1,188 results on '"Kovar P"'
Search Results
2. Micro-cold Spray Deposition of YSZ Films from Ultrafine Powders Using a Pressure Relief Channel Nozzle
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Bierschenk, Stephen G. and Kovar, Desiderio
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- 2024
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3. Kinetic formulation of Tolman-Ehrenfest effect: Non-ideal fluids in Schwarzschild and Kerr space-times
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Cremaschini, Claudio, Kovář, Jiří, Stuchlík, Zdeněk, and Tessarotto, Massimo
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General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena ,Condensed Matter - Statistical Mechanics - Abstract
A review of the original thermodynamic formulation of the Tolman-Ehrenfest effect prescribing the temperature profile of uncharged fluid at thermal equilibrium forming stationary configurations in curved space-time is proposed. A statistical description based on relativistic kinetic theory is implemented. In this context the Tolman-Ehrenfest relation arises in the Schwarzschild space-time for collisionless uncharged particles at Maxwellian kinetic equilibrium. However, the result changes considerably when non-ideal fluids, i.e., non-Maxwellian distributions, are treated, whose statistical temperature becomes non-isotropic and gives rise to a tensor pressure. This is associated with phase-space anisotropies in the distribution function, occurring both for diagonal and non-diagonal metric tensors, exemplified by the Schwarzschild and Kerr metrics respectively. As a consequence, it is shown that for these systems it is not possible to define a Tolman-Ehrenfest relation in terms of an isotropic scalar temperature. Qualitative properties of the novel solution are discussed., Comment: 7 pages. arXiv admin note: text overlap with arXiv:2306.10434
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- 2023
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4. Polytropic representation of the kinetic pressure tensor of non-ideal magnetized fluids in equilibrium toroidal structures
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Cremaschini, Claudio, Kovář, Jiří, Stuchlík, Zdeněk, and Tessarotto, Massimo
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Physics - Plasma Physics ,Astrophysics - High Energy Astrophysical Phenomena ,Condensed Matter - Statistical Mechanics - Abstract
Non-ideal fluids are generally subject to the occurrence of non-isotropic pressure tensors, whose determination is fundamental in order to characterize their dynamical and thermodynamical properties. This requires the implementation of theoretical frameworks provided by appropriate microscopic and statistical kinetic approaches in terms of which continuum fluid fields are obtained. In this paper the case of non-relativistic magnetized fluids forming equilibrium toroidal structures in external gravitational fields is considered. Analytical solutions for the kinetic distribution function are explicitly constructed, to be represented by a Chapman-Enskog expansion around a Maxwellian equilibrium. In this way, different physical mechanisms responsible for the generation of non-isotropic pressures are identified and proved to be associated with the kinetic constraints imposed on single and collective particle dynamics by phase-space symmetries and magnetic field. As a major outcome, the validity of a polytropic representation for the kinetic pressure tensors corresponding to each source of anisotropy is established, whereby directional pressures exhibit a specific power-law functional dependence on fluid density. The astrophysical relevance of the solution for the understanding of fluid plasma properties in accretion-disc environments is discussed., Comment: 16 pages
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- 2023
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5. The Addition of Boron to Melt-Spun Fe−6.5%Si Ribbons
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Ouyang, Gaoyuan, Claude, Roger, Kovar, Alexander, Hillard, Ben, Kramer, Matthew J., Anderson, Iver E., and Cui, Jun
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- 2024
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6. Influence of Crystallographic Orientation on the Deformation of Ag Nanoparticles During High-Speed Impact
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Chitrakar, T. V., Becker, Michael F., and Kovar, Desiderio
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- 2023
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7. Cultivar-dependent and drought-induced modulation of secondary metabolites, adaptative defense in Fagopyrum esculentum L
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Oksana, Sytar, Marek, Kovar, Marian, Brestic, and Marek, Zivcak
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- 2023
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8. Losing weight to achieve joint or hernia surgery: is the intragastric balloon the answer?
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Abbitt, Danielle, Netsanet, Adom, Kovar, Alexandra, Choy, Kevin, Jones, Teresa S., Cassell, Benjamin, Hammad, Hazem, Reveille, Robert Matthew, Wikiel, Krzysztof J., and Jones, Edward L.
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- 2023
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9. Symptom profiles of community cases infected by influenza, RSV, rhinovirus, seasonal coronavirus, and SARS-CoV-2 variants of concern
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Geismar, Cyril, Nguyen, Vincent, Fragaszy, Ellen, Shrotri, Madhumita, Navaratnam, Annalan M. D., Beale, Sarah, Byrne, Thomas E., Fong, Wing Lam Erica, Yavlinsky, Alexei, Kovar, Jana, Hoskins, Susan, Braithwaite, Isobel, Aldridge, Robert W., and Hayward, Andrew C.
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- 2023
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10. Incidence of muscle wasting in the critically ill: a prospective observational cohort study
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Hrdy, Ondrej, Vrbica, Kamil, Kovar, Marek, Korbicka, Tomas, Stepanova, Radka, and Gal, Roman
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- 2023
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11. Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales
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Beale, Sarah, Hoskins, Susan, Byrne, Thomas, Fong, Wing Lam Erica, Fragaszy, Ellen, Geismar, Cyril, Kovar, Jana, Navaratnam, Annalan M. D., Nguyen, Vincent, Patel, Parth, Yavlinsky, Alexei, Johnson, Anne M., Van Tongeren, Martie, Aldridge, Robert W., and Hayward, Andrew
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- 2023
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12. Geometry Limitations in Indirect Selective Laser Sintering of Alumina
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Sassaman, Douglas, Ide, Matthew, Beaman, Joseph J, Kovar, Desiderio, and Seepersad, Carolyn
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Physics - Applied Physics ,Condensed Matter - Materials Science - Abstract
Ceramics containing open channels with complex geometries can be manufactured by additive manufacturing (AM) and are of great interest in clean energy technologies. However, design limitations and guidelines for manufacturing these architectures with AM have not yet been established. In this work, we compare previously proposed geometry limitations for polymer selective laser sintering (SLS) to the geometries produced using indirect SLS in alumina. We focus on a subset of model shapes that are simple to produce and measure. We show that these rules provide a starting point for the design and manufacture of ceramic geometries using indirect SLS. However, there are additional considerations for AM of ceramics by indirect SLS that further limit the geometries that can be produced., Comment: Submitted to Solid Freeform Fabrication Symposium, August 2021
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- 2021
13. Unraveling the role of ruzigrass in soil K cycling in tropical cropping systems
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Volf, Marcelo R., Crusciol, Carlos A. C., Kovar, John L., and Rosolem, Ciro A.
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- 2023
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14. Interventions Increase Vaccination Rates in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Systematic Review and Meta-Analysis
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Patel, Jalpa, Noureldin, Mohamed, Fakhouri, Dina, Farraye, Francis A., Kovar-Gough, Iris, Warren, Bradley, Waljee, Akbar K., and Piper, Marc S.
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- 2023
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15. Charged fluids encircling compact objects: force representations and conformal geometries
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Kovář, Jiří, Kojima, Yasufumi, Slaný, Petr, Stuchlík, Zdeněk, and Karas, Vladimír
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General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
Charged fluids rotating around compact objects can form unique equilibrium structures when ambient large-scale electromagnetic fields combine with strong gravity. Equatorial as well as off-equatorial toroidal structures are among such figures of equilibrium with a direct relevance for astrophysics. To investigate their geometrical shapes and physical properties in the near-horizon regime, where effects of general relativity play a significant role, we commonly employ a scheme based on the energy-momentum conservation written in a standard representation. Here, we develop its interesting alternatives in terms of two covariant force representations, both based on a hypersurface projection of the energy-momentum conservation. In a proper hypersurface, space-like forces can be defined, following from a decomposition of the fluid four-acceleration. Each of the representations provides us with an insight into properties of the fluid flow, being well reflected in related conformal hypersurface geometries; we find behaviour of centrifugal forces directly related to geodesics of these conformal hypersurfaces and their embedding diagrams. We also reveal correspondence between the charged fluid flow world-lines from an ordinary spacetime, and world-lines determined by a charged test particles equation of motion in a conformal spacetime., Comment: 23 pages, 3 figures
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- 2020
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16. Factors Influencing Socially Responsible Leadership Development in College of Agriculture Students
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Kovar, Kristin A. and Simonsen, Jon C.
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The purpose of this study was to examine factors impacting college student leadership development within a college of agriculture at the University of Missouri. This study employed descriptive relational survey methods to examine the impact of involvement factors (participation in organizations, community service and leadership education) on college student leadership development. The target population was all junior and senior students in the College of Agricutlure, Food and Natural Resources at the University of Missouri (N=1,124). Out of the calculated sample size (n=287), 107 participants completed the online instrument (37.3%). In the examination of the leadership outcomes, the greatest mean was reported for the outcome of commitment and the lowest mean was reported for the outcome of change. Most students were involved with two to five different organizations during their college career. A majority (92.5%) of the students reported that they have engaged in community service during their college career, although 44.9% of respondents did not participate in community service on a regular basis. Students responded as being involved in one to two short-term leadership education programs, but no long-term leadership education programs. Eight separate linear regression models were analyzed to determine the impact of involvement factors on the development of socially responsible leadership.
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- 2019
17. Emotional Intelligence in Undergraduate Medical Students: A Scoping Review
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Toriello, Helga V., Van de Ridder, J. M. Monica, Brewer, Patricia, Mavis, Brian, Allen, Renoulte, Arvidson, Cindy, Kovar-Gough, Iris, Novak, Elizabeth, O'Donnell, John, Osuch, Janet, and Ulrich, Brian
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Purpose: To perform a scoping review to determine what is known about emotional intelligence (EI) in undergraduate medical education (UME). Two main questions were asked: (1) What medical student characteristics are associated with EI? Are there correlations with demographic or other factors?; and (2) What research studies have been done on EI in UME? For example, is there evidence EI changes over time as a result of personal experiences? Should EI be used as an admission criterion? Can EI improve as a result of experiences or deliberate interventions? Method: The authors searched four databases (PubMed, PsycInfo, Education Resources Information Center, and Web of Science) for all papers published up to and including December 2020. Two reviewers independently screened articles to determine if they met inclusion criteria. All authors extracted and analyzed data. Results: A set of 1520 papers on the topic of emotional intelligence was identified, with 119 papers meeting inclusion criteria. Most studies were done at international locations with only 17 done at US medical schools. Seventy-five were cohort or cross-sectional studies. Study populations were mixed among the studies, with year of medical study, inclusion of other healthcare students, and participation rates among the inter-study differences noted. Conclusions: Numerous gaps in the literature on EI exist with several points being clear: (1) there is disagreement on the definition of EI; (2) it is undetermined whether EI is a trait or an ability; and (3) there is marked variability among the instruments used to measure EI. It is also becoming apparent that using EI determination may be helpful as a component of the admission process, higher EI is likely related to improved clinical reasoning, and higher EI contributes to more effective stress management.
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- 2022
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18. Characterization of the Si(Li) detector for Monte Carlo calculations of beta spectra
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Novotny, Pavel, Dryak, Pavel, Solc, Jaroslav, Kovar, Petr, and Vykydal, Zdenek
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Physics - Instrumentation and Detectors ,Nuclear Experiment - Abstract
A precise model of a Si(Li) detector ORTEC model SLP-06165P-OPT-0.5 was created for beta spectra calculations using the Monte Carlo (MC) code MCNPX. Detector parameters were determined from X-ray radiograms obtained with a film and a Timepix detector. The MC model of the detector was validated by comparison of calculated and experimental full-energy peak efficiencies in the energy range from 5 to 136 keV using a range of point-like photon emitting radionuclide standards. A comparison of measured and calculated beta spectrum of a radionuclide Pm-147 is presented., Comment: EMPIR project 15SIB10 "Radionuclide beta spectra metrology"
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- 2019
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19. Relativistic and Newtonian fluid tori with electric charge
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Karas, Vladimir, Kopacek, Ondrej, Trova, Audrey, Kovar, Jiri, Slany, Petr, and Stuchlik, Zdenek
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We discuss the effects of electric charging on the equilibrium configurations of magnetized, rotating fluid tori around black holes of different mass. In the context of gaseous/dusty tori in galactic nuclei, the central black hole dominates the gravitational field and it remains electrically neutral, while the surrounding material acquires some electric charge and exhibits non-negligible self-gravitational effect on the torus structure. The structure of the torus is influenced by the balance between the gravitational and electromagnetic forces. A cusp may develop even in Newtonian tori due to the charge distribution., Comment: 5 pages, 1 figure; to appear in Proceedings of the 15th Marcel Grossman Meeting on General Relativity - the session AC3 on "Accretion Discs and Jets" by Eva Hackmann & Audrey Trova (Rome, 1-7 July 2018), edited by Elia Battistelli, Robert T. Jantzen, and Remo Ruffini, in preparation
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- 2019
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20. Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth.
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Krivanek, Jan, Soldatov, Ruslan A, Kastriti, Maria Eleni, Chontorotzea, Tatiana, Herdina, Anna Nele, Petersen, Julian, Szarowska, Bara, Landova, Marie, Matejova, Veronika Kovar, Holla, Lydie Izakovicova, Kuchler, Ulrike, Zdrilic, Ivana Vidovic, Vijaykumar, Anushree, Balic, Anamaria, Marangoni, Pauline, Klein, Ophir D, Neves, Vitor CM, Yianni, Val, Sharpe, Paul T, Harkany, Tibor, Metscher, Brian D, Bajénoff, Marc, Mina, Mina, Fried, Kaj, Kharchenko, Peter V, and Adameyko, Igor
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Odontoblasts ,Epithelial Cells ,Stem Cells ,Tooth ,Incisor ,Molar ,Mesoderm ,Animals ,Mice ,Inbred C57BL ,Humans ,Mice ,Models ,Animal ,Cell Differentiation ,Gene Expression Regulation ,Developmental ,Genetic Heterogeneity ,Adolescent ,Adult ,Female ,Male ,Young Adult - Abstract
Understanding cell types and mechanisms of dental growth is essential for reconstruction and engineering of teeth. Therefore, we investigated cellular composition of growing and non-growing mouse and human teeth. As a result, we report an unappreciated cellular complexity of the continuously-growing mouse incisor, which suggests a coherent model of cell dynamics enabling unarrested growth. This model relies on spatially-restricted stem, progenitor and differentiated populations in the epithelial and mesenchymal compartments underlying the coordinated expansion of two major branches of pulpal cells and diverse epithelial subtypes. Further comparisons of human and mouse teeth yield both parallelisms and differences in tissue heterogeneity and highlight the specifics behind growing and non-growing modes. Despite being similar at a coarse level, mouse and human teeth reveal molecular differences and species-specific cell subtypes suggesting possible evolutionary divergence. Overall, here we provide an atlas of human and mouse teeth with a focus on growth and differentiation.
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- 2020
21. Comprehensive Parent–Metabolite PBPK/PD Modeling Insights into Nicotine Replacement Therapy Strategies
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Kovar, Lukas, Selzer, Dominik, Britz, Hannah, Benowitz, Neal, St. Helen, Gideon, Kohl, Yvonne, Bals, Robert, and Lehr, Thorsten
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Drug Abuse (NIDA only) ,Tobacco ,Tobacco Smoke and Health ,Brain Disorders ,Prevention ,Substance Misuse ,Good Health and Well Being ,Cotinine ,Electronic Nicotine Delivery Systems ,Humans ,Nicotine ,Smoking Cessation ,Tobacco Use Cessation Devices ,Pharmacology & Pharmacy ,Pharmacology and pharmaceutical sciences - Abstract
BackgroundNicotine, the pharmacologically active substance in both tobacco and many electronic cigarette (e-cigarette) liquids, is responsible for the addiction that sustains cigarette smoking. With 8 million deaths worldwide annually, smoking remains one of the major causes of disability and premature death. However, nicotine also plays an important role in smoking cessation strategies.ObjectivesThe aim of this study was to develop a comprehensive, whole-body, physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of nicotine and its major metabolite cotinine, covering various routes of nicotine administration, and to simulate nicotine brain tissue concentrations after the use of combustible cigarettes, e-cigarettes, nicotine gums, and nicotine patches.MethodsA parent-metabolite, PBPK/PD model of nicotine for a non-smoking and a smoking population was developed using 91 plasma and brain tissue concentration-time profiles and 11 heart rate profiles. Among others, cytochrome P450 (CYP) 2A6 and 2B6 enzymes were implemented, including kinetics for CYP2A6 poor metabolizers.ResultsThe model is able to precisely describe and predict both nicotine plasma and brain tissue concentrations, cotinine plasma concentrations, and heart rate profiles. 100% of the predicted area under the concentration-time curve (AUC) and maximum concentration (Cmax) values meet the twofold acceptance criterion with overall geometric mean fold errors of 1.12 and 1.15, respectively. The administration of combustible cigarettes, e-cigarettes, nicotine patches, and nicotine gums was successfully implemented in the model and used to identify differences in steady-state nicotine brain tissue concentration patterns.ConclusionsOur PBPK/PD model may be helpful in further investigations of nicotine dependence and smoking cessation strategies. As the model represents the first nicotine PBPK/PD model predicting nicotine concentration and heart rate profiles after the use of e-cigarettes, it could also contribute to a better understanding of the recent increase in youth e-cigarette use.
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- 2020
22. Type I interferon signaling in malignant blasts contributes to treatment efficacy in AML patients
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Holicek, Peter, Truxova, Iva, Rakova, Jana, Salek, Cyril, Hensler, Michal, Kovar, Marek, Reinis, Milan, Mikyskova, Romana, Pasulka, Josef, Vosahlikova, Sarka, Remesova, Hana, Valentova, Iva, Lysak, Daniel, Holubova, Monika, Kaspar, Petr, Prochazka, Jan, Kasikova, Lenka, Spisek, Radek, Galluzzi, Lorenzo, and Fucikova, Jitka
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- 2023
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23. Early identification of patients at risk for delayed recovery of ambulation after elective abdominal surgery
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Kovar, Alexandra, Carmichael, Heather, Jones, Teresa S., Hosokawa, Patrick, Goode, Christina M., Overbey, Douglas M., Jones, Edward L., and Robinson, Thomas N.
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- 2022
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24. Baby Friendly Hospital Designation and Breastfeeding Outcomes Among Maryland WIC Participants
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Gross, Susan M., Orta-Aleman, Dania, Resnik, Amy Kovar, Ducharme-Smith, Kirstie, Augustyn, Marycatherine, Silbert-Flagg, JoAnne, Rosenblum, Nadine, and Caulfield, Laura E.
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- 2022
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25. Epithelial Wound Healing Coordinates Distinct Actin Network Architectures to Conserve Mechanical Work and Balance Power
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Ajeti, Visar, Tabatabai, A. Pasha, Fleszar, Andrew J., Staddon, Michael F., Seara, Daniel S., Suarez, Cristian, Yousafzai, M. Sulaiman, Bi, Dapeng, Kovar, David R., Banerjee, Shiladitya, and Murrell, Michael P.
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Physics - Biological Physics - Abstract
How cells with diverse morphologies and cytoskeletal architectures modulate their mechanical behaviors to drive robust collective motion within tissues is poorly understood. During wound repair within epithelial monolayers in vitro, cells coordinate the assembly of branched and bundled actin networks to regulate the total mechanical work produced by collective cell motion. Using traction force microscopy, we show that the balance of actin network architectures optimizes the wound closure rate and the magnitude of the mechanical work. These values are constrained by the effective power exerted by the monolayer, which is conserved and independent of actin architectures. Using a cell-based physical model, we show that the rate at which mechanical work is done by the monolayer is limited by the transformation between actin network architectures and differential regulation of cell-substrate friction. These results and our proposed molecular mechanisms provide a robust quantitative model for how cells collectively coordinate their non-equilibrium behaviors to dynamically regulate tissue-scale mechanical output., Comment: 34 pages, 6 figures
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- 2018
26. Equilibrium configurations of charged fluid around Kerr black hole
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Trova, A., Schroven, K., Hackmann, E., Karas, V., Kovar, J., and Slany, P.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
Equilibrium configurations of electrically charged perfect fluid surrounding a central rotating black hole endowed with a test electric charge and embedded in a large-scale asymptotically uniform magnetic field are presented. Following our previous studies considering the central black hole non-rotating, we show that in the rotating case, conditions for the configurations existence change according to the spin of the black hole. We focus our attention on the charged fluid in rigid rotation which can form toroidal configurations centered in the equatorial plane or the ones hovering above the black hole, along the symmetry axis. We conclude that a non-zero value of spin changes the existence conditions and the morphology of the solutions significantly. In the case of fast rotation, the morphology of the structures is close to an oblate shape., Comment: 12 pages, 10 figures
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- 2018
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27. Spike-antibody responses to COVID-19 vaccination by demographic and clinical factors in a prospective community cohort study
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Shrotri, Madhumita, Fragaszy, Ellen, Nguyen, Vincent, Navaratnam, Annalan M. D., Geismar, Cyril, Beale, Sarah, Kovar, Jana, Byrne, Thomas E., Fong, Wing Lam Erica, Patel, Parth, Aryee, Anna, Braithwaite, Isobel, Johnson, Anne M., Rodger, Alison, Hayward, Andrew C., and Aldridge, Robert W.
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- 2022
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28. An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma
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Shulman, David S., Whittle, Sarah B., Surdez, Didier, Bailey, Kelly M., de Álava, Enrique, Yustein, Jason T., Shlien, Adam, Hayashi, Masanori, Bishop, Alexander J. R., Crompton, Brian D., DuBois, Steven G., Shukla, Neerav, Leavey, Patrick J., Lessnick, Stephen L., Kovar, Heinrich, Delattre, Olivier, Grünewald, Thomas G. P., Antonescu, Cristina R., Roberts, Ryan D., Toretsky, Jeffrey A., Tirode, Franck, Gorlick, Richard, Janeway, Katherine A., Reed, Damon, Lawlor, Elizabeth R., and Grohar, Patrick J.
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- 2022
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29. Metformin treatment is associated with improved outcome in patients with diabetes and advanced heart failure (HFrEF)
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Benes, Jan, Kotrc, Martin, Kroupova, Katerina, Wohlfahrt, Peter, Kovar, Jan, Franekova, Janka, Hegarova, Marketa, Hoskova, Lenka, Hoskova, Eva, Pelikanova, Terezie, Jarolim, Petr, Kautzner, Josef, and Melenovsky, Vojtech
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- 2022
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30. SARS-CoV-2 antibodies and breakthrough infections in the Virus Watch cohort
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Aldridge, Robert W., Yavlinsky, Alexei, Nguyen, Vincent, Eyre, Max T., Shrotri, Madhumita, Navaratnam, Annalan M. D., Beale, Sarah, Braithwaite, Isobel, Byrne, Thomas, Kovar, Jana, Fragaszy, Ellen, Fong, Wing Lam Erica, Geismar, Cyril, Patel, Parth, Rodger, Alison, Johnson, Anne M., and Hayward, Andrew
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- 2022
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31. Plunging neutron stars as origin of organised magnetic field in galactic nuclei
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Karas, V., Kopacek, O., Kunneriath, D., Zajacek, M., Araudo, A., Eckart, A., and Kovar, J.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
Black holes cannot support their own internal magnetic field like, for example, compact stars can. Despite this fact observations indicate that event horizons of supermassive black holes (SMBH) are threaded by field lines along which plasma streams flow. Various magnetohydrodynamical mechanisms have been suggested to generate turbulent magnetic fields on small scales, however, the origin of the large-scale component is unclear. In this write-up we describe our progress in an on-going work and discuss the possibility of dipole-type magnetic fields being brought onto SMBH by magnetized neutron stars, which are expected to drift inward from a hidden population in the Nuclear Star Cluster. This can contribute to an organised component of the magnetic field on the characteristic length-scale of the stellar size, which thread the horizon during the final stages of the magnetized star plunge into or its close flyby around SMBH. Because of mass--size scaling relations for black holes, the effect is more important for lower-mass SMBH., Comment: 9 pages, 2 figures; to appear in Proceedings of the 14th INTEGRAL/BART Workshop in Karlovy Vary (Czech Republic, 3-7 April 2017)
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- 2017
32. Attitudes and perceived barriers toward store-and-forward teledermatology among primary care providers of the rural Mississippi
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Morrissette, Summer, Pearlman, Ross L., Kovar, Margaret, Sisson, William T., Brodell, Robert T., and Nahar, Vinayak K.
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- 2022
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33. Engineering a Single-Agent Cytokine/Antibody Fusion That Selectively Expands Regulatory T Cells for Autoimmune Disease Therapy
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Spangler, Jamie B, Trotta, Eleonora, Tomala, Jakub, Peck, Ariana, Young, Tracy A, Savvides, Christina S, Silveria, Stephanie, Votavova, Petra, Salafsky, Joshua, Pande, Vijay S, Kovar, Marek, Bluestone, Jeffrey A, and Garcia, K Christopher
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Infectious Diseases ,Autoimmune Disease ,1.1 Normal biological development and functioning ,Underpinning research ,Animals ,Antibodies ,Autoimmune Diseases ,Cell Proliferation ,Cells ,Cultured ,Colitis ,Cytokines ,Disease Models ,Animal ,Humans ,Immunotherapy ,Lymphocyte Activation ,Mice ,Protein Engineering ,Receptors ,Interleukin-2 ,Recombinant Fusion Proteins ,T-Lymphocytes ,Regulatory ,Immunology - Abstract
IL-2 has been used to treat diseases ranging from cancer to autoimmune disorders, but its concurrent immunostimulatory and immunosuppressive effects hinder efficacy. IL-2 orchestrates immune cell function through activation of a high-affinity heterotrimeric receptor (composed of IL-2Rα, IL-2Rβ, and common γ [γc]). IL-2Rα, which is highly expressed on regulatory T (TReg) cells, regulates IL-2 sensitivity. Previous studies have shown that complexation of IL-2 with the JES6-1 Ab preferentially biases cytokine activity toward TReg cells through a unique mechanism whereby IL-2 is exchanged from the Ab to IL-2Rα. However, clinical adoption of a mixed Ab/cytokine complex regimen is limited by stoichiometry and stability concerns. In this study, through structure-guided design, we engineered a single agent fusion of the IL-2 cytokine and JES6-1 Ab that, despite being covalently linked, preserves IL-2 exchange, selectively stimulating TReg expansion and exhibiting superior disease control to the mixed IL-2/JES6-1 complex in a mouse colitis model. These studies provide an engineering blueprint for resolving a major barrier to the implementation of functionally similar IL-2/Ab complexes for treatment of human disease.
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- 2018
34. Actin Cross-Linking Toxin Is a Universal Inhibitor of Tandem-Organized and Oligomeric G-Actin Binding Proteins
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Kudryashova, Elena, Heisler, David B, Williams, Blake, Harker, Alyssa J, Shafer, Kyle, Quinlan, Margot E, Kovar, David R, Vavylonis, Dimitrios, and Kudryashov, Dmitri S
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Biochemistry and Cell Biology ,Biological Sciences ,Infectious Diseases ,Emerging Infectious Diseases ,Orphan Drug ,Rare Diseases ,Generic health relevance ,Actin Cytoskeleton ,Actin-Related Protein 2-3 Complex ,Actins ,Amino Acid Motifs ,Bacterial Toxins ,Microfilament Proteins ,Vibrio cholerae ,Ena/VASP ,WH2-domain ,actin cytoskeleton ,actin-binding proteins ,bacterial toxins ,cross-linking ,multivalent interaction ,nucleation promoting factors ,single-molecule speckle live-cell microscopy ,toxicity amplification ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Psychology - Abstract
Delivery of bacterial toxins to host cells is hindered by host protective barriers. This obstruction dictates a remarkable efficiency of toxins, a single copy of which may kill a host cell. Efficiency of actin-targeting toxins is further hampered by an overwhelming abundance of their target. The actin cross-linking domain (ACD) toxins of Vibrio species and related bacterial genera catalyze the formation of covalently cross-linked actin oligomers. Recently, we reported that the ACD toxicity can be amplified via a multivalent inhibitory association of actin oligomers with actin assembly factors formins, suggesting that the oligomers may act as secondary toxins. Importantly, many proteins involved in nucleation, elongation, severing, branching, and bundling of actin filaments contain G-actin-binding Wiskott-Aldrich syndrome protein (WASP)-homology motifs 2 (WH2) organized in tandem and therefore may act as a multivalent platform for high-affinity interaction with the ACD-cross-linked actin oligomers. Using live-cell single-molecule speckle (SiMS) microscopy, total internal reflection fluorescence (TIRF) microscopy, and actin polymerization assays, we show that, in addition to formins, the oligomers bind with high affinity and potently inhibit several families of actin assembly factors: Ena/vasodilator-stimulated phosphorprotein (VASP); Spire; and the Arp2/3 complex, both in vitro and in live cells. As a result, ACD blocks the actin retrograde flow and membrane dynamics and disrupts association of Ena/VASP with adhesion complexes. This study defines ACD as a universal inhibitor of tandem-organized G-actin binding proteins that overcomes the abundance of actin by redirecting the toxicity cascade toward less abundant targets and thus leading to profound disorganization of the actin cytoskeleton and disruption of actin-dependent cellular functions.
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- 2018
35. Partitioning and Enhanced Self-Assembly of Actin in Polypeptide Coacervates
- Author
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McCall, Patrick M, Srivastava, Samanvaya, Perry, Sarah L, Kovar, David R, Gardel, Margaret L, and Tirrell, Matthew V
- Subjects
Actins ,Cytoskeleton ,Peptides ,Polylysine ,Protein Multimerization ,Protein Structure ,Quaternary ,Physical Sciences ,Chemical Sciences ,Biological Sciences ,Biophysics - Abstract
Biomolecules exist and function in cellular microenvironments that control their spatial organization, local concentration, and biochemical reactivity. Due to the complexity of native cytoplasm, the development of artificial bioreactors and cellular mimics to compartmentalize, concentrate, and control the local physico-chemical properties is of great interest. Here, we employ self-assembling polypeptide coacervates to explore the partitioning of the ubiquitous cytoskeletal protein actin into liquid polymer-rich droplets. We find that actin spontaneously partitions into coacervate droplets and is enriched by up to ∼30-fold. Actin polymerizes into micrometer-long filaments and, in contrast to the globular protein BSA, these filaments localize predominately to the droplet periphery. We observe up to a 50-fold enhancement in the actin filament assembly rate inside coacervate droplets, consistent with the enrichment of actin within the coacervate phase. Together these results suggest that coacervates can serve as a versatile platform in which to localize and enrich biomolecules to study their reactivity in physiological environments.
- Published
- 2018
36. Interaction between light availability and grazing enhances species richness and turnover of vascular plants in shrubby pastures in Romania
- Author
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Vojta, J., Volařík, D., and Kovář, P.
- Published
- 2020
37. Electrically charged matter in permanent rotation around magnetized black hole: A toy model for self-gravitating fluid tori
- Author
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Trova, A., Karas, V., Slany, P., and Kovar, J.
- Subjects
Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present an analytical approach for the equilibrium of a self-gravitating charged fluid embedded in a spherical gravitational and dipolar magnetic fields produced by a central mass. Our scheme is proposed, as a toy-model, in the context of gaseous/dusty tori surrounding supermassive black holes in galactic nuclei. While the central black hole dominates the gravitational field and it remains electrically neutral, the surrounding material has a non-negligible self-gravitational effect on the torus structure. By charging mechanisms it also acquires non-zero electric charge density, so the two influences need to be taken into account to achieve a self-consistent picture. With our approach we discuss the impact of self-gravity, represented by the term dt (ratio of the torus total mass to the mass of the central body), on the conditions for existence of the equilibrium and the morphology and typology of the tori. By comparison with a previous work without self-gravity, we show that the conditions can be different. Although the main aim of the present paper is to discuss a framework for the classification of electrically charged, magnetized, self-gravitating tori, we also mention potential astrophysical applications to vertically stratified fluid configurations., Comment: ApJS accepted, 17 pages and 9 figures
- Published
- 2016
- Full Text
- View/download PDF
38. Bolidozor - Distributed radio meteor detection system
- Author
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Kakona, Jakub, Kovar, Pavel, and Kakona, Martin
- Subjects
Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Most of the meteor radioastronomical radars are backscatter radars which cover only a small area of the atmosphere. Therefore a daytime meteor flux models are based on sparse data collected by only a few radar systems. To solve this issue, a radar system with a wide coverage is required. We present a new approach of open-source multi-static radio meteor detection system which could be distributed over a large area. This feature allows us to detect meteor events taking place over a larger area as well and gather more uniform data about meteor flux and possibly about meteor trajectories., Comment: this article supersedes 2015pimo.conf..157K
- Published
- 2016
39. Application of a symplectic integrator in a non-integrable relativistic system
- Author
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Kopáček, Ondřej, Karas, Vladimír, Kovář, Jiří, and Stuchlík, Zdeněk
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General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present a detailed comparison of several integration schemes applied to the dynamic system consisting of a charged particle on the Kerr background endowed with the axisymmetric electromagnetic test field. In particular, we compare the performance of the symplectic integrator with several non-symplectic routines and discuss under which circumstances we should choose the symplectic one and when we should switch to some other scheme. We are basically concerned with two crucial, yet opposing aspects - accuracy of the integration and CPU time consumption. The latter is generally less critical in our application while the highest possible accuracy is strongly demanded., Comment: 11 pages, 5 figures, 2 tables, prepared in 2011 for the Proceedings of RAGtime 10-13: Workshops on black holes and neutron stars (Opava, September 15 - 17, 2010)
- Published
- 2016
40. Combined experience of six independent laboratories attempting to create an Ewing sarcoma mouse model
- Author
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Minas, Tsion Zewdu, Surdez, Didier, Javaheri, Tahereh, Tanaka, Miwa, Howarth, Michelle, Kang, Hong-Jun, Han, Jenny, Han, Zhi-Yan, Sax, Barbara, Kream, Barbara E, Hong, Sung-Hyeok, Çelik, Haydar, Tirode, Franck, Tuckermann, Jan, Toretsky, Jeffrey A, Kenner, Lukas, Kovar, Heinrich, Lee, Sean, Sweet-Cordero, E Alejandro, Nakamura, Takuro, Moriggl, Richard, Delattre, Olivier, and Üren, Aykut
- Subjects
Genetics ,Pediatric ,Adenoviridae ,Animals ,Cell Line ,Tumor ,Disease Models ,Animal ,Gene Expression Regulation ,Neoplastic ,Gene Knock-In Techniques ,Humans ,Mice ,Mice ,Transgenic ,Neoplasm Transplantation ,Oncogene Proteins ,Fusion ,Promoter Regions ,Genetic ,Proto-Oncogene Protein c-fli-1 ,RNA-Binding Protein EWS ,Sarcoma ,Ewing ,Ewing sarcoma ,EWS-FLI1 ,EWS-FLI1 driven transgenic mouse model ,Oncology and Carcinogenesis - Abstract
Ewing sarcoma (ES) involves a tumor-specific chromosomal translocation that produces the EWS-FLI1 protein, which is required for the growth of ES cells both in vitro and in vivo. However, an EWS-FLI1-driven transgenic mouse model is not currently available. Here, we present data from six independent laboratories seeking an alternative approach to express EWS-FLI1 in different murine tissues. We used the Runx2, Col1a2.3, Col1a3.6, Prx1, CAG, Nse, NEFL, Dermo1, P0, Sox9 and Osterix promoters to target EWS-FLI1 or Cre expression. Additional approaches included the induction of an endogenous chromosomal translocation, in utero knock-in, and the injection of Cre-expressing adenovirus to induce EWS-FLI1 expression locally in multiple lineages. Most models resulted in embryonic lethality or developmental defects. EWS-FLI1-induced apoptosis, promoter leakiness, the lack of potential cofactors, and the difficulty of expressing EWS-FLI1 in specific sites were considered the primary reasons for the failed attempts to create a transgenic mouse model of ES.
- Published
- 2017
41. C/EBPβ-1 promotes transformation and chemoresistance in Ewing sarcoma cells
- Author
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Gardiner, Jamie D, Abegglen, Lisa M, Huang, Xiaomeng, Carter, Bryce E, Schackmann, Elizabeth A, Stucki, Marcus, Paxton, Christian N, Randall, R Lor, Amatruda, James F, Putnam, Angelica R, Kovar, Heinrich, Lessnick, Stephen L, and Schiffman, Joshua D
- Subjects
Rare Diseases ,Cancer ,Stem Cell Research ,Pediatric ,Genetics ,Pediatric Cancer ,Aldehyde Dehydrogenase ,Aldehyde Dehydrogenase 1 Family ,Antineoplastic Agents ,CCAAT-Enhancer-Binding Protein-beta ,Cell Line ,Tumor ,Cell Proliferation ,Cell Survival ,Cell Transformation ,Neoplastic ,Drug Resistance ,Neoplasm ,Gene Expression Profiling ,Gene Expression Regulation ,Neoplastic ,Humans ,Oncogene Proteins ,Fusion ,Protein Binding ,Proto-Oncogene Protein c-fli-1 ,RNA-Binding Protein EWS ,Retinal Dehydrogenase ,Sarcoma ,Ewing ,ALDH1A1 ,C/EBPβ ,Ewing sarcoma ,biomarker ,chemoresistance ,Oncology and Carcinogenesis - Abstract
CEBPB copy number gain in Ewing sarcoma was previously shown to be associated with worse clinical outcome compared to tumors with normal CEBPB copy number, although the mechanism was not characterized. We employed gene knockdown and rescue assays to explore the consequences of altered CEBPB gene expression in Ewing sarcoma cell lines. Knockdown of EWS-FLI1 expression led to a decrease in expression of all three C/EBPβ isoforms while re-expression of EWS-FLI1 rescued C/EBPβ expression. Overexpression of C/EBPβ-1, the largest of the three C/EBPβ isoforms, led to a significant increase in colony formation when cells were grown in soft agar compared to empty vector transduced cells. In addition, depletion of C/EBPβ decreased colony formation, and re-expression of either C/EBPβ-1 or C/EBPβ-2 rescued the phenotype. We identified the cancer stem cell marker ALDH1A1 as a target of C/EBPβ in Ewing sarcoma. Furthermore, increased expression of C/EBPβ led to resistance to chemotherapeutic agents. In summary, we have identified CEBPB as an oncogene in Ewing sarcoma. Overexpression of C/EBPβ-1 increases transformation, upregulates expression of the cancer stem cell marker ALDH1A1, and leads to chemoresistance.
- Published
- 2017
42. Cracked actin filaments as mechanosensitive receptors
- Author
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Zsolnay, Vilmos, Gardel, Margaret L., Kovar, David R., and Voth, Gregory A.
- Abstract
Actin filament networks are exposed to mechanical stimuli, but the effect of strain on actin filament structure has not been well established in molecular detail. This is a critical gap in understanding because the activity of a variety of actin-binding proteins has recently been determined to be altered by actin filament strain. We therefore used all-atom molecular dynamics simulations to apply tensile strains to actin filaments and find that changes in actin subunit organization are minimal in mechanically strained, but intact, actin filaments. However, a conformational change disrupts the critical D-loop to W-loop connection between longitudinal neighboring subunits, which leads to a metastable cracked conformation of the actin filament whereby one protofilament is broken prior to filament severing. We propose that the metastable crack presents a force-activated binding site for actin regulatory factors that specifically associate with strained actin filaments. Through protein-protein docking simulations, we find that 43 evolutionarily diverse members of the dual zinc-finger-containing LIM-domain family, which localize to mechanically strained actin filaments, recognize two binding sites exposed at the cracked interface. Furthermore, through its interactions with the crack, LIM domains increase the length of time damaged filaments remain stable. Our findings propose a new molecular model for mechanosensitive binding to actin filaments.
- Published
- 2024
- Full Text
- View/download PDF
43. Engineering of the unfolded protein response pathway in Pichia pastoris: enhancing production of secreted recombinant proteins
- Author
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Raschmanová, Hana, Weninger, Astrid, Knejzlík, Zdeněk, Melzoch, Karel, and Kovar, Karin
- Published
- 2021
- Full Text
- View/download PDF
44. Long-chain branched polypropylene: crystallization under high pressure and polymorphic composition
- Author
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Navratilova, Jana, Gajzlerova, Lenka, Kovar, Lukas, and Cermak, Roman
- Published
- 2021
- Full Text
- View/download PDF
45. Fire Salamander, Salamandra salamandra, niche selection in Central European conditions.
- Author
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KOVAR, ROMAN, BRABEC, MAREK, MORAVEC, PAVEL, and HUSAK, TOMAS
- Abstract
We analyzed data from 3,546 occurrence records of Fire Salamanders (Salamandra salamandra) from the territory of the Czech Republic where it has a heterogeneous distribution pattern. Its occurrence in terrestrial habitats adjacent to breeding streams is characterized by a mean distance of 103 m, maximum 1,321 m, from the nearest stream. Based on a logistic GLM (generalized linear model) analysis we determined the Fire Salamanders' climatic and habitat associations at landscape scale in the Czech Republic. The main limiting factors for its dispersal include the proximity of small shallow streams in rolling landscapes, the pH of these streams, the presence of broad-leaf or mixed forests, humidity, solar irradiation, and severity of winters. While the absence of suitable breeding habitats is the main limiting factor for their occurrence in more expansive lowlands, factors such as lower temperatures, lower humidity, and the absence of broad-leaf and mixed forests begin to play a role with increasing altitude. Unlike cold temperatures, low amounts of precipitation and higher temperatures do not act as limiters in the Czech Republic. Fire Salamanders respond to the colder climate of higher altitudes with intensified summer activity and the purely bimodal nature of their activity (with spring and autumn peaks) tends to fade at higher altitudes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
46. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta
- Author
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Kanost, Michael R, Arrese, Estela L, Cao, Xiaolong, Chen, Yun-Ru, Chellapilla, Sanjay, Goldsmith, Marian R, Grosse-Wilde, Ewald, Heckel, David G, Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose L, Vogel, Heiko, Walters, James, Waterhouse, Robert M, Ahn, Seung-Joon, Almeida, Francisca C, An, Chunju, Aqrawi, Peshtewani, Bretschneider, Anne, Bryant, William B, Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne M, Clarke, David F, Dittmer, Neal T, Ferguson, Laura CF, Garavelou, Spyridoula, Gordon, Karl HJ, Gunaratna, Ramesh T, Han, Yi, Hauser, Frank, He, Yan, Heidel-Fischer, Hanna, Hirsh, Ariana, Hu, Yingxia, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, König, Christopher, Kovar, Christie, Kroll, Ashley R, Kuwar, Suyog S, Lee, Sandy L, Lehman, Rüdiger, Li, Kai, Li, Zhaofei, Liang, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer H, McCulloch, Kyle J, Mathew, Tittu, Morton, Brian, Muzny, Donna M, Neunemann, David, Ongeri, Fiona, Pauchet, Yannick, Pu, Ling-Ling, Pyrousis, Ioannis, Rao, Xiang-Jun, Redding, Amanda, Roesel, Charles, Sanchez-Gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yang, Xiong, Guang-Hua, Traut, Walther, Walsh, Tom K, Worley, Kim C, Wu, Di, Wu, Wenbi, Wu, Yuan-Qing, Zhang, Xiufeng, Zou, Zhen, Zucker, Hannah, Briscoe, Adriana D, Burmester, Thorsten, Clem, Rollie J, Feyereisen, René, Grimmelikhuijzen, Cornelis JP, Hamodrakas, Stavros J, Hansson, Bill S, Huguet, Elisabeth, Jermiin, Lars S, Lan, Que, Lehman, Herman K, Lorenzen, Marce, Merzendorfer, Hans, Michalopoulos, Ioannis, Morton, David B, Muthukrishnan, Subbaratnam, Oakeshott, John G, Palmer, Will, Park, Yoonseong, and Passarelli, A Lorena
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Tobacco ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Animals ,Gene Expression ,Gene Expression Profiling ,Genome ,Insect ,Larva ,Manduca ,Pupa ,Sequence Analysis ,DNA ,Synteny ,Lepidoptera ,Insect ,Tobacco hornworm ,Moth ,Insect biochemistry ,Innate immunity ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Zoology ,Entomology ,Biochemistry and cell biology - Abstract
Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.
- Published
- 2016
47. Electrically charged matter in rigid rotation around magnetized black hole
- Author
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Kovář, Jiří, Slaný, Petr, Cremaschini, Claudio, Stuchlík, Zdeněk, Karas, Vladimír, and Trova, Audrey
- Subjects
General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We study charged-fluid toroidal structures surrounding a non-rotating charged black hole immersed in a large-scale, asymptotically uniform magnetic field. In continuation of our former study on electrically charged matter in approximation of zero conductivity, we demonstrate existence of orbiting structures in permanent rigid rotation in the equatorial plane, and charged clouds hovering near the symmetry axis. We constrain the range of parameters that allow stable configurations and derive the geometrical shape of equi-pressure surfaces. Our simplified analytical study suggests that these regions of stability may be relevant for trapping electrically charged particles and dust grains in some areas of the black hole magnetosphere, being thus important in some astrophysical situations., Comment: 14 pages, 5 figures
- Published
- 2014
- Full Text
- View/download PDF
48. Regular and Chaotic Motion in General Relativity: The Case of a Massive Magnetic Dipole
- Author
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Kopáček, Ondřej, Kovář, Jiří, Karas, Vladimír, and Kojima, Yasufumi
- Subjects
Astrophysics - High Energy Astrophysical Phenomena ,General Relativity and Quantum Cosmology - Abstract
Circular motion of particles, dust grains and fluids in the vicinity of compact objects has been investigated as a model for accretion of gaseous and dusty environment. Here we further discuss, within the framework of general relativity, figures of equilibrium of matter under the influence of combined gravitational and large-scale magnetic fields, assuming that the accreted material acquires a small electric charge due to interplay of plasma processes and photoionization. In particular, we employ an exact solution describing the massive magnetic dipole and we identify the regions of stable motion. We also investigate situations when the particle dynamics exhibits the onset of chaos. In order to characterize the measure of chaoticness we employ techniques of Poincar\'e surfaces of section and of recurrence plots., Comment: 11 pages, 6 figures, published in the proceedings of the conference "Relativity and Gravitation: 100 Years after Einstein in Prague" (25. - 29. 6. 2012, Prague)
- Published
- 2014
- Full Text
- View/download PDF
49. Hemichordate genomes and deuterostome origins.
- Author
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Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Mitros, Therese, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert M, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth W, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens H, Pani, Ariel M, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen H, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini N, Kovar, Christie L, Lee, Sandra L, Lewis, Lora R, Morton, Donna, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna M, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas H, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Worley, Kim C, Gibbs, Richard A, Kirschner, Marc W, Lowe, Christopher J, Satoh, Noriyuki, Rokhsar, Daniel S, and Gerhart, John
- Subjects
Animals ,Chordata ,Nonvertebrate ,Echinodermata ,Transforming Growth Factor beta ,Evolution ,Molecular ,Phylogeny ,Signal Transduction ,Conserved Sequence ,Synteny ,Multigene Family ,Genome ,Chordata ,Nonvertebrate ,Evolution ,Molecular ,General Science & Technology - Abstract
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
- Published
- 2015
50. Two Decades of Agricultural Literacy Research: A Synthesis of the Literature
- Author
-
Kovar, Kristin A. and Ball, Anna L.
- Abstract
The purpose of this investigation was to identify and synthesize research related to agricultural literacy since the publication of Understanding Agriculture--New Directions for Education (1988). The researchers sought to determine where agricultural literacy research was published, which populations were targeted, the purpose of the research, and the findings of agricultural literacy studies published between 1988 and 2011. Overall, a total of 49 studies were found - 17 studies in the Journal of Agricultural Education, seven studies in the NACTA Journal, three studies in the Journal of Extension, 18 studies in national or regional American Association for Agricultural Education (AAAE) conference proceedings, and four miscellaneous studies. The populations targeted in agricultural literacy research were teachers, students, and non-educator adults with elementary teachers and students being the most frequently targeted populations. The purposes of the respective studies were coded into three specific areas: (a) assess agricultural literacy; (b) test the effectiveness of an agricultural literacy program; or (c) develop a framework or guide used to assist educators. While the programs were found to be successful in increasing agricultural literacy, many populations assessed were found to be agriculturally illiterate. Further research is warranted to explain areas of deficiency in agricultural literacy.
- Published
- 2013
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