Browsing by Author "Zhang, H."

Now showing 1 - 12 of 12
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    Application of approximate matrix factorization to high order linearly implicit Runge-Kutta methods
    Zhang, H.; Sandu, Adrian; Tranquilli, Paul (Elsevier, 2015-10-01)
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    Armored kinorhynch-like scalidophoran animals from the early Cambrian
    Zhang, H.; Xiao, S.; Liu, Y.; Yuan, X.; Wan, B.; Muscente, A. D.; Shao, T.; Gong, H.; Cao, G. (2015-11-26)
    Morphology-based phylogenetic analyses support the monophyly of the Scalidophora (Kinorhyncha, Loricifera, Priapulida) and Nematoida (Nematoda, Nematomorpha), together constituting the monophyletic Cycloneuralia that is the sister group of the Panarthropoda. Kinorhynchs are unique among living cycloneuralians in having a segmented body with repeated cuticular plates, longitudinal muscles, dorsoventral muscles, and ganglia. Molecular clock estimates suggest that kinorhynchs may have diverged in the Ediacaran Period. Remarkably, no kinorhynch fossils have been discovered, in sharp contrast to priapulids and loriciferans that are represented by numerous Cambrian fossils. Here we describe several early Cambrian (~535 million years old) kinorhynch-like fossils, including the new species Eokinorhynchus rarus and two unnamed but related forms. E. rarus has characteristic scalidophoran features, including an introvert with pentaradially arranged hollow scalids. Its trunk bears at least 20 annuli each consisting of numerous small rectangular plates, and is armored with five pairs of large and bilaterally placed sclerites. Its trunk annuli are reminiscent of the epidermis segments of kinorhynchs. A phylogenetic analysis resolves E. rarus as a stem-group kinorhynch. Thus, the fossil record confirms that all three scalidophoran phyla diverged no later than the Cambrian Period.
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    Coupled Reversible and Irreversible Bistable Switches Underlying TGF beta-induced Epithelial to Mesenchymal Transition
    Tian, X. J.; Zhang, H.; Xing, Jianhua (CELL PRESS, 2013-08)
    Epithelial to mesenchymal transition (EMT) plays an important role in embryonic development, tissue regeneration, and cancer metastasis. Whereas several feedback loops have been shown to regulate EMT, it remains elusive how they coordinately modulate EMT response to TGF-beta treatment. We construct a mathematical model for the core regulatory network controlling TGF-beta-induced EMT. Through deterministic analyses and stochastic simulations, we show that EMT is a sequential two-step program in which an epithelial cell first is converted to partial EMT then to the mesenchymal state, depending on the strength and duration of TGF-beta stimulation. Mechanistically the system is governed by coupled reversible and irreversible bistable switches. The SNAIL1/miR-34 double-negative feedback loop is responsible for the reversible switch and regulates the initiation of EMT, whereas the ZEB/nniR-200 feedback loop is accountable for the irreversible switch and controls the establishment of the mesenchymal state. Furthermore, an autocrine TGF-beta/miR-200 feedback loop makes the second switch irreversible, modulating the maintenance of EMT. Such coupled bistable switches are robust to parameter variation and molecular noise. We provide a mechanistic explanation on multiple experimental observations. The model makes several explicit predictions on hysteretic dynamic behaviors, system response to pulsed stimulation, and various perturbations, which can be straightforwardly tested.
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    Decomposition squared
    Sharpe, Eric R.; Zhang, H. (2024-10-23)
    Abstract In this paper, we test and extend a proposal of Gu, Pei, and Zhang for an application of decomposition to three-dimensional theories with one-form symmetries and to quantum K theory. The theories themselves do not decompose, but, OPEs of parallel one-dimensional objects (such as Wilson lines) and dimensional reductions to two dimensions do decompose, sometimes in two independent ways. We apply this to extend conjectures for quantum K theory rings of gerbes (realized by three-dimensional gauge theories with one-form symmetries) via both orbifold partition functions and gauged linear sigma models.
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    Extrapolation-based implicit-explicit general linear methods
    Cardone, A.; Jackiewicz, Z.; Sandu, Adrian; Zhang, H. (Springer, 2014-03-01)
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    High Order Implicit-Explicit General Linear Methods with Optimized Stability Regions
    Zhang, H.; Sandu, Adrian; Blaise, S. (Siam Publications, 2016-01-01)
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    Light Sterile Neutrinos: A White Paper
    Abazajian, Kevork N.; Acero, M. A.; Agarwalla, S. K.; Aguilar-Arevalo, A. A.; Albright, C. H.; Antusch, S.; Arguelles, C. A.; Balantekin, A. B.; Barenboim, G.; Barger, V.; Bernardini, P.; Bezrukov, F.; Bjaelde, O. E.; Bogacz, S. A.; Bowden, N. S.; Boyarsky, A.; Bravar, A.; Berguno, D. B.; Brice, S. J.; Bross, A. D.; Caccianiga, B.; Cavanna, F.; Chun, E. J.; Cleveland, B. T.; Collin, A. P.; Coloma, P.; Conrad, Janet M.; Cribier, M.; Cucoanes, A. S.; D'Olivo, J. C.; Das, S.; Gouvea, A. D.; Derbin, A. V.; Dharmapalan, R.; Diaz, J. S.; Ding, X. J.; Djurcic, Zelimir; Donini, A.; Duchesneau, D.; Ejiri, H.; Elliott, S. R.; Ernst, D. J.; Esmaili, A.; Evans, J. J.; Fernandez-Martinez, Enrique; Figueroa-Feliciano, E.; Fleming, B. T.; Formaggio, J. A.; Franco, D.; Gaffiot, J.; Gandhi, R.; Gao, Y.; Garvey, G. T.; Gavrin, V. N.; Ghoshal, P.; Gibin, D.; Giunti, C.; Gninenko, S. N.; Gorbachev, V. V.; Gorbunov, D. S.; Guenette, R.; Guglielmi, A.; Halzen, F.; Hamann, J.; Hannestad, S.; Haxton, W.; Heeger, K. M.; Henning, R.; Hernandez, P.; Huber, Patrick; Huelsnitz, W.; Ianni, A.; Ibragimova, T. V.; Karadzhov, Y.; Karagiorgi, Georgia S.; Keefer, G.; Kim, Y. D.; Kopp, J.; Kornoukhov, V. N.; Kusenko, A.; Kyberd, P.; Langacker, P.; Lasserre, T.; Laveder, M.; Letourneau, A.; Lhuillier, D.; Li, Y. F.; Lindner, M.; Link, Jonathan M.; Littlejohn, B. L.; Lombardi, Paolo; Long, K.; Lopez-Pavon, J.; Louis, W. C.; Ludhova, L.; Lykken, J. D.; Machado, P. A. N.; Maltoni, M.; Mann, W. A.; Marfatia, D.; Mariani, Camillo; Matveev, V. A.; Mavromatos, N. E.; Melchiorri, A.; Meloni, David; Mena, O.; Mention, G.; Merle, A.; Meroni, E.; Mezzetto, M.; Mills, G. B.; Minic, Djordje; Miramonti, L.; Mohapatra, D.; Mohapatra, R. N.; Montanari, C.; Mori, Y.; Mueller, T. A.; Mumm, H. P.; Muratova, V. N.; Nelson, A. E.; Nico, J. S.; Noah, E.; Nowak, J.; Smirnov, O. Y.; Obolensky, M.; Pakvasa, S.; Palamara, O.; Pallavicini, M.; Pascoli, S.; Patrizii, L.; Pavlovic, Z.; Peres, O. L. G.; Pessard, H.; Pietropaolo, F.; Pitt, M. L.; Popovic, M.; Pradler, J.; Ranucci, G.; Ray, H.; Razzaque, S.; Rebel, B.; Robertson, R. G. H.; Rodejohann, W.; Rountree, S. D.; Rubbia, C.; Ruchayskiy, O.; Sala, P. R.; Scholberg, K.; Schwetz, T.; Shaevitz, Marjorie Hansen; Shaposhnikov, M.; Shrock, R.; Simone, S.; Skorokhvatov, Mikhail D.; Sorel, M.; Sousa, A.; Spergel, D. N.; Spitz, Joshua; Stanco, L.; Stancu, Ion; Suzuki, A.; Takeuchi, Tatsu; Tamborra, Irene; Tang, J.; Testera, G.; Tian, X. C.; Tonazzo, A.; Tunnell, C. D.; Water, R. G. V. D.; Verde, L.; Veretenkin, E. P.; Vignoli, C.; Vivier, M.; Vogelaar, R. Bruce; Wascko, M. O.; Wilkerson, J. F.; Winter, W.; Wong, Y. Y. Y.; Yanagida, T. T.; Yasuda, O.; Yeh, M.; Yermia, F.; Yokley, Z. W.; Zeller, Geralyn P.; Zhan, L.; Zhang, H. (2012-04)
    This white paper addresses the hypothesis of light sterile neutrinos based on recent anomalies observed in neutrino experiments and the latest astrophysical data.
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    LIRK-W: Linearly-implicit Runge-Kutta methods with approximate matrix factorization
    Tranquilli, Paul; Sandu, Adrian; Zhang, H. (2016-11-22)
    This paper develops a new class of linearly implicit time integration schemes called Linearly-Implicit Runge-Kutta-W (LIRK-W) methods. These schemes are based on an implicit-explicit approach which does not require a splitting of the right hand side and allow for arbitrary, time dependent, and stage varying approximations of the linear systems appearing in the method. Several formulations of LIRK-W schemes, each designed for specific approximation types, and their associated order condition theories are presented.
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    A Meta Analysis on Risks of Adverse Pregnancy Outcomes in Toxoplasma gondii Infection
    Li, X.-L.; Wei, H.-X.; Zhang, H.; Peng, H. J.; Lindsay, David S. (PLOS, 2014-05-15)
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    Partitioned and Implicit-Explicit General Linear Methods for Ordinary Differential Equations
    Zhang, H.; Sandu, Adrian; Blaise, S. (Springer/Plenum Publishers, 2014-10-01)
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    Prolonged voluntary wheel running reveals unique adaptations in mdx mice treated with microdystrophin constructs +/- the nNOS-binding site
    Hamm, S. E.; Yuan, C.; McQueen, L. F.; Wallace, M. A.; Zhang, H.; Arora, A.; Garafalo, A. M.; McMillan, Ryan P.; Lawlor, M. W.; Prom, M. J.; Ott, E. M.; Yan, J.; Addington, A. K.; Morris, C. A.; Gonzalez, J. P.; Grange, R. W. (Frontiers, 2023-06-26)
    We tested the effects of prolonged voluntary wheel running on the muscle function of mdx mice treated with one of two different microdystrophin constructs. At 7 weeks of age mdx mice were injected with a single dose of AAV9-CK8-microdystrophin with (gene therapy 1, GT1) or without (gene therapy 2, GT2) the nNOS-binding domain and were assigned to one of four gene therapy treated groups: mdxRGT1 (run, GT1), mdxGT1 (no run, GT1), or mdxRGT2 (run,GT2), mdxGT2 (no run, GT2). There were two mdx untreated groups injected with excipient: mdxR (run, no gene therapy) and mdx (no run, no gene therapy). A third no treatment group, Wildtype (WT) received no injection and did not run. mdxRGT1, mdxRGT2 and mdxR performed voluntary wheel running for 52 weeks; WT and remaining mdx groups were cage active. Robust expression of microdystrophin occurred in diaphragm, quadriceps, and heart muscles of all treated mice. Dystrophic muscle pathology was high in diaphragms of non-treated mdx and mdxR mice and improved in all treated groups. Endurance capacity was rescued by both voluntary wheel running and gene therapy alone, but their combination was most beneficial. All treated groups increased in vivo plantarflexor torque over both mdx and mdxR mice. mdx and mdxR mice displayed ∼3-fold lower diaphragm force and power compared to WT values. Treated groups demonstrated partial improvements in diaphragm force and power, with mdxRGT2 mice experiencing the greatest improvement at ∼60% of WT values. Evaluation of oxidative red quadriceps fibers revealed the greatest improvements in mitochondrial respiration in mdxRGT1 mice, reaching WT levels. Interestingly, mdxGT2 mice displayed diaphragm mitochondrial respiration values similar to WT but mdxRGT2 animals showed relative decreases compared to the no run group. Collectively, these data demonstrate that either microdystrophin construct combined with voluntary wheel running increased in vivo maximal muscle strength, power, and endurance. However, these data also highlighted important differences between the two microdystrophin constructs. GT1, with the nNOS-binding site, improved more markers of exercise-driven adaptations in metabolic enzyme activity of limb muscles, while GT2, without the nNOS-binding site, demonstrated greater protection of diaphragm strength after chronic voluntary endurance exercise but decreased mitochondrial respiration in the context of running.
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