• Ocean tidal heating in icy satellites with solid shells

      Matsuyama, Isamu; Beuthe, Mikael; Hay, Hamish C.F.C.; Nimmo, Francis; Kamata, Shunichi; Univ Arizona, Lunar & Planetary Lab (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018-09-15)
      As a long-term energy source, tidal heating in subsurface oceans of icy satellites can influence their thermal, rotational, and orbital evolution, and the sustainability of oceans. We present a new theoretical treatment for tidal heating in thin subsurface oceans with overlying incompressible elastic shells of arbitrary thickness. The stabilizing effect of an overlying shell damps ocean tides, reducing tidal heating. This effect is more pronounced on Enceladus than on Europa because the effective rigidity on a small body like Enceladus is larger. For the range of likely shell and ocean thicknesses of Enceladus and Europa, the thin shell approximation of Beuthe (2016) is generally accurate to less than about 4%. Explaining Enceladus' endogenic power radiated from the south polar terrain by ocean tidal heating requires ocean and shell thicknesses that are significantly smaller than the values inferred from gravity and topography constraints. The time-averaged surface distribution of ocean tidal heating is distinct from that due to dissipation in the solid shell, with higher dissipation near the equator and poles for eccentricity and obliquity forcing, respectively. This can lead to unique horizontal shell thickness variations if the shell is conductive. The surface displacement driven by eccentricity and obliquity forcing can have a phase lag relative to the forcing tidal potential due to the delayed ocean response. For Europa and Enceladus, eccentricity forcing generally produces greater tidal amplitudes due to the large eccentricity values relative to the obliquity values. Despite the small obliquity values, obliquity forcing generally produces larger phase lags due to the generation of Rossby-Haurwitz waves. If Europa's shell and ocean are, respectively, 10 and 100 km thick, the tide amplitude and phase lag are 26.5 m and <1 degrees for eccentricity forcing, and <2.5 m and <18 degrees for obliquity forcing. Measurement of the obliquity phase lag (e.g. by Europa Clipper) would provide a probe of ocean thickness (C) 2018 Elsevier Inc. All rights reserved.
    • Debiased orbit and absolute-magnitude distributions for near-Earth objects

      Granvik, Mikael; Morbidelli, Alessandro; Jedicke, Robert; Bolin, Bryce; Bottke, William F.; Beshore, Edward; Vokrouhlický, David; Nesvorný, David; Michel, Patrick; Univ Arizona (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018-09-15)
      The debiased absolute-magnitude and orbit distributions as well as source regions for near-Earth objects (NEOs) provide a fundamental frame of reference for studies of individual NEOs and more complex population-level questions. We present a new four-dimensional model of the NEO population that describes debiased steady-state distributions of semimajor axis, eccentricity, inclination, and absolute magnitude H in the range 17 < H < 25. The modeling approach improves upon the methodology originally developed by Bottke et al. (2000, Science 288, 2190-2194) in that it is, for example, based on more realistic orbit distributions and uses source-specific absolute-magnitude distributions that allow for a power-law slope that varies with H. We divide the main asteroid belt into six different entrance routes or regions (ER) to the NEO region: the v(6), 3:1J, 5:2J and 2:1J resonance complexes as well as Hungarias and Phocaeas. In addition we include the Jupiter-family comets as the primary cometary source of NEOs. We calibrate the model against NEO detections by Catalina Sky Surveys' stations 703 and G96 during 2005-2012, and utilize the complementary nature of these two systems to quantify the systematic uncertainties associated to the resulting model. We find that the (fitted) H distributions have significant differences, although most of them show a minimum power-law slope at H similar to 20. As a consequence of the differences between the ER-specific H distributions we find significant variations in, for example, the NEO orbit distribution, average lifetime, and the relative contribution of different ERs as a function of H. The most important ERs are the v(6) and 3:1J resonance complexes with JFCs contributing a few percent of NEOs on average. A significant contribution from the Hungaria group leads to notable changes compared to the predictions by Bottke et al. in, for example, the orbit distribution and average lifetime of NEOs. We predict that there are 962(-56)(+52) (802(-42)(+48) x 10(3)) NEOs with H < 17.75 (H < 25) and these numbers are in agreement with the most recent estimates found in the literature (the uncertainty estimates only account for the random component). Based on our model we find that relative shares between different NEO groups (Amor, Apollo, Aten, Atira, Vatira) are (39.4,54.4,3.5,1.2,0.3)%, respectively, for the considered H range and that these ratios have a negligible dependence on H. Finally, we find an agreement between our estimate for the rate of Earth impacts by NEOs and recent estimates in the literature, but there remains a potentially significant discrepancy in the frequency of Tunguska-sized and Chelyabinsk-sized impacts. (C) 2018 The Authors. Published by Elsevier Inc.
    • Profiling caregivers: Hormonal variation underlying allomaternal care in wild red-bellied lemurs, Eulemur rubriventer

      Tecot, Stacey R.; Baden, Andrea L.; Univ Arizona, Sch Anthropol; Univ Arizona, Laboratory for the Evolutionary Endocrinology of Primates (Elsevier, 2018-09-01)
    • Antiwindup Terminal Sliding Mode Control for Mars Entry Using Supertwisting Sliding Mode Disturbance Observer

      Jiang, Xiuqiang; Li, Shuang (AMER SOC CIVIL ENGINEERS, 2018-09)
      Uncertainty and external disturbance during the Mars entry process inevitably degrade the performance of Mars entry guidance and control algorithms. Traditional approaches focus on suppressing disturbances and compensating uncertainties, which usually results in larger control responses beyond the limited control capability of a Mars entry vehicle. This paper further takes the limited actuator ability into consideration and proposes the Mars entry robust attitude control strategy using the terminal sliding mode control (TSMC) with antiwindup (AW) and a supertwisting sliding mode disturbance observer (SMDO). First, terminal sliding mode control with antiwindup is developed to robustly track the nominal attitude command under uncertainty and limited control capability. Then, the supertwisting sliding mode disturbance observer is introduced to online estimate the disturbances and further enhance the attitude control accuracy and robustness. Finally, the comparison simulation results illustrate that the proposed control strategy not only performs well in tracking the reference commands even in the presence of uncertain disturbance, but also avoids the control saturation issue.
    • A lattice QCD study of pion-nucleon scattering in the Roper channel

      Leskovec, Luka; Lang, Christian, B; Padmanath, M.; Prelovsek, Sasa; University of Graz; Regensburg University; University of Ljubljana; Univ Arizona, Dept Phys, Tucson, AZ 85721 USA (SPRINGER WIEN, 2018-09)
      We present a lattice QCD study of the puzzling positive-parity nucleon channel, where the Roper resonance N∗(1440) resides in experiment. The study is based on an ensemble of gauge configurations with Nf=2+1 Wilson-clover fermions with a pion mass of 156 MeV and lattice size L=2.9 fm. We use several qqq interpolating fields combined with Nπ and Nσ two-hadron operators in calculating the energy spectrum in the rest frame. Combining experimental Nπ phase shifts with elastic approximation and the Lüscher formalism suggests in the spectrum an additional energy level near the Roper mass mR=1.43 GeV for our lattice. We do not observe any such additional energy level, which implies that Nπ elastic scattering alone does not render a low-lying Roper resonance. The current status indicates that the N∗(1440) might arise as dynamically generated resonance from coupling to other channels, most notably the Nππ .
    • The cAMP-induced G protein subunits dissociation monitored in live Dictyostelium cells by BRET reveals two activation rates, a positive effect of caffeine and potential role of microtubules

      Tariqul Islam, A.F.M.; Yue, Haicen; Scavello, Margarethakay; Haldeman, Pearce; Rappel, Wouter-Jan; Charest, Pascale G.; Univ Arizona, Dept Chem & Biochem (ELSEVIER SCIENCE INC, 2018-08)
      To study the dynamics and mechanisms controlling activation of the heterotrimeric G protein G alpha 2 beta gamma in Dictyostelium in response to stimulation by the chemoattractant cyclic AMP (cAMP), we monitored the G protein subunit interaction in live cells using bioluminescence resonance energy transfer (BRET). We found that CAMP induces the cAR1-mediated dissociation of the G protein subunits to a similar extent in both undifferentiated and differentiated cells, suggesting that only a small number of cAR1 (as expressed in undifferentiated cells) is necessary to induce the full activation of G alpha 2 beta gamma. In addition, we found that treating cells with caffeine increases the potency of cAMP-induced G alpha 2 beta gamma activation; and that disrupting the microtubule network but not F-actin inhibits the cAMP-induced dissociation of G alpha 2 beta gamma. Thus, microtubules are necessary for efficient cAR1-mediated activation of the heterotrimeric G protein. Finally, kinetics analyses of G alpha 2 beta gamma subunit dissociation induced by different cAMP concentrations indicate that there are two distinct rates at which the heterotrimeric G protein subunits dissociate when cells are stimulated with cAMP concentrations above 500 nM versus only one rate at lower cAMP concentrations. Quantitative modeling suggests that the kinetics profile of G alpha 2 beta gamma subunit dissociation results from the presence of both uncoupled and G protein pre-coupled cAR1 that have differential affinities for CAMP and, consequently, induce G protein subunit dissociation through different rates. We suggest that these different signaling kinetic profiles may play an important role in initial chemoattractant gradient sensing.
    • An ecohydrological stream type classification of intermittent and ephemeral streams in the southwestern United States

      Levick, Lainie; Hammer, Samantha; Lyon, Russell; Murray, Joel; Birtwistle, Amy; Guertin, Phillip; Goodrich, David; Bledsoe, Brian; Laituri, Melinda; Univ Arizona (ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2018-08)
      An ecohydrological stream type classification was developed to improve decision making for ephemeral and intermittent streams at four military reservations in the southwestern U.S.: Fort Irwin, Yuma Proving Ground (YPG), Fort Huachuca, and Fort Bliss. Agglomerative hierarchical cluster analysis was used to classify stream reaches by ecohydrologic properties (vegetation, hydrologic, and geomorphic attributes derived using geographic information system analyses), and Classification and Regression Trees (CART) were used to determine thresholds for each variable for a predictive model. Final stream types were determined from statistical analyses, cluster validity tests, examination of mapped clusters, and site knowledge. Climate regime and geomorphology were most important for YPG and Fort Irwin where annual precipitation is low. Vegetation variables were important at Fort Bliss and hydrologic variables were important at Fort Huachuca where higher annual precipitation and a bimodal rainfall pattern occur. The classification results and input variables are spatially linked to specific stream reaches, allowing managers to identify locations with similar attributes to support management actions. These methods enable the development of a stream type classification in gauged or ungauged watersheds and for areas where intensive field data collection is not feasible.
    • Global deletion of tetraspanin CD82 attenuates bone growth and enhances bone marrow adipogenesis

      Bergsma, Alexis; Ganguly, Sourik S.; Dick, Daniel; Williams, Bart O.; Miranti, Cindy K.; Univ Arizona, Ctr Canc (ELSEVIER SCIENCE INC, 2018-08)
      CD82 is a widely expressed member of the tetraspanin family of transmembrane proteins known to control cell signaling, adhesion, and migration. Tetraspanin CD82 is induced over 9-fold during osteoclast differentiation in vitro; however, its role in bone homeostasis is unknown. A globally deleted CD82 mouse model was used to assess the bone phenotype. Based on microCT and 4-point bending tests, CD82-deficient bones are smaller in diameter and weaker, but display no changes in bone density. Histomorphometry shows a decrease in size, erosion perimeter, and number of osteoclasts in situ, with a corresponding increase in trabecular surface area, specifically in male mice. Male-specific alterations are observed in trabecular structure by microCT and in vitro differentiated osteoclasts are morphologically abnormal. Histomorphometry did not reveal a significant reduction in osteoblast number; however, dynamic labeling reveals a significant decrease in bone growth. Consistent with defects in OB function, OB differentiation and mineralization are defective in vitro, whereas adipogenesis is enhanced. There is a corresponding increase in bone marrow adipocytes in situ. Thus, combined defects in both osteoclasts and osteoblasts can account for the observed bone phenotypes, and suggests a role for CD82 in both bone mesenchyme and myeloid cells.
    • “Loser” aesthetics: Korean internet freaks and gender politics

      Yang, Sunyoung; Univ Arizona, Dept East Asian Studies (Taylor & Francis Group, 2018-07-31)
      In the aftermath of the 1997 Asian Financial Crisis, a new Internet freak culture emerged in South Korea in response to the rapid development of the Internet as well as the country’s neoliberal reforms. At this time, images of losers, freaks, and other surplus populations circulated online. This article examines the gender politics of Internet freaks through an analysis of one online fan forum, the Lee Joon Gi gallery of DCinside.com. Lee’s fan forum acquired a reputation through sexually charged posts from its female-user base in the late 2000s and is still active today. By appropriating attributes of online male culture and forms of communication, such as absurd statements, rudeness, and aggressive sexual expression, the users of this fan community created a carnivalesque space for themselves and subverted rigid Korean gender ideologies. Such parodies have transformed the fear of misogyny and sexism in the offline world into laughter online and become fertile ground for changes in gender politics in online spaces.
    • A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics

      Hanish, Bentley J; Hackney Price, Jennifer F; Kaneko, Ichiro; Ma, Ning; van der Vaart, Arjan; Wagner, Carl E; Jurutka, Peter W; Marshall, Pamela A; Arizona State University; Univ Arizona, Coll Med Phoenix, Dept Basic Med Sci, Phoenix, AZ USA; Univ Arizona, Canc Ctr, Tucson, AZ USA (ELSEVIER SCIENCE INC, 2018-07-01)
      Rexinoids are powerful ligands that bind to retinoid-X-receptors (RXRs) and show great promise as therapeutics for a wide range of diseases, including cancer. However, only one rexinoid, bexarotene (Targretin TM) has been successfully transitioned from the bench to the clinic and used to treat cutaneous T-cell lymphoma (CTCL). Our goal is to develop novel potent rexinoids with a less untoward side effect profile than bexarotene. To this end, we have synthesized a wide array of rexinoids with EC50 values and biological activity similar to bexarotene. In order to determine their suitability for additional downstream analysis, and to identify potential candidate analogs for clinical translation, we treated human CTCL cells in culture and employed microarray technology to assess gene expression profiles. We analyzed twelve rexinoids and found they could be stratified into three distinct categories based on their gene expression: similar to bexarotene, moderately different from bexarotene, and substantially different from bexarotene. Surprisingly, small changes in the structure of the bexarotene parent compound led to marked differences in gene expression profiles. Furthermore, specific analogs diverged markedly from our hypothesis in expression of genes expected to be important for therapeutic promise. However, promoter analysis of genes whose expression was analyzed indicates general regulatory trends along structural frameworks. Our results suggest that certain structural motifs, particularly the basic frameworks found in analog 4 and analog 9, represent important starting points to exploit in generating additional rexinoids for future study and therapeutic applications.
    • Action of automorphisms on irreducible characters of symplectic groups

      Taylor, Jay; Univ Arizona, Dept Math, 617 N Santa Rita Ave, Tucson, AZ 85721 USA (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2018-07-01)
      Assume G is a finite symplectic group Sp(2n)(q) over a finite field F-q of odd characteristic. We describe the action of the automorphism group Aut(G) on the set Irr(G) of ordinary irreducible characters of G. This description relies on the equivariance of Deligne-Lusztig induction with respect to automorphisms. We state a version of this equivariance which gives a precise way to compute the automorphism on the corresponding Levi subgroup; this may be of independent interest. As an application we prove that the global condition in Spath's criterion for the inductive McKay condition holds for the irreducible characters of Sp(2n)(q). (C) 2018 Elsevier Inc. All rights reserved.
    • Rotation-dependent nonlinear absorption of orbital angular momentum beams in ruby

      Musarra, G.; Wilson, K. E.; Faccio, D.; Wright, E. M.; Univ Arizona, Coll Opt Sci (OPTICAL SOC AMER, 2018-07-01)
      We investigate the effect of a rotating medium on orbital angular momentum (OAM)-carrying beams by combining a weak probe beam shifted in frequency relative to a strong pump beam. We show how the rotational Doppler effect modifies the light-matter interaction through the external rotation of the medium. This interaction leads to an absorption that increases with the mechanical rotation velocity of the medium and with a rate that depends on the OAM of the light beam. (C) 2018 Optical Society of America
    • Cuticular wax variants in a population of switchgrass ( Panicum virgatum L.)

      Weaver, Joshua M.; Lohrey, Greg; Tomasi, Pernell; Dyer, John M.; Jenks, Matthew A.; Feldmann, Kenneth A.; Univ Arizona, Sch Plant Sci (ELSEVIER SCIENCE BV, 2018-07)
      Leaf cuticular waxes are known to influence both biotic and abiotic stress tolerances of plants. The objective of this work was to characterize the wax phenotypic diversity present in a population of 1849 switchgrass plants. We identified 92 visually distinct variant plants that possessed altered leaf glaucousness relative to the common standard type (ST), which exhibited a bluish-white (glaucous) leaf color. The variants could be grouped into three classes: 1) non-glaucous types (NG) that possessed a shiny green leaf surface, 2) reduced glaucous types (RG) that appeared less glaucous than ST, and 3) highly glaucous types (HG) that exhibited more intense bluish white color than ST. Analyses of total cuticular wax content averaged over each of three NG (mean 304.79 +/- 15.16 mu g/dm(2)), RG (mean 533.33 +/- 21.62 mu g/dm(2)) and HG types (mean 1228.23 +/- 45.74 mu g/dm(2)) showed significant differences (P < 0.001) from three selected STs (mean 810.92 +/- 30.57 mu g/dm(2)). Analysis of wax composition among these selected types revealed that the C-33 beta-diketones were the most abundant wax compounds in all but NG types. Field emission scanning electron microscopy showed that abaxial leaf surfaces exhibited predominantly rod-shaped crystals, and adaxial surfaces exhibited predominantly plate-shaped wax crystals on all lines, except for NG that lacked wax crystals on the abaxial leaf surface. As a target for crop improvement, this study reveals that a large amount of variation for cuticle waxes exists within this switchgrass germplasm.
    • Process modeling for economic optimization of a solar driven sweeping gas membrane distillation desalination system

      Moore, Sarah E.; Mirchandani, Sera D.; Karanikola, Vasiliki; Nenoff, Tina M.; Arnold, Robert G.; Eduardo Sáez, A.; Univ Arizona, Dept Environm Chem & Engn (ELSEVIER SCIENCE BV, 2018-07)
      Water scarcity is especially impactful in remote and impoverished communities without access to centralized water treatment plants. In areas with access to a saline water source, point-of-use desalination by solar-driven membrane distillation (MD) is a possible method for mitigating water scarcity. To evaluate the applicability of MD, a comprehensive process model was developed and used to design an economically optimal system. Thermal energy for distillation was provided by solar thermal collectors, and electricity was provided using photovoltaic collectors. Distillation was performed using sweeping-gas membrane distillation. The cost of water in the optimized system was approximately $85/m(3). Membrane modules and solar thermal collectors made up the largest portion of the cost. Neither thermal nor electrical energy storage was economical within current technologies. The model developed provides a template to optimize MD membrane characteristics specialized for point-of-use applications.
    • Characterization of carfilzomib-resistant non-small cell lung cancer cell lines.

      Hanke, Neale T; Imler, Elliot; Marron, Marilyn T; Seligmann, Bruce E; Garland, Linda L; Baker, Amanda F; Univ Arizona, Ctr Canc, Coll Med, Tucson, AZ 85721 USA (SPRINGER, 2018-07)
      We previously showed that carfilzomib (CFZ) has potent anti-proliferative and cytotoxic activity in a broad range of lung cancer cell lines. Here we investigate possible mechanisms of CFZ acquired resistance in lung cancer cell lines. CFZ-resistant non-small cell lung cancer (NSCLC) cell lines were developed by exposing A549 and H520 cells to stepwise increasing concentrations of CFZ. Resistance to CFZ and cross-resistance to bortezomib and other chemotherapy drugs was measured using the MTT assay. Cytotoxicity to CFZ was determined using a CytoTox assay. Western blot was used to measure apoptosis, autophagy, and drug efflux transporter-related proteins. Quantitative targeted whole transcriptome sequencing and quantitative RT-PCR was used to measure gene expression. Flow cytometry was used to analyze intracellular accumulation of doxorubicin. The CFZ IC Upregulation of Pgp appears to be an important, but not the only, mechanism of CFZ resistance in NSCLC cell lines.
    • Analysing baryon acoustic oscillations in sparse spectroscopic samples via cross-correlation with dense photometry

      Patej, A; Eisenstein, D J; Univ Arizona, Steward Observ (OXFORD UNIV PRESS, 2018-07)
      We develop a formalism for measuring the cosmological distance scale from baryon acoustic oscillations (BAO) using the cross-correlation of a sparse redshift survey with a denser photometric sample. This reduces the shot noise that would otherwise affect the autocorrelation of the sparse spectroscopic map. As a proof of principle, we make the first on-sky application of this method to a sparse sample defined as the z > 0.6 tail of the Sloan Digital Sky Survey's (SDSS) BOSS/CMASS sample of galaxies and a dense photometric sample from SDSS DR9. We find a 2.8 sigma preference for the BAO peak in the cross-correlation at an effective z = 0.64, from which we measure the angular diameter distance D-M(z = 0.64) = (2418 +/- 73 Mpc)(r(s)/r(s, fid)). Accordingly, we expect that using this method to combine sparse spectroscopy with the deep, high-quality imaging that is just now becoming available will enable higher precision BAO measurements than possible with the spectroscopy alone.
    • A new wave front shape-based approach for acoustic source localization in an anisotropic plate without knowing its material properties

      Sen, Novonil; Kundu, Tribikram; Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ 85721, USA; Department of Civil Engineering and Engineering Mechanics, University of Arizona, Tucson, AZ 85721, USA (ELSEVIER SCIENCE BV, 2018-07)
      Estimating the location of an acoustic source in a structure is an important step towards passive structural health monitoring. Techniques for localizing an acoustic source in isotropic structures are well developed in the literature. Development of similar techniques for anisotropic structures, however, has gained attention only in the recent years and has a scope of further improvement. Most of the existing techniques for anisotropic structures either assume a straight line wave propagation path between the source and an ultrasonic sensor or require the material properties to be known. This study considers different shapes of the wave front generated during an acoustic event and develops a methodology to localize the acoustic source in an anisotropic plate from those wave front shapes. An elliptical wave front shape-based technique was developed first, followed by the development of a parametric curve-based technique for non-elliptical wave front shapes. The source coordinates are obtained by minimizing an objective function. The proposed methodology does not assume a straight line wave propagation path and can predict the source location without any knowledge of the elastic properties of the material. A numerical study presented here illustrates how the proposed methodology can accurately estimate the source coordinates. (C) 2018 Elsevier B.V. All rights reserved.
    • Influence of Nitrosative Stress on Fatigue During Childhood Leukemia Treatment

      Hockenberry, Marilyn J.; Moore, Ida M. (Ki); Scheurer, Michael E.; Hooke, Mary C.; Taylor, Olga A.; Koerner, Kari M.; Gundy, Patricia M.; Pan, Wei; Univ Arizona, Coll Nursing, Biobehav Hlth Sci Div (SAGE PUBLICATIONS INC, 2018-07)
      The focus on a cure for childhood leukemia over the last three decades has resulted in survival rates of more than 80%. However, efforts to manage leukemia-treatment symptoms have not kept pace with new therapies. Symptom toxicity during treatment can result in complications, treatment delays, and therapy dose reductions. Compromise in therapy can negatively influence the quality of life and, even more notably, jeopardize chances for long-term survival. This study examined biologic mechanisms that influence fatigue caused by increased reactive oxidative species (ROS) or actual failure of the antioxidant defense system due to genetic variation by investigating reactive nitrosative species, a downstream consequence of ROS. The specific aims of this study were to characterize the trajectory of nitrosative stress during acute lymphoblastic leukemia treatment and evaluate the influence of nitrosative stress on fatigue. A repeated measures design was used to evaluate the fatigue experienced by 186 children and adolescents, 3-18 years of age, with a diagnosis of leukemia during the most intense phase of treatment. An established biomarker of nitrosative stress, protein 3-nitrotyrosine (3NT) residues in the cerebral spinal fluid, was evaluated at diagnosis, postinduction, and consolidation phases of treatment. Higher fatigue was associated with higher 3NT levels at the beginning of treatment. Two distinct groups of children experienced either consistently high or consistently low 3NT levels across the treatment trajectory, from diagnosis to 12 months postinduction. Findings from this study support continued exploration into the phenotypic biochemical mechanisms that influence a reactive response to childhood cancer treatment.
    • Homogenization of dissipative, noisy, Hamiltonian dynamics

      Birrell, Jeremiah; Wehr, Jan; Univ Arizona, Dept Math; Univ Arizona, Program Appl Math (ELSEVIER SCIENCE BV, 2018-07)
      We study the dynamics of a class of Hamiltonian systems with dissipation, coupled to noise, in a singular (small mass) limit. We derive the homogenized equation for the position degrees of freedom in the limit, including the presence of a noise-induced drift term. We prove convergence to the solution of the homogenized equation in probability and, under stronger assumptions, in an L-P-norm. Applications cover the overdamped limit of particle motion in a time-dependent electromagnetic field, on a manifold with time-dependent metric, and the dynamics of nuclear matter. (C) 2017 Elsevier B.V. All rights reserved.
    • Adaptive Local Realignment of Protein Sequences

      DeBlasio, Dan; Kececioglu, John; Univ Arizona, Dept Comp Sci (MARY ANN LIEBERT, INC, 2018-07)
      While mutation rates can vary markedly over the residues of a protein, multiple sequence alignment tools typically use the same values for their scoring-function parameters across a protein's entire length. We present a new approach, called adaptive local realignment, that in contrast automatically adapts to the diversity of mutation rates along protein sequences. This builds upon a recent technique known as parameter advising, which finds global parameter settings for an aligner, to now adaptively find local settings. Our approach in essence identifies local regions with low estimated accuracy, constructs a set of candidate realignments using a carefully-chosen collection of parameter settings, and replaces the region if a realignment has higher estimated accuracy. This new method of local parameter advising, when combined with prior methods for global advising, boosts alignment accuracy as much as 26% over the best default setting on hard-to-align protein benchmarks, and by 6.4% over global advising alone. Adaptive local realignment has been implemented within the Opal aligner using the Facet accuracy estimator.