• 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.
    • 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.
    • Chance-constrained economic dispatch with renewable energy and storage

      Cheng, Jianqiang; Chen, Richard Li-Yang; Najm, Habib N.; Pinar, Ali; Safta, Cosmin; Watson, Jean-Paul; Univ Arizona, Dept Syst & Ind Engn (SPRINGER, 2018-06)
      Increasing penetration levels of renewables have transformed how power systems are operated. High levels of uncertainty in production make it increasingly difficulty to guarantee operational feasibility; instead, constraints may only be satisfied with high probability. We present a chance-constrained economic dispatch model that efficiently integrates energy storage and high renewable penetration to satisfy renewable portfolio requirements. Specifically, we require that wind energy contribute at least a prespecified proportion of the total demand and that the scheduled wind energy is deliverable with high probability. We develop an approximate partial sample average approximation (PSAA) framework to enable efficient solution of large-scale chance-constrained economic dispatch problems. Computational experiments on the IEEE-24 bus system show that the proposed PSAA approach is more accurate, closer to the prescribed satisfaction tolerance, and approximately 100 times faster than standard sample average approximation. Finally, the improved efficiency of our PSAA approach enables solution of a larger WECC-240 test system in minutes.
    • On triangle cover contact graphs

      Sultana, Shaheena; Hossain, Md. Iqbal; Rahman, Md. Saidur; Moon, Nazmun Nessa; Hashem, Tahsina; Univ Arizona (ELSEVIER SCIENCE BV, 2018-06)
      Let S = {P-1, p(2), ..., p(n)} be a set of pairwise disjoint geometric objects of some type in a 2D plane and let C = {c(1), c(2), ..., c(n)} be a set of dosed objects of some type in the same plane with the property that each element in C covers exactly one element in S and any two elements in C are interior-disjoint. We call an element in S a seed and an element in C a cover. A cover contact graph (CCG) has a vertex for each element of C and an edge between two vertices whenever the corresponding cover elements touch. It is known how to construct, for any given point seed set, a disk or triangle cover whose contact graph is 1- or 2-connected but the problem of deciding whether a k-connected CCG can be constructed or not for k > 2 is still unsolved. A triangle cover contact graph (TCCG) is a cover contact graph whose cover elements are triangles. In this paper, we give algorithms to construct a 3-connected TCCG and a 4-connected TCCG for a given set of point seeds. We also show that any connected outerplanar graph has a realization as a TCCG on a given set of collinear point seeds. Note that, under this restriction, only trees and cycles are known to be realizable as CCG. (C) 2017 Elsevier B.V. All rights reserved.
    • Fracture Through a Distal Fibular Tunnel Used for an Anatomic Lateral Ankle Ligament Reconstruction

      Roward, Zachary; Latt, L. Daniel; Univ Arizona, Dept Orthopaedic Surgery (Sage, 2018-06)
      Anatomic lateral ankle ligament reconstruction using free tendon graft with osseous tunnels has become a popular technique for revision reconstruction of the lateral ankle ligaments. With the procedure’s burgeoning popularity, an accompanying increase in postoperative complications is likely to occur. We report on one such complication: traumatic distal fibula fracture through the transosseous tunnels.
    • Increased O-GlcNAcylation of SNAP29 Drives Arsenic-Induced Autophagic Dysfunction

      Dodson, Matthew; Liu, Pengfei; Jiang, Tao; Ambrose, Andrew J.; Luo, Gang; Rojo de la Vega, Montserrat; Cholanians, Aram B.; Wong, Pak Kin; Chapman, Eli; Zhang, Donna D.; Univ Arizona, Coll Pharm, Dept Pharmacol & Toxicol; Univ Arizona, Arizona Canc Ctr (AMER SOC MICROBIOLOGY, 2018-06)
      Environmental exposure to arsenic is linked to adverse health effects, including cancer and diabetes. Pleiotropic cellular effects are observed with arsenic exposure. Previously, we demonstrated that arsenic dysregulated the autophagy pathway at low, environmentally relevant concentrations. Here we show that arsenic blocks autophagy by preventing autophagosome-lysosome fusion. Specifically, arsenic disrupts formation of the STX17-SNAP29-VAMP8 SNARE complex, where SNAP29 mediates vesicle fusion through bridging STX17- containing autophagosomes to VAMP8-bearing lysosomes. Mechanistically, arsenic inhibits SNARE complex formation, at least in part, by enhancing O-GlcNAcylation of SNAP29. Transfection of O-GlcNAcylation-defective, but not wild-type, SNAP29 into clustered regularly interspaced short palindromic repeat (CRISPR)-mediated SNAP29 knockout cells abolishes arsenic-mediated autophagy inhibition. These findings reveal a mechanism by which low levels of arsenic perturb proteostasis through inhibition of SNARE complex formation, providing a possible therapeutic target for disease intervention in the more than 200 million people exposed to unsafe levels of arsenic.
    • Blast Exposure Disrupts the Tonotopic Frequency Map in the Primary Auditory Cortex

      Masri, Samer; Zhang, Li S.; Luo, Hao; Pace, Edward; Zhang, Jinsheng; Bao, Shaowen; Univ Arizona, Neurosci Grad Program; Univ Arizona, Dept Physiol (PERGAMON-ELSEVIER SCIENCE LTD, 2018-05-21)
      Blast exposure can cause various auditory disorders including tinnitus, hyperacusis, and other central auditory processing disorders. While this is suggestive of pathologies in the central auditory system, the impact of blast exposure on central auditory processing remains poorly understood. Here we examined the effects of blast shockwaves on acoustic response properties and the tonotopic frequency map in the auditory cortex. We found that multiunits recorded from the auditory cortex exhibited higher acoustic thresholds and broader frequency tuning in blast-exposed animals. Furthermore, the frequency map in the primary auditory cortex was distorted. These changes may contribute to central auditory processing disorders. (C) 2018 IBRO. Published by Elsevier Ltd. All rights reserved.
    • Deep millimeter spectroscopy observations toward NGC 1068

      Qiu, Jianjie; Wang, Junzhi; Shi, Yong; Zhang, Jiangshui; Fang, Min; Li, Fei; Univ Arizona, Dept Astron (EDP SCIENCES S A, 2018-05-15)
      Aims. We aim for a better understanding of gas properties in the circum-nuclear disk (CND) region of the nearby gas-rich Seyfert 2 galaxy NGC 1068. We focus on line identification and the basic physical parameters estimation of molecular gas in the CND region. Methods. We used the IRAM 30 m telescope to conduct deep millimeter spectroscopy observations toward the center of NGC 1068. Results. Thirty-two lines were detected in this galaxy, 15 lines of wich were detected for the first time. With a sensitivity better by about a factor of 4 than observations in the literature for this source at 3 mm band, we detected several weak lines for the first time in this source, such as lines from CH3CCH, CH3OCH3, and (HCO+)-O-18. Column densities of these molecules were estimated based on line emissions. Some marginal detections in the literature, such as (HNC)-C-13 (1-0), were confirmed. CH3OCH3 was detected for the first time in external galaxies. Lines from several carbon chain molecules and shock-related molecules were also detected in this source.
    • Effects of climatic seasonality on the isotopic composition of evaporating soil waters

      Benettin, Paolo; Volkmann, Till H. M.; von Freyberg, Jana; Frentress, Jay; Penna, Daniele; Dawson, Todd E.; Kirchner, James W.; Univ Arizona, Biosphere 2 (COPERNICUS GESELLSCHAFT MBH, 2018-05-15)
      Stable water isotopes are widely used in ecohydrology to trace the transport, storage, and mixing of water on its journey through landscapes and ecosystems. Evaporation leaves a characteristic signature on the isotopic composition of the water that is left behind, such that in dual-isotope space, evaporated waters plot below the local meteoric water line (LMWL) that characterizes precipitation. Soil and xylem water samples can often plot below the LMWL as well, suggesting that they have also been influenced by evaporation. These soil and xylem water samples frequently plot along linear trends in dual-isotope space. These trend lines are often termed "evaporation lines" and their intersection with the LMWL is often interpreted as the isotopic composition of the precipitation source water. Here we use numerical experiments based on established isotope fractionation theory to show that these trend lines are often by-products of the seasonality in evaporative fractionation and in the isotopic composition of precipitation. Thus, they are often not true evaporation lines, and, if interpreted as such, can yield highly biased estimates of the isotopic composition of the source water.
    • Multiple episodes of fast exhumation since Cretaceous in southeast Tibet, revealed by low-temperature thermochronology

      Liu-Zeng, Jing; Zhang, Jinyu; McPhillips, Devin; Reiners, Peter; Wang, Wei; Pik, Raphael; Zeng, Lingsen; Hoke, Greg; Xie, Kejia; Xiao, Ping; Zheng, Dewen; Ge, Yukui; Univ Arizona, Dept Geosci (ELSEVIER SCIENCE BV, 2018-05-15)
      The southeast margin of the Tibetan plateau is characterized by deeply incised river valleys separated by a perched low relief landscape that gently descends from the high Tibetan plateau towards the southeast. When and how this unique landscape formed is debated. The onset of increased river incision is often interpreted as a proxy for the timing of surface uplift. Here, apatite and zircon (U-Th)/He and apatite fission track thermochronometries are employed to map the spatial and temporal pattern of exhumation in the region. Vertical profiles of granitic rocks were collected near Deqin (similar to 28.5 degrees N) and Weixi (similar to 27.5 degrees N). The two transects share a similar exhumation history, with two episodes of relatively fast exhumation (similar to 100-300 m/Myr) in the Cenozoic: during the Paleocene to Eocene (60-40 Ma) and Miocene to present (20-0 Ma), separated by an intervening period of slow exhumation. A pulse of moderate to high exhumation (70-300 m/Myr) during the mid- to late-Cretaceous (120-80 Ma) is also present in the data. However, the rate and total amount of exhumation near Deqin is larger than at Weixi and is especially pronounced in the interval between 20 Ma to present. We interpret this difference as possibly related to differences in erosion rates between the Lancang (Deqin) and the Jinsha (Weixi) rivers. The Paleocene to Eocene episode of fast exhumation is likely in response to early Cenozoic deformation along tectonic boundary structures, related to the transpressional collision of the Indian plate with this region. Pre-Miocene episodes of fast exhumation corroborate recent paleoaltimetric studies, which show that the southeast margin of the Tibetan plateau was elevated prior to the Oligocene. (C) 2018 Elsevier B.V. All rights reserved.
    • Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

      Song, Hongshuo; Giorgi, Elena E.; Ganusov, Vitaly V.; Cai, Fangping; Athreya, Gayathri; Yoon, Hyejin; Carja, Oana; Hora, Bhavna; Hraber, Peter; Romero-Severson, Ethan; Jiang, Chunlai; Li, Xiaojun; Wang, Shuyi; Li, Hui; Salazar-Gonzalez, Jesus F.; Salazar, Maria G.; Goonetilleke, Nilu; Keele, Brandon F.; Montefiori, David C.; Cohen, Myron S.; Shaw, George M.; Hahn, Beatrice H.; McMichael, Andrew J.; Haynes, Barton F.; Korber, Bette; Bhattacharya, Tanmoy; Gao, Feng; Univ Arizona, Off Res & Discovery (NATURE PUBLISHING GROUP, 2018-05-15)
      Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo.
    • Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women

      Łaniewski, Paweł; Barnes, Dominique; Goulder, Alison; Cui, Haiyan; Roe, Denise J.; Chase, Dana M.; Herbst-Kralovetz, Melissa M.; Univ Arizona, Coll Med Phoenix, Dept Basic Med Sci; Univ Arizona, Coll Med Phoenix, Dept Obstet & Gynecol; Univ Arizona, UA Canc Ctr (NATURE PUBLISHING GROUP, 2018-05-15)
      While high-risk human papillomavirus (HPV) infection is a well-established risk factor for cervical cancer, there are likely other factors within the local microenvironment that contribute to cervical carcinogenesis. Here we investigated relationships between HPV, vaginal pH, vaginal microbiota (VMB) composition, level of genital immune mediators and severity of cervical neoplasm. We enrolled women with low- and high-grade cervical dysplasia (LGD, HGD), invasive cervical carcinoma (ICC), and healthy controls. HPV16, HPV45, HPV58, and HPV31 were the most prevalent in our cohort with HPV16 and HPV31 genotypes more prevalent in Hispanics. Vaginal pH was associated with ethnicity and severity of cervical neoplasm. Lactobacillus dominance decreased with the severity of cervical neoplasm, which correlated with elevated vaginal pH. Hispanic ethnicity was also associated with decreased Lactobacillus dominance. Furthermore, Sneathia was enriched in all precancerous groups, ICC, abnormal pH and Hispanic origin. Patients with ICC, but not LGD and HGD, exhibited increased genital inflammatory scores and elevated specific immune mediators. Notably, IL-36 gamma was significantly associated with ICC. Our study revealed local, host immune and microbial signatures associated with cervical carcinogenesis and provides an initial step to understanding the complex interplay between mucosal inflammation, HPV persistence and the VMB.
    • Long non-coding RNA expression patterns in lung tissues of chronic cigarette smoke induced COPD mouse model

      Zhang, Haiyun; Sun, Dejun; Li, Defu; Zheng, Zeguang; Xu, Jingyi; Liang, Xue; Zhang, Chenting; Wang, Sheng; Wang, Jian; Lu, Wenju; Univ Arizona, Div Translat & Regenerat Med (NATURE PUBLISHING GROUP, 2018-05-15)
      Long non-coding RNAs (lncRNAs) have critical regulatory roles in protein-coding gene expression. Aberrant expression profiles of lncRNAs have been observed in various human diseases. In this study, we investigated transcriptome profiles in lung tissues of chronic cigarette smoke (CS)-induced COPD mouse model. We found that 109 lncRNAs and 260 mRNAs were significantly differential expressed in lungs of chronic CS-induced COPD mouse model compared with control animals. GO and KEGG analyses indicated that differentially expressed lncRNAs associated protein-coding genes were mainly involved in protein processing of endoplasmic reticulum pathway, and taurine and hypotaurine metabolism pathway. The combination of high throughput data analysis and the results of qRT-PCR validation in lungs of chronic CS-induced COPD mouse model, 16HBE cells with CSE treatment and PBMC from patients with COPD revealed that NR_102714 and its associated protein-coding gene UCHL1 might be involved in the development of COPD both in mouse and human. In conclusion, our study demonstrated that aberrant expression profiles of lncRNAs and mRNAs existed in lungs of chronic CS-induced COPD mouse model. From animal models perspective, these results might provide further clues to investigate biological functions of lncRNAs and their potential target protein-coding genes in the pathogenesis of COPD.
    • The Immediate Early Gene Egr3 Is Required for Hippocampal Induction of Bdnf by Electroconvulsive Stimulation

      Meyers, Kimberly T.; Marballi, Ketan K.; Brunwasser, Samuel J.; Renda, Briana; Charbel, Milad; Marrone, Diano F.; Gallitano, Amelia L.; Univ Arizona, Coll Med Phoenix, Dept Basic Med Sci; Univ Arizona, Evelyn F McKnight Brain Inst (FRONTIERS MEDIA SA, 2018-05-11)
      Early growth response 3 (Egr3) is an immediate early gene (IEG) that is regulated downstream of a cascade of genes associated with risk for psychiatric disorders, and dysfunction of Egr3 itself has been implicated in schizophrenia, bipolar disorder, and depression. As an activity-dependent transcription factor, EGR3 is poised to regulate the neuronal expression of target genes in response to environmental events. In the current study, we sought to identify a downstream target of EGR3 with the goal of further elucidating genes in this biological pathway relevant for psychiatric illness risk. We used electroconvulsive stimulation (ECS) to induce high-level expression of IEGs in the brain, and conducted expression microarray to identify genes differentially regulated in the hippocampus of Egr3-deficient (-/-) mice compared to their wildtype (WT) littermates. Our results replicated previous work showing that ECS induces high-level expression of the brain-derived neurotrophic factor (Bdnf) in the hippocampus of WT mice. However, we found that this induction is absent in Egr3-/- mice. Quantitative real-time PCR (qRT-PCR) validated the microarray results (performed in males) and replicated the findings in two separate cohorts of female mice. Follow-up studies of activity-dependent Bdnf exons demonstrated that ECS-induced expression of both exons IV and VI requires Egr3. In situ hybridization demonstrated high-level cellular expression of Bdnf in the hippocampal dentate gyrus following ECS in WT, but not Egr3-/-, mice. Bdnf promoter analysis revealed eight putative EGR3 binding sites in the Bdnf promoter, suggesting a mechanism through which EGR3 may directly regulate Bdnf gene expression. These findings do not appear to result from a defect in the development of hippocampal neurons in Egr3-/- mice, as cell counts in tissue sections stained with anti-NeuN antibodies, a neuron-specific marker, did not differ between Egr3-/- and WT mice. In addition, Sholl analysis and counts of dendritic spines in golgi-stained hippocampal sections revealed no difference in dendritic morphology or synaptic spine density in Egr3-/-, compared to WT, mice. These findings indicate that Egr3 is required for ECS-induced expression of Bdnf in the hippocampus and suggest that Bdnf may be a downstream gene in our previously identified biologically pathway for psychiatric illness susceptibility.
    • Exploring the Connection between Parsec-scale Jet Activity and Broadband Outbursts in 3C 279

      Rani, B.; Jorstad, S. G.; Marscher, A. P.; Agudo, I.; Sokolovsky, K. V.; Larionov, V. M.; Smith, P.; Mosunova, D. A.; Borman, G. A.; Grishina, T. S.; Kopatskaya, E. N.; Mokrushina, A. A.; Morozova, D. A.; Savchenko, S. S.; Troitskaya, Yu. V.; Troitsky, I. S.; Thum, C.; Molina, S. N.; Casadio, C.; Univ Arizona, Steward Observ (IOP PUBLISHING LTD, 2018-05-10)
      We use a combination of high-resolution very long baseline interferometry (VLBI) radio and multiwavelength flux density and polarization observations to constrain the physics of the dissipation mechanism powering the broadband flares in 3C 279 during an episode of extreme flaring activity in 2013-2014. Six bright flares superimposed on a long-term outburst are detected at gamma-ray energies. Four of the flares have optical and radio counterparts. The two modes of flaring activity (faster flares sitting on top of a long-term outburst) present at radio, optical, and gamma-ray frequencies are missing in X-rays. X-ray counterparts are only observed for two flares. The first three flares are accompanied by ejection of a new VLBI component (NC2), suggesting the 43 GHz VLBI core as the site of energy dissipation. Another new component, NC3, is ejected after the last three flares, which suggests that the emission is produced upstream from the core (closer to the black hole). The study therefore indicates multiple sites of energy dissipation in the source. An anticorrelation is detected between the optical percentage polarization (PP) and optical/gamma-ray flux variations, while the PP has a positive correlation with optical/gamma-ray spectral indices. Given that the mean polarization is inversely proportional to the number of cells in the emission region, the PP versus optical/gamma-ray anticorrelation could be due to more active cells during the outburst than at other times. In addition to the turbulent component, our analysis suggests the presence of a combined turbulent and ordered magnetic field, with the ordered component transverse to the jet axis.
    • Summer dry-down modulates the isotopic composition of soil CO2 production in snow-dominated landscapes.

      Riveros-Iregui, Diego A; Lorenzo, Theresa M; Liang, Liyin L; Hu, Jia; Univ Arizona, Sch Nat Resources & Environm (PUBLIC LIBRARY SCIENCE, 2018-05-10)
      In mountainous landscapes, soil moisture is highly dynamic due to the effects of topography and the temporal variability imposed by seasonal precipitation, including rainfall and snow. Soil moisture is known to affect ecosystem carbon exchange both aboveground and belowground, as well as the stable isotopic composition of exchanged CO2. In this study we used an extensive suite of measurements to examine the effects of seasonal changes in soil moisture on the isotopic composition of soil CO2 production at the landscape level. We show that the seasonal decline in soil moisture (i.e., summer dry-down) appeared to impose a trend in the δ13C of soil CO2 production (δP) with more negative δP early in the growing season when soils were wet, and more positive δP as the growing season progressed and soils dried out. This seemingly generalizable pattern for a snow-dominated watershed is likely to represent the variability of recently assimilated C, tracked through the plant-soil system and imprinted in the respired CO2. Thus, our observations suggest that, at least for mountainous environments, seasonal changes in δP are largely mediated by soil moisture and their spatial variability is partially organized by topography.
    • VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements

      Christley, Scott; Scarborough, Walter; Salinas, Eddie; Rounds, William H.; Toby, Inimary T.; Fonner, John M.; Levin, Mikhail K.; Kim, Min; Mock, Stephen A.; Jordan, Christopher; Ostmeyer, Jared; Buntzman, Adam; Rubelt, Florian; Davila, Marco L.; Monson, Nancy L.; Scheuermann, Richard H.; Cowell, Lindsay G.; Univ Arizona, Inst Bio5 (FRONTIERS MEDIA SA, 2018-05-08)
      Background: Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. Results: VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. Conclusion: VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.
    • Inferring giant planets from ALMA millimeter continuum and line observations in (transition) disks

      Facchini, S.; Pinilla, P.; van Dishoeck, E. F.; de Juan Ovelar, M.; Univ Arizona, Dept Astron (EDP SCIENCES S A, 2018-05-07)
      Context. Radial gaps or cavities in the continuum emission in the IR-mm wavelength range are potential signatures of protoplanets embedded in their natal protoplanetary disk are. Hitherto, models have relied on the combination of mm continuum observations and near-infrared scattered light images to put constraints on the properties of embedded planets. Atacama Large Millimeter/submillimeter Array (ALMA) observations are now probing spatially resolved rotational line emission of CO and other chemical species. These observations can provide complementary information on the mechanism carving the gaps in dust and additional constraints on the purported planet mass. Aims. We investigate whether the combination of ALMA continuum and CO line observations can constrain the presence and mass of planets embedded in protoplanetary disks. Methods. We post-processed azimuthally averaged 2D hydrodynamical simulations of planet-disk models, in which the dust densities and grain size distributions are computed with a dust evolution code that considers radial drift, fragmentation, and growth. The simulations explored various planet masses (1 M-J <= M-p <= 15 M-J) and turbulent parameters (10(-4) <= alpha <= 10(-3)). The outputs were then post-processed with the thermochemical code DALI, accounting for the radially and vertically varying dust properties. We obtained the gas and dust temperature structures, chemical abundances, and synthetic emission maps of both thermal continuum and CO rotational lines. This is the first study combining hydrodynamical simulations, dust evolution, full radiative transfer, and chemistry to predict gas emission of disks hosting massive planets. Results. All radial intensity profiles of (CO)-C-12, (CO)-C-13, and (CO)-O-18 show a gap at the planet location. The ratio between the location of the gap as seen in CO and the peak in the mm continuum at the pressure maximum outside the orbit of the planet shows a clear dependence on planet mass and is independent of disk viscosity for the parameters explored in this paper. Because of the low dust density in the gaps, the dust and gas components can become thermally decoupled and the gas becomes colder than the dust. The gaps seen in CO are due to a combination of gas temperature dropping at the location of the planet and of the underlying surface density profile. Both effects need to be taken into account and disentangled when inferring gas surface densities from observed CO intensity profiles; otherwise, the gas surface density drop at the planet location can easily be overestimated. CO line ratios across the gap are able to quantify the gas temperature drop in the gaps in observed systems. Finally, a CO cavity not observed in any of the models, only CO gaps, indicating that one single massive planet is not able to explain the CO cavities observed in transition disks, at least without additional physical or chemical mechanisms.
    • Feature-based data assimilation in geophysics

      Morzfeld, Matthias; Adams, Jesse; Lunderman, Spencer; Orozco, Rafael; Univ Arizona, Dept Math (COPERNICUS GESELLSCHAFT MBH, 2018-05-03)
      Many applications in science require that computational models and data be combined. In a Bayesian framework, this is usually done by defining likelihoods based on the mismatch of model outputs and data. However, matching model outputs and data in this way can be unnecessary or impossible. For example, using large amounts of steady state data is unnecessary because these data are redundant. It is numerically difficult to assimilate data in chaotic systems. It is often impossible to assimilate data of a complex system into a low-dimensional model. As a specific example, consider a low-dimensional stochastic model for the dipole of the Earth's magnetic field, while other field components are ignored in the model. The above issues can be addressed by selecting features of the data, and defining likelihoods based on the features, rather than by the usual mismatch of model output and data. Our goal is to contribute to a fundamental understanding of such a feature-based approach that allows us to assimilate selected aspects of data into models. We also explain how the feature-based approach can be interpreted as a method for reducing an effective dimension and derive new noise models, based on perturbed observations, that lead to computationally efficient solutions. Numerical implementations of our ideas are illustrated in four examples.