagen alone, RTEC grown on LM-332/collagen displayed a significant increase in dye transfer. Although mechanical stimulation of RTEC grown on either LM-332/collagen or collagen alone resulted in intercellular Ca2+ waves, the mechanism of transfer was dependent on matrix: RTEC grown on LM-332/collagen propagated Ca2+waves via extracellular purinergic signaling whereas RTEC grown on collagen used gap junctions. Comparison of RTEC grown on collagen or LM-332/collagen matrices revealed a reorganization of Cx26, Cx43 and Cx46 proteins.CONCLUSION:Alterations in airway basement membrane proteins such as LM-332 can induce connexin reorganizations and result in altered cellular communication mechanisms that could contribute to airway tissue function.
    • Laminin-binding integrin gene copy number alterations in distinct epithelial-type cancers.

      Harryman, William L; Pond, Erika; Singh, Parminder; Little, Andrew S; Eschbacher, Jennifer M; Nagle, Raymond B; Cress, Anne E; The University of Arizona Cancer Center, 1515 N. Campbell Ave., Tucson, Arizona, United States (e-Century Publishing, 2016-01-01)
      The laminin-binding integrin (LBI) family are cell adhesion molecules that are essential for invasion and metastasis of human epithelial cancers and cell adhesion mediated drug resistance. We investigated whether copy number alteration (CNA) or mutations of a five-gene signature (ITGB4, ITGA3, LAMB3, PLEC, and SYNE3), representing essential genes for LBI adhesion, would correlate with patient outcomes within human epithelial-type tumor data sets currently available in an open access format. We investigated the relative alteration frequency of an LBI signature panel (integrin β4 (ITGB4), integrin α3 (ITGA3), laminin β3 chain (LAMB3), plectin (PLEC), and nesprin 3 (SYNE3)), independent of the epithelial cancer type, within publically available and published data using cBioPortal and Oncomine software. We rank ordered the results using a 20% alteration frequency cut-off and limited the analysis to studies containing at least 100 samples. Kaplan-Meier survival curves were analyzed to determine if alterations in the LBI signature correlated with patient survival. The Oncomine data mining tool was used to compare the heat map expression of the LBI signature without SYNE3 (as this was not included in the Oncomine database) to drug resistance patterns. Twelve different cancer types, representing 5,647 samples, contained at least a 20% alteration frequency of the five-gene LBI signature. The frequency of alteration ranged from 38.3% to 19.8%. Within the LBI signature, PLEC was the most commonly altered followed by LAMB3, ITGB4, ITGA3, and SYNE3 across all twelve cancer types. Within cancer types, there was little overlap of the individual amplified genes from each sample, suggesting different specific amplicons may alter the LBI adhesion structures. Of the twelve cancer types, overall survival was altered by CNA presence in bladder urothelial carcinoma (p=0.0143*) and cervical squamous cell carcinoma and endocervical adenocarcinoma (p=0.0432*). Querying the in vitro drug resistance profiles with the LBI signature demonstrated a positive correlation with cells resistant to inhibitors of HDAC (Vorinostat, Panobinostat) and topoisomerase II (Irinotecan). No correlation was found with the following agents: Bleomycin, Doxorubicin, Methotrexate, Gemcitabine, Docetaxel, Bortezomib, and Shikonen. Our work has identified epithelial-types of human cancer that have significant CNA in our selected five-gene signature, which was based on the essential and genetically-defined functions of the protein product networks (in this case, the LBI axis). CNA of the gene signature not only predicted overall survival in bladder, cervical, and endocervical adenocarcinoma but also response to chemotherapy. This work suggests that future studies designed to optimize the gene signature are warranted.
    • Laminin-binding integrin gene copy number alterations in distinct epithelial-type cancers.

      Harryman, William L; Pond, Erika; Singh, Parminder; Little, Andrew S; Eschbacher, Jennifer M; Nagle, Raymond B; Cress, Anne E; Univ Arizona, Ctr Canc (E-CENTURY PUBLISHING CORP, 2016)
      The laminin-binding integrin (LBI) family are cell adhesion molecules that are essential for invasion and metastasis of human epithelial cancers and cell adhesion mediated drug resistance. We investigated whether copy number alteration (CNA) or mutations of a five-gene signature (ITGB4, ITGA3, LAMB3, PLEC, and SYNE3), representing essential genes for LBI adhesion, would correlate with patient outcomes within human epithelial-type tumor data sets currently available in an open access format.
    • LAMOST Observations in 15 K2 Campaigns. I. Low-resolution Spectra from LAMOST DR6

      Wang, J.; Fu, J.-N.; Zong, W.; Smith, M.C.; De Cat, P.; Shi, J.; Luo, A.; Zhang, H.; Frasca, A.; Corbally, C.J.; et al. (IOP Publishing Ltd, 2020)
      The Large Sky Area Multi-object Fiber Spectroscopic Telescope (LAMOST)-K2 (LK2) project, initiated in 2015, aims to collect low-resolution spectra of targets in the K2 campaigns, similar to the LAMOST-Kepler project. By the end of 2018, a total of 126 LK2 plates had been observed by LAMOST. After cross-matching the catalog of the LAMOST data release 6 (DR6) with that of the K2 approved targets, we found 160,619 usable spectra of 84,012 objects, most of which had been observed more than once. The effective temperature, surface gravity, metallicity, and radial velocity from 129,974 spectra for 70,895 objects are derived through the LAMOST Stellar Parameter Pipeline (LASP). The internal uncertainties were estimated to be 81 K, 0.15 dex, 0.09 dex, and 5 km s-1, respectively, when derived from a spectrum with a signal-to-noise ratio in the g band (S/N g ) of 10. These estimates are based on results for targets with multiple visits. The external accuracies were assessed by comparing the parameters of targets in common with the APOGEE and Gaia surveys, for which we generally found linear relationships. A final calibration is provided, combining external and internal uncertainties for giants and dwarfs, separately. We foresee that these spectroscopic data will be used widely in different research fields, especially in combination with K2 photometry. © 2020. The American Astronomical Society. All rights reserved.
    • Land Surface Climate in the Regional Arctic System Model

      Hamman, Joseph; Nijssen, Bart; Brunke, Michael; Cassano, John; Craig, Anthony; DuVivier, Alice; Hughes, Mimi; Lettenmaier, Dennis P.; Maslowski, Wieslaw; Osinski, Robert; et al. (AMER METEOROLOGICAL SOC, 2016-09)
      The Regional Arctic System Model (RASM) is a fully coupled, regional Earth system model applied over the pan-Arctic domain. This paper discusses the implementation of the Variable Infiltration Capacity land surface model (VIC) in RASM and evaluates the ability of RASM, version 1.0, to capture key features of the land surface climate and hydrologic cycle for the period 1979-2014 in comparison with uncoupled VIC simulations, reanalysis datasets, satellite measurements, and in situ observations. RASM reproduces the dominant features of the land surface climatology in the Arctic, such as the amount and regional distribution of precipitation, the partitioning of precipitation between runoff and evapotranspiration, the effects of snow on the water and energy balance, and the differences in turbulent fluxes between the tundra and taiga biomes. Surface air temperature biases in RASM, compared to reanalysis datasets ERA-Interim and MERRA, are generally less than 2 degrees C; however, in the cold seasons there are local biases that exceed 6 degrees C. Compared to satellite observations, RASM captures the annual cycle of snow-covered area well, although melt progresses about two weeks faster than observations in the late spring at high latitudes. With respect to derived fluxes, such as latent heat or runoff, RASM is shown to have similar performance statistics as ERA-Interim while differing substantially from MERRA, which consistently overestimates the evaporative flux across the Arctic region.
    • Land-use changes associated with large-scale land transactions in Ethiopia

      Williams, T.G.; Trush, S.A.; Sullivan, J.A.; Liao, C.; Chesterman, N.; Agrawal, A.; Guikema, S.D.; Brown, D.G.; School of Geography, Development and Environment, University of Arizona (Resilience Alliance, 2021)
      Large-scale land transactions (LSLTs) can precipitate dramatic changes in land systems. Ethiopia has experienced one of the largest amounts of LSLTs in Africa, yet their effects on local land systems are poorly understood. In this study, we quantify the direct and indirect land use and land cover (LULC) changes associated with LSLTs at eight socio-environmentally diverse sites in central and western Ethiopia. To estimate these effects, we employ a novel, two-stage counterfactual analysis. We first use a region-growing procedure to identify a “control” site with comparable landscape-level characteristics to each LSLT. Then, we sample and reweight points within each control site to further improve covariate balance. This two-stage approach both controls for potential confounding factors at multiple spatial levels and reduces the costs of extensive LULC data classification. Our results show that the majority of the reported transacted area (62%) remained unconverted to large-scale agriculture. Most of the land that was developed into large-scale agriculture displaced smallholder agriculture (53%), followed by conversion of woodland/shrubland (35%) and forest (9%). Beyond their boundaries, LSLTs indirectly influenced rates of smallholder agricultural expansion and abandonment, pointing to site dependence in how LSLTs affect adjacent land systems. In particular, the low prevalence of forest within and around these LSLTs underscores a need to move beyond measures of deforestation as proxies for LSLT effects on land systems. Our two-stage approach shows promise as an efficient method for generating robust counterfactuals and thereby LULC change estimates in systems lacking wall-to-wall LULC data. © 2021 by the author(s). Published here under license by the Resilience Alliance.