cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
OLIGOSACCHARIDES AND MOLECULAR RECOGNITION
Creators: name: CATTANEO, VITTORIO
Publisher: name: Universit� degli Studi di Milano
Year: 2014

description: Carbohydrates have been established as the most abundant ? and arguably the most structural diverse ? organic molecules found in nature. They are chiral molecules readily available in nature in a variety of diastereomeric forms. Their conformational rigidity provides a well defined three-dimensional spatial arrangement of substituents with various multi-configured hydroxyl groups for chemical modification. Carbohydrates play a fundamental role in signal transduction and vital molecular recognition phenomena, they dominate the landscape of the cell and are responsible for cell-cell interaction, the recognition of virus and bacteria, binding of toxins and are involved in cell growth. For these reasons they are an attractive material for the development of new therapeutic agents, such as their application as antigenic material in vaccines formulation. In this framework we focused our attention in a troublesome nosocomial pathogen: Acinetobacter baumannii, a Gram-negative coccobacillus, in particular on the strain ATCC 17961. We synthesized three different fragments of the O-chain LPS of this bacterium, containing the unusual sugar residue 2,3-diacetamido-2,3- dideoxy-D-glucuronic acid. The binding affinity of these fragments will be evaluated by competitive ELISA assay against the anti-LPS serum of Acinetobacter baumannii ATCC 17961. Furthermore, thanks to chemical flexibility of carbohydrates, they are attractive chiral molecular scaffolds in asymmetric catalysis. They could be employed as metal ligands for enantioselective catalysis or themselves as metal-free organocatalysts. Sugars are an attractive material in this field for their low cost, potential polyfunctionalization, and the possibility to modify the chemical structure of the molecule in order to tune the chemical and physical properties for example the steric hindrance, the electronic and solubility properties of the catalyst. We synthesized two different carbohydrate-based organocatalyst, and we tested their activity in reaction between acetylacetone or diethylmalonate with ?-nitrostyrene. e5
Risk Based Framework for Haul Vehicle and Light Vehicle Interaction Within Surface Mining Operations
Creators: name: Birkbeck, Samuel
Publisher: name: University of Southern Queensland
Year: 2021
Subjects: Mining, Safety, Risk, Traffic Modelling, LV

description: Mining is an important industry in the Australian economy. However, the mining industry had the 3rd highest fatality rate of all Australian industries. Collisions between light and haul vehicles are a significant contributor to the injury rate with fatal collisions occurring in 2008 in Western Australia and 2013 in New South Wales. Research into government databases from these regions has identified numerous reportable incidents because of light vehicle and haul vehicle interaction. With such a high rate of incidents and fatalities within the industry, the research sets out to develop and test a risk-based framework for mitigating vehicle interaction risk with the use of separated road networks. A review of literature identified numerous road design guidelines for light vehicles through Austroads publications and mining specific haul road design guidelines. However, industry wide standards are not currently available for the design of haul vehicle and light vehicle interaction situations. Vehicle separation can be achieved with the use of physical delineation devices such as earth berms and the use of separate roads for the two vehicle types. This risk mitigation method requires a significant investment from mining companies and therefore a profit optimisation approach was incorporated into the risk-based framework. The research tests a risk-based framework with the use of an existing mine. The framework examines the employer, societal and employee costs and benefits using discounted cash flow quantitative methods over a timeframe for an incident to statistically occur. Traffic modelling is utilised to determine the layout efficiencies through improved speeds and reduced vehicle density. Different scenarios were considered altering the framework inputs, including by increasing the mine size (Case Study 2), reducing the volumes of haul vehicle traffic (Cases Study 3), and reducing the volumes of light vehicle traffic (Case Study 4). All the case studies showed a financial benefit of a separated network if there was a high likelihood of a light vehicle- haul vehicle collision in the short to medium term. Incidents between light vehicles and haul vehicles are prevalent in the mining industry however the number of fatal collisions has reduced over recent years due to technological improvements such as the use of vehicle detection systems. Current advances in technology, such as the use of autonomous vehicles, will have a role to play in improving safety, however such technological advances do not eliminate risk, and vehicle separation could also be an effective strategy to utilise if financially feasible.
Type I and type II second harmonic generation of conically refracted beams
Creators: name: Turpin, Alex
name: Loiko, Yury V.
name: Kalkandjiev, Todor K.
name: Trull, Jose
name: Cojocaru, Crina
name: Mompart, Jordi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Type I and type II second harmonic generation (SHG) of a beam transformed by the conical refraction phenomenon are presented. We show that, for type I, the second harmonic intensity pattern is a light ring with a point of null intensity while, for type II, the light ring possesses two dark regions. Taking into account the different two-photon processes involved in SHG, we have derived analytical expressions for the resulting transverse intensity patterns that are in good agreement with the experimental data. Finally, we have investigated the spatial evolution of the second harmonic signals, showing that they behave as conically refracted beams.
High Order Cell-Centered Lagrangian-Type Finite Volume Schemes with Time-Accurate Local Time Stepping on Unstructured Triangular Meshes
Creators: name: Boscheri, Walter
name: Dumbser, Michael
name: Zanotti, Olindo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: We present a novel cell-centered direct Arbitrary-Lagrangian-Eulerian (ALE) finite volume scheme on unstructured triangular meshes that is high order accurate in space and time and that also allows for time-accurate local time stepping (LTS). The new scheme uses the following basic ingredients: a high order WENO reconstruction in space on unstructured meshes, an element-local high-order accurate space-time Galerkin predictor that performs the time evolution of the reconstructed polynomials within each element, the computation of numerical ALE fluxes at the moving element interfaces through approximate Riemann solvers, and a one-step finite volume scheme for the time update which is directly based on the integral form of the conservation equations in space-time. The inclusion of the LTS algorithm requires a number of crucial extensions, such as a proper scheduling criterion for the time update of each element and for each node; a virtual projection of the elements contained in the reconstruction stencils of the element that has to perform the WENO reconstruction; and the proper computation of the fluxes through the space-time boundary surfaces that will inevitably contain hanging nodes in time due to the LTS algorithm. We have validated our new unstructured Lagrangian LTS approach over a wide sample of test cases solving the Euler equations of compressible gasdynamics in two space dimensions, including shock tube problems, cylindrical explosion problems, as well as specific tests typically adopted in Lagrangian calculations, such as the Kidder and the Saltzman problem. When compared to the traditional global time stepping (GTS) method, the newly proposed LTS algorithm allows to reduce the number of element updates in a given simulation by a factor that may depend on the complexity of the dynamics, but which can be as large as 4.7.
description: 31 pages, 13 figures
On an elliptic-parabolic MEMS model with two free boundaries
Creators: name: Kohlmann, Martin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35R35, 35M33, 35B30, 35Q74, 74M05

description: We discuss an evolution free boundary problem of mixed type with two free boundaries modeling an idealized electrostatically actuated MEMS device. While the electric potential is the solution of an elliptic equation, the dynamics of the membranes' displacement is modeled by two parabolic equations. It is shown that the model is locally well-posed in time and that solutions exist globally for small source voltages whereas non-existence holds for large voltage values. Moreover, our model possesses a steady state solution that is asymptotically stable. Finally, we show that in the vanishing aspect ratio limit, solutions of the model converge towards solutions of the associated small aspect ratio problem.
description: 25 pages; submitted
Theoretical overview of kaon decays
Creators: name: Pich, Antonio
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Kaon decays are an important testing ground of the electroweak flavour theory. They can provide new signals of CP violation and, perhaps, a window into physics beyond the Standard Model. At the same time, they exhibit an interesting interplay of long-distance QCD effects in flavour-changing transitions. A brief overview is presented, focusing on a few selected topics of particular interest. A more detailed and comprehensive review can be found in arXiv:1107.6001.
description: Invited talk at the XI International Conference on Hyperons, Charm and Beauty Hadrons -Beach 2014- (Birmingham, UK, 21-26 July 2014). 6 pages, 4 figures
Varicella-Zoster Virus Fc Receptor Component gI Is Phosphorylated on Its Endodomain by a Cyclin-Dependent Kinase
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: Varicella-zoster virus (VZV) glycoprotein gI is a type 1 transmembrane glycoprotein which is one component of the heterodimeric gE:gI Fc receptor complex. Like VZV gE, VZV gI was phosphorylated in both VZV-infected cells and gI-transfected cells. Preliminary studies demonstrated that a serine 343-proline 344 sequence located within the gI cytoplasmic tail was the most likely phosphorylation site. To determine which protein kinase catalyzed the gI phosphorylation event, we constructed a fusion protein, consisting of glutathione-S-transferase (GST) and the gI cytoplasmic tail, called GST-gI-wt. When this fusion protein was used as a substrate for gI phosphorylation in vitro, the results demonstrated that GST-gI-wt fusion protein was phosphorylated by a representative cyclin-dependent kinase (CDK) called P-TEFb, a homologue of CDK1 (cdc2). When serine 343 within the serine-proline phosphorylation site was replaced with an alanine residue, the level of phosphorylation of the gI fusion protein was greatly reduced. Subsequent experiments with individually immunoprecipitated mammalian CDKs revealed that the VZV gI fusion protein was phosphorylated best by CDK1, to a lesser degree by CDK2, and not at all by CDK6. Transient-transfection assays carried out in the presence of the specific CDK inhibitor roscovitine strongly supported the prior results by demonstrating a marked decrease in gI phosphorylation while gI protein expression was unaffected. Finally, the possibility that VZV gI contained a CDK phosphorylation site in its endodomain was of further interest because its partner, gE, contains a casein kinase II phosphorylation site in its endodomain; prior studies have established that CDK1 can phosphorylate casein kinase II.
Temperature-Dependent Hysteresis in One-Dimensional Thermovisco-Elastoplasticity
Creators: name: Krejčí, Pavel
name: Sprekels, Jürgen
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Thermoplasticity
subject: viscoelasticity
subject: hysteresis
subject: Prandtl-Ishlinskii operator
subject: PDEs with hysteresis
subject: thermodynamical consistency
subject: 35G25
subject: 73B30
subject: 73E60
subject: 73B05

description: In this paper, we develop a thermodynamically consistent description of the uniaxial behavior of thermovisco-elastoplastic materials for which the total stress σ contains, in addition to elastic, viscous and thermic contributions, a plastic component σp of the form σp(x,t) = 풫 [ε,θ(x,t)](x,t). Here, ε and θ are the fields of strain and absolute temperature, respectively, and {풫[·,θ]}θ>0 denotes a family of (rate-independent) hysteresis operators of Prandtl-Ishlinskii type, parametrized by the absolute temperature. The system of momentum and energy balance equations governing the space-time evolution of the material form a system of two highly nonlinearly coupled partial differential equations involving partial derivatives of hysteretic nonlinearities at different places. It is shown that an initial-boundary value problem for this system admits a unique global strong solution which depends continuously on the data.
A Single Amino Acid Change in nsP1 Attenuates Neurovirulence of the Sindbis-Group Alphavirus S.A.AR86
Creators: name: Heise, M. T.
name: Johnston, R. E.
name: Simpson, D. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: S.A.AR86, a member of the Sindbis group of alphaviruses, is neurovirulent in adult mice and has a unique threonine at position 538 of nsP1; nonneurovirulent members of this group of alphaviruses encode isoleucine. Isoleucine was introduced at position 538 in the wild-type S.A.AR86 infectious clone, ps55, and virus derived from this mutant clone, ps51, was significantly attenuated for neurovirulence compared to that derived from ps55. Intracranial (i.c.) s55 infection resulted in severe disease, including hind limb paresis, conjunctivitis, weight loss, and death in 89% of animals. In contrast, s51 caused fewer clinical signs and no mortality. Nevertheless, comparison of the virus derived from the mutant (ps51) and wild-type (ps55) S.A.AR86 molecular clones demonstrated that s51 grew as well as or better than the wild-type s55 virus in tissue culture and that viral titers in the brain following i.c. infection with s51 were equivalent to those of wild-type s55 virus. Analysis of viral replication within the brain by in situ hybridization revealed that both viruses established infection in similar regions of the brain at early times postinfection (12 to 72 h). However, at late times postinfection, the wild-type s55 virus had spread throughout large areas of the brain, while the s51 mutant exhibited a restricted pattern of replication. This suggests that s51 is either defective in spreading throughout the brain at late times postinfection or is cleared more rapidly than s55. Further evidence for the contribution of nsP1 Thr 538 to S.A.AR86 neurovirulence was provided by experiments in which a threonine residue was introduced at nsP1 position 538 of Sindbis virus strain TR339, which is nonneurovirulent in weanling mice. The resulting virus, 39ns1, demonstrated significantly increased neurovirulence and morbidity, including weight loss and hind limb paresis. These results demonstrate a role for alphavirus nonstructural protein genes in adult mouse neurovirulence.
The Direct and Converse Inequalities for Jackson-Type Operators on Spherical Cap
Creators: name: Wang, Yuguang
name: Cao, Feilong
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 41A17

description: Approximation on the spherical cap is different from that on the sphere which requires us to construct new operators. This paper discusses the approximation on the spherical cap. That is, so called Jackson-type operator $\{J_{k,s}^m\}_{k=1}^{\infty}$ is constructed to approximate the function defined on the spherical cap $D(x_0,γ)$. We thus establish the direct and inverse inequalities and obtain saturation theorems for $\{J_{k,s}^m\}_{k=1}^{\infty}$ on the cap $D(x_0,γ)$. Using methods of $K$-functional and multiplier, we obtain the inequality \begin{eqnarray*} C_1\:\| J_{k,s}^m(f)-f\|_{D,p}\leq ω^2\left(f,\:k^{-1}\right)_{D,p} \leq C_2 \max_{v\geq k}\| J_{v,s}^m(f) - f\|_{D,p} \end{eqnarray*} and that the saturation order of these operators is $O(k^{-2})$, where $ω^2\left(f,\:t\right)_{D,p}$ is the modulus of smoothness of degree 2, the constants $C_1$ and $C_2$ are independent of $k$ and $f$.
Alpha/Beta Interferon Protects Adult Mice from Fatal Sindbis Virus Infection and Is an Important Determinant of Cell and Tissue Tropism
Creators: name: Nguyen, K. B.
name: Johnston, R. E.
name: Klimstra, W. B.
name: Biron, C. A.
name: Ryman, K. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: Infection of adult 129 Sv/Ev mice with consensus Sindbis virus strain TR339 is subclinical due to an inherent restriction in early virus replication and viremic dissemination. By comparing the pathogenesis of TR339 in 129 Sv/Ev mice and alpha/beta interferon receptor null (IFN-α/βR−/−) mice, we have assessed the contribution of IFN-α/β in restricting virus replication and spread and in determining cell and tissue tropism. In adult 129 Sv/Ev mice, subcutaneous inoculation with 100 PFU of TR339 led to extremely low-level virus replication and viremia, with clearance under way by 96 h postinoculation (p.i.). In striking contrast, adult IFN-α/βR−/− mice inoculated subcutaneously with 100 PFU of TR339 succumbed to the infection within 84 h. By 24 h p.i. a high-titer serum viremia had seeded infectious virus systemically, coincident with the systemic induction of the proinflammatory cytokines interleukin-12 (IL-12) p40, IFN-γ, tumor necrosis factor alpha, and IL-6. Replicating virus was located in macrophage-dendritic cell (DC)-like cells at 24 h p.i. in the draining lymph node and in the splenic marginal zone. By 72 h p.i. virus replication was widespread in macrophage-DC-like cells in the spleen, liver, lung, thymus, and kidney and in fibroblast-connective tissue and periosteum, with sporadic neuroinvasion. IFN-α/β-mediated restriction of TR339 infection was mimicked in vitro in peritoneal exudate cells from 129 Sv/Ev versus IFN-α/βR−/− mice. Thus, IFN-α/β protects the normal adult host from viral infection by rapidly conferring an antiviral state on otherwise permissive cell types, both locally and systemically. Ablation of the IFN-α/β system alters the apparent cell and tissue tropism of the virus and renders macrophage-DC-lineage cells permissive to infection.
title: Effect of Combined Forming and Aging Processes on the Mechanical Properties of the Precipitation-Hardenable High-Strength Aluminum Alloys AA6082 and AA7075
Creators: name: Lotz, Steffen
name: Scharifi, Emad
name: Weidig, Ursula
name: Steinhoff, Kurt
Publisher: name: Universität Kassel
Year: 2022
Subjects: subject: thermo-mechanical aging
subject: high strength aluminum alloys
subject: precipitation-hardening
subject: 620
subject: Aluminiumlegierung
subject: Thermomechanik
subject: Aushärtung
subject: Aluminiumbauelement
subject: Zugfestigkeit
subject: Dehnung
subject: Luft- und Raumfahrtindustrie
subject: Fahrzeugindustrie
subject: Alterung

description: Gefördert durch den Publikationsfonds der Universität Kassel
Frequency Regions for Forced Locking of Self-Pulsating Multi-Section DFB Lasers
Creators: name: Bandelow, Uwe
name: Recke, Lutz
name: Sandstede, Björn
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Frequency locking
subject: Self-Pulsations
subject: Clock Recovery
subject: DFB Lasers
subject: Optical Communication Systems
subject: 42.55.Px
subject: 42.60.Gd
subject: 42.60.Mi
subject: 42.79.Sz

description: A method is developed which allows for the calculation of locking regions of self-pulsating multi-section lasers which are exposed to external optical data sequences. In particular, resonant locking is investigated where both wavelength detuning and detuning of the power frequencies are important.
Novel Propagation Technologies for Australian Macadamia
Creators: name: Wong, Albert Chern Sun
name: Hu, Zhangpan
name: Hiti-Bandaralage, Jayeni
name: O'Brien, Chris
name: Hayward, Alice
name: Mitter, Neena
Publisher: name: Zenodo
Year: 2022
Subjects: Macadamia, tissue culture

description: Australia’s macadamia industry is worth around A$855M in 2021, with both global demand and production set to increase in the future. However, the expansion of the industry faces several hurdles, such as slow tree growth, resources and environmental costs of increasing tree supply, and the preservation of cultivar and germplasm resources in the face of climate change. While current industry-wide initiatives have enabled productivity improvements to meet increasing global demand, novel technologies that could help push production barriers would still be required to meet future demand and address climate uncertainties. This project is developing a novel high-throughput tissue culture-based propagation system for macadamia, and is critical for addressing limitations in macadamia tree production, aiming to minimize resources and the carbon footprint for propagation. This system requires innovative plant tissue culture techniques, optimized culture conditions, and novel media composition to enable high shoot multiplication capacity and large-scale propagation of multiple healthy plants from minimal plant material. It will address existing issues such as loss of shoot vigor, poor survivability, and rooting difficulty reported in previous attempts of macadamia tissue culture, while facilitating the study of underlying molecular mechanisms regulating root induction in woody plant species. This system is also being leveraged for cryopreservation of macadamia germplasm, for long-term preservation. At present two cultivars; Beaumont and MCT1, have been initiated into tissue culture, with shoot production and multiplication optimisation ongoing. Successful development and employment of this system in the industry will enhance the productivity and sustainability of the macadamia industry in Australia.
description: This research project is being funded by the Australian Research Council Linkage program in partnership with the Department of Agriculture and Fisheries, Royal Botanic Gardens and Domain Trust, MacQ Pty Ltd, Aurora Macadamias Pty Ltd, MACS Network Operations Pty Ltd, Bush Holdings Pty Ltd, Macadamia Conservation Trust and the Australian Macadamia Society Ltd. Figure of tissue culture stages was created with BioRender.com
RPC Gap Production and Performance for CMS RE4 Upgrade
Creators: name: Park, Sung Keun
name: Kang, Min Ho
name: Lee, Kyong Sei
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: CMS experiment constructed the fourth Resistive Plate Chamber (RPC) trigger station composed of 144 RPCs to enhance the high momentum muon trigger efficiency at both endcap regions. All new CMS endcap RPC gaps are produced in accordance with QA and QC at the Korea Detector Laboratory (KODEL) in Korea. All qualified gaps have been delivered to three assembly sites: CERN in Switzerland, BARC in India, and Ghent University in Belgium for the RPC detector assembly. In this paper, we present the detailed procedures used in the production of RPC gaps adopted for the CMS upgrade.
description: RPC2014 conference contribution, 7 pages, 8 figures
MPEC 2023-U237 : 2023 US8
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2023
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2023 US8

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
On the mean-square approximation of a diffusion process in a bounded domain
Creators: name: Milstein, Grigori N.
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: mean-square approximation
subject: random walk
subject: exit point
subject: 60H10
subject: 60J15
subject: 65U05

description: The problem of simulating phase trajectories of a diffusion process in a bounded domain is considered. Unlike usual approximation of SDE when a time-discretization is exploited, here a space-discretization is recommended. For systems with zero drift the next approximate point on the phase trajectory is found as a solution of the system with coefficients frozen at the previous point by a random walk over the boundary of a small ellipsoid. Theorems on mean-square order of accuracy for such an approximation are proved. An algorithm for approximate construction of exit points from the bounded domain is given.
Observed Cosmological Reexpansion in Minimal QFT with Bose and Fermi Fields
Creators: name: Gruber, Christine
name: Kleinert, Hagen
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this work we aim at explaining the re-acceleration of the expansion of the universe, or equivalently, the hierarchy problem, with the help of a simple field-theoretical model. In particular, we want to account for the notorious discrepancy between the observed value of the cosmological expansion term and theoretical values of the vacuum energy of free quantum fields. Rendered infinite by short-wavelength fluctuations, evaluation up to a cutoff in momentum space at the Planck scale leads to contributions of the order of $10^{76} \,\mathrm{GeV}^4$. The observed value of the cosmic expansion being of the order of $10^{-47} \mathrm{GeV}^4$, this is a difference of $123$ orders of magnitude. We propose a possible resolution of the hierarchy problem by a cancelation of divergences by equivalent contributions of bosonic and fermionic fields of the system, albeit after some fine-tuning of the parameters of the field theory. We show that in principle nothing beyond conventional ingredients of quantum field theory is necessary to provide us with a possible explanation of the observed dark energy, and thus with a solution to the hierarchy problem.
description: 13 pages, no figures; to be published in Astropart. Phys
Core Protein-Coding Sequence, but Not Core Protein, Modulates the Efficiency of Cap-Independent Translation Directed by the Internal Ribosome Entry Site of Hepatitis C Virus
Creators: name: Rijnbrand, R. C. A.
name: Lemon, S. M.
name: Wang, T.-H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: Among a myriad of putative functions assigned to the hepatitis C virus (HCV) core protein, several studies suggest that it may modulate internal ribosome entry site (IRES)-mediated initiation of translation. We compared the translational activity of dicistronic reporter transcripts containing the HCV IRES within the intercistronic space fused to downstream sequence encoding either 22 amino acids (aa) or 173 aa of the core protein. The inclusion of the nearly full-length core protein-coding sequence significantly suppressed translation in vitro and in transfected HepG2 cells. However, this suppression was not eliminated by frameshift mutations introduced into the core sequence, suggesting that it occurred at the RNA level and not as a result of core protein expression in cis. Similarly, the expression of core protein (aa 1 to 191) in trans from a recombinant baculovirus did not suppress IRES-directed translation from any of these transcripts in transfected Huh-7 cells. While core protein expression did decrease IRES activity in HepG2 cells (up to 79% suppression), the expression of β-galactosidase from a control baculovirus also suppressed IRES activity (up to 56%), strongly suggesting that this suppression was nonspecific. Finally, the addition of purified recombinant core protein (aa 1 to 179) to in vitro translation reactions at concentrations up to a 10-fold molar excess over the RNA transcripts resulted in no significant reduction in IRES activity. Consistent with these results, a gel retention assay indicated no difference in the affinities of the recombinant HCV core protein and a recombinant Venezuelan equine encephalitis virus capsid protein for HCV IRES-containing RNA transcripts. We conclude that while the inclusion of core protein-coding sequence downstream of the IRES may reduce the efficiency of cap-independent translation on HCV RNA, the core protein itself has no biologically relevant activity in modulating HCV IRES activity.
Effects of Genital Tract Inflammation on Human Immunodeficiency Virus Type 1 V3 Populations in Blood and Semen
Creators: name: Ping, L.-H.
name: Maida, M.
name: Cohen, M. S.
name: Swanstrom, R.
name: Eron, J. J.
name: Zimba, D.
name: Vernazza, P.
name: Kazembe, P.
name: Seillier-Moiseiwitsch, F.
name: Chakraborty, H.
name: Nelson, J. A. E.
name: Fiscus, S. A.
name: Hoffman, I.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: We have examined cell-free viral populations in the blood plasma and seminal plasma compartments of men infected with subtype C human immunodeficiency virus type 1 (HIV-1) using the V3-specific heteroduplex tracking assay (V3-HTA). We studied two cohorts of subjects who had visited either a sexually transmitted disease (STD) clinic for genital tract inflammation in the form of urethritis (n = 43) or a dermatology clinic (controls, n = 14) in Malawi. We have previously shown that the presence of urethritis is associated with an eightfold increase in virus load in the seminal plasma compartment (M. S. Cohen et al., Lancet 349:1868–1873, 1997). The purpose of this study was to determine whether genital tract inflammation and its treatment caused genetic instability in cell-free HIV-1 populations. In a cross-sectional analysis at study entry, three-fourths of the STD and control subjects had multiple V3 populations in their blood while 60% of the STD subjects and 79% of the control subjects had multiple V3 populations in their semen. Overall, one-fourth of all of the subjects showed discordance between results with blood and semen specimens when samples were compared for the presence and absence of subpopulations. When differences in the relative levels of abundance of bands were also taken into account, two-fifths of all of the subjects showed discordance between the compartments. Among the subset of subjects in whom multiple virus populations could be detected, half showed discordance between the compartments. There were no differences between STD and control cohorts for these comparisons of the compartments in this cross-sectional analysis at study entry. Longitudinal analysis of the viral populations from two separate clinic visits over 1 to 4 weeks showed that the complexity of each V3 population as measured by Shannon entropy was different in blood and semen at the two time points, indicating that the blood and semen constitute different compartments for HIV-1. The seminal plasma compartment was more dynamic than the blood plasma compartment for the STD subjects who were treated for urethritis, with changes being noted in the presence or absence of V3-HTA bands in the semen of 29% of these subjects but in the blood of only 9% of these subjects. However, the changes were generally small. Overall, our results suggest that 40% of male subjects show discordance between seminal and blood viral populations and that the complexity of each V3 population was different between the two compartments. Both of these results point to the partial independence of the seminal compartment as a viral niche within the body.
Properties of QSO Metal Line Absorption Systems at High Redshifts: Nature and Evolution of the Absorbers and New Evidence on Escape of Ionizing Radiation from Galaxies
Creators: name: Boksenberg, Alec
name: Sargent, Wallace L. W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Using Voigt-profile-fitting procedures on Keck HIRES spectra of nine QSOs we identify 1099 CIV absorber components clumped in 201 systems outside the Lyman forest over 1.6 < z < 4.4. With associated SiIV, CII, SiII and NV where available we investigate bulk statistical and ionization properties of the components and systems and find no significant change in redshift for CIV and SiIV while CII, SiII and NV change substantially. The CIV components exhibit strong clustering but no clustering is detected for systems on scales from 150 km/s out to 50000 km/s. We conclude the clustering is due entirely to the peculiar velocities of gas present in the circumgalactic media of galaxies. Using specific combinations of ionic ratios we compare our observations with model ionization predictions for absorbers exposed to the metagalactic ionizing radiation background augmented by proximity radiation from their associated galaxies and find the generally accepted means of radiative escape by transparent channels from the internal star-forming sites is spectrally not viable for our stronger absorbers. We develop an active scenario based on runaway stars with resulting changes in the efflux of radiation that naturally enable the needed spectral convergence and in turn provide empirical indicators of morphological evolution in the associated galaxies. Together with a coexisting population of relatively compact galaxies indicated by the weaker absorbers in our sample the collective escape of radiation is sufficient to maintain the IGM ionized over the full range 1.9 < z < 4.4.
description: 131 pages including 46 pages of figures and 33 pages of tables. Accepted for publication by the Astrophysical Journal (Supplement). arXiv admin note: text overlap with arXiv:astro-ph/0307557
The Kac version of the Sherrington-Kirkpatrick model at high temperatures
Creators: name: Bovier, Anton
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Spin glasses
subject: Kac limits
subject: central limit theorems
subject: 82B44
subject: 60K35
subject: 82C32

description: We study the Kac version of the Sherrington-Kirkpatrick (SK) model of a spin glass, i.e. a spin glass with long but finite range interaction on ℤd and gaussian mean zero couplings. We prove that for all β < 1, the free energy of this model converges to that of the SK model as the range of the interaction tends to infinity. Moreover, we prove that for all temperatures for which the infinite volume Gibbs state is unique, the free energy scaled by the square root of the volume converges to a gaussian with variance cγ, β, where γ-1 is the range of the interaction. Moreover, at least for almost all values of β, this variance tends to zero as γ goes to zero, the value in the SK model. We interpret our finding as a weak indication that at least at high temperatures, the SK model can be seen as a reasonable asymptotic model for lattice spin glasses.
Long-term behavior of a critical multitype spatially homogeneous branching particle process and a related reaction-diffusion system
Creators: name: Fleischmann, Klaus
name: Vatutin, Vladimir A.
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: extinction
subject: survival
subject: persistence
subject: systems of reaction-diffusion equations
subject: steady state
subject: genealogical tree
subject: reduced tree
subject: marked particle
subject: 60J80
subject: 60J15

description: A dichotomy concerning extinction and survival (even persistence) at late times is established for critical multitype spatially homogeneous branching particle systems in continuous time under natural conditions on the branching mechanism known from the "classical" processes without motion component. This generalizes results of López-Mimbela and Wakolbinger [LMW96] and others. Our simplified approach is based on some genealogical tree analysis combined with the study of the long-term behavior of L1-norms of solutions of related systems of reaction-"diffusion" equations, which is perhaps also of some independent interest.
Expression proteomics reveals protein targets and highlights mechanisms of action of small molecule drugs
Creators: name: Chernobrovkin, Alexey
name: Vicente, Consuelo Marin
name: Visa, Neus
name: Zubarev, Roman A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Biological sciences

description: Phenomenological screening of small molecule libraries for anticancer activity yields potentially interesting candidate molecules, with a bottleneck in the determination of drug targets and the mechanism of anticancer action. A novel approach to drug target deconvolution compares the abundance profiles of proteins expressed in a panel of cells treated with different drugs, and identifies proteins with cell-type independent and drug-specific regulation that is exceptionally strong in relation to the other proteins. Mapping top candidates on known protein networks reveals the mechanism of drug action, while abundant proteins provide a signature of cellular death/survival pathways. The above approach can significantly shorten drug target identification, and thus facilitate the emergence of novel anticancer treatments.
description: 26 pages, 3 figures, 3 supplementary figures. Raw mass-spectrometry files were deposited to chorusproject.org. Supplementary tables and figures available upon request
Epstein-Barr Virus Immediate-Early Proteins BZLF1 and BRLF1 Activate the ATF2 Transcription Factor by Increasing the Levels of Phosphorylated p38 and c-Jun N-Terminal Kinases
Creators: name: Adamson, A. L.
name: Swenson, J.
name: Kenney, S.
name: Johnson, R. A.
name: Mauser, A.
name: Darr, D.
name: Holley-Guthrie, E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: Expression of either Epstein-Barr virus (EBV) immediate-early protein BZLF1 (Z) or BRLF1 (R) is sufficient to convert EBV infection from the latent to lytic form. Disruption of viral latency requires transcriptional activation of the Z and R promoters. The Z and R proteins are transcriptional activators, and each immediate-early protein activates expression of the other immediate-early protein. Z activates the R promoter through a direct binding mechanism. However, R does not bind directly to the Z promoter. In this study, we demonstrate that the ZII element (a cyclic AMP response element site) in the Z promoter is required for efficient activation by R. The ZII element has been shown to be important for induction of lytic EBV infection by tetradecanoyl phorbol acetate and surface immunoglobulin cross-linking and is activated by Z through an indirect mechanism. We demonstrate that both R and Z activate the cellular stress mitogen-activated protein (MAP) kinases, p38 and JNK, resulting in phosphorylation (and activation) of the cellular transcription factor ATF2. Furthermore, we show that the ability of R to induce lytic EBV infection in latently infected cells is significantly reduced by inhibition of either the p38 kinase or JNK pathways. In contrast, inhibition of stress MAP kinase pathways does not impair the ability of Z expression vectors to disrupt viral latency, presumably because expression of Z under the control of a strong heterologous promoter bypasses the need to activate Z transcription. Thus, both R and Z can activate the Z promoter indirectly by inducing ATF2 phosphorylation, and this activity appears to be important for R-induced disruption of viral latency.
Atomically Resolved Imaging of Highly Ordered Alternating Fluorinated Graphene
Creators: name: Kashtiban, Reza J.
name: Dyson, M. Adam
name: Nair, Rahul R.
name: Zan, Recep
name: Wong, Swee L.
name: Ramasse, Quentin
name: Geim, Andre K.
name: Bangert, Ursel
name: Sloan, Jeremy
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: One of the most desirable goals of graphene research is to produce ordered 2D chemical derivatives of suitable quality for monolayer device fabrication. Here we reveal, by focal series exit wave reconstruction, that C2F chair is a stable graphene derivative and demonstrates pristine long-range order limited only by the size of a functionalized domain. Focal series of images of graphene and C2F chair formed by reaction with XeF2 were obtained at 80 kV in an aberration-corrected transmission electron microscope. EWR images reveal that single carbon atoms and carbon-fluorine pairs in C2F chair alternate strictly over domain sizes of at least 150 nm^2 with electron diffraction indicating ordered domains >/= 0.16 square micrometer. Our results also indicate that, within an ordered domain, functionalization occurs on one side only as theory predicts. Additionally we show that electron diffraction provides a quick and easy method for distinguishing between graphene, C2F chair and fully fluorinated stoichiometric CF 2D phases.
Epstein-Barr Virus LMP2A Transforms Epithelial Cells, Inhibits Cell Differentiation, and Activates Akt
Creators: name: Bendt, K. M.
name: Scholle, F.
name: Raab-Traub, N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: The Epstein-Barr virus LMP2A protein was expressed in a human keratinocyte cell line, HaCaT, and effects on epithelial cell growth were detected in organotypic raft cultures and in vivo in nude mice. Raft cultures derived from LMP2A-expressing cells were hyperproliferative, and epithelial differentiation was inhibited. The LMP2A-expressing HaCaT cells were able to grow anchorage independently and formed colonies in soft agar. HaCaT cells expressing LMP2A were highly tumorigenic and formed aggressive tumors in nude mice. The LMP2A tumors were poorly differentiated and highly proliferative, in contrast to occasional tumors that arose from parental HaCaT cells and vector control cells, which grew slowly and remained highly differentiated. Animals injected with LMP2A-expressing cells developed frequent metastases, which predominantly involved lymphoid organs. Involucrin, a marker of epithelial differentiation, and E-cadherin, involved in the maintenance of intercellular contact, were downregulated in LMP2A tumors. Whereas activation of the mitogen-activated protein kinase pathway was not observed, phosphatidylinositol-3-kinase (PI3-kinase)-dependent activation of the serine-threonine kinase Akt was detected in LMP2A-expressing cells and LMP2A tumors. Inhibition of this pathway blocked growth in soft agar. These data indicate that LMP2A greatly affects cell growth and differentiation pathways in epithelial cells, in part through activation of the PI3-kinase–Akt pathway.
Expression of the Two Major Envelope Proteins of Equine Arteritis Virus as a Heterodimer Is Necessary for Induction of Neutralizing Antibodies in Mice Immunized with Recombinant Venezuelan Equine Encephalitis Virus Replicon Particles
Creators: name: Hedges, J. F.
name: Balasuriya, U. B. R.
name: Davis, N. L.
name: Williams, J. C.
name: Johnston, R. E.
name: Heidner, H. W.
name: MacLachlan, N. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: RNA replicon particles derived from a vaccine strain of Venezuelan equine encephalitis virus (VEE) were used as a vector for expression of the major envelope proteins (GL and M) of equine arteritis virus (EAV), both individually and in heterodimer form (GL/M). Open reading frame 5 (ORF5) encodes the GL protein, which expresses the known neutralizing determinants of EAV (U. B. R. Balasuriya, J. F. Patton, P. V. Rossitto, P. J. Timoney, W. H. McCollum, and N. J. MacLachlan, Virology 232:114–128, 1997). ORF5 and ORF6 (which encodes the M protein) of EAV were cloned into two different VEE replicon vectors that contained either one or two 26S subgenomic mRNA promoters. These replicon RNAs were packaged into VEE replicon particles by VEE capsid protein and glycoproteins supplied in trans in cells that were coelectroporated with replicon and helper RNAs. The immunogenicity of individual replicon particle preparations (pVR21-GL, pVR21-M, and pVR100-GL/M) in BALB/c mice was determined. All mice developed antibodies against the recombinant proteins with which they were immunized, but only the mice inoculated with replicon particles expressing the GL/M heterodimer developed antibodies that neutralize EAV. The data further confirmed that authentic posttranslational modification and conformational maturation of the recombinant GL protein occur only in the presence of the M protein and that this interaction is necessary for induction of neutralizing antibodies.
Functional Characterization of the Dimer Linkage Structure RNA of Moloney Murine Sarcoma Virus
Creators: name: Ly, H.
name: Olsen, J. C.
name: Kaplan, A. H.
name: Nierlich, D. P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: Several determinants that appear to promote the dimerization of murine retroviral genomic RNA have been identified. The interaction between these determinants has not been extensively examined. Previously, we proposed that dimerization of the Moloney murine sarcoma virus genomic RNAs relies upon the concentration-dependent interactions of a conserved palindrome that is initiated by separate G-rich stretches (H. Ly, D. P. Nierlich, J. C. Olsen, and A. H. Kaplan, J. Virol. 73:7255–7261, 1999). The cooperative action of these two elements was examined using a combination of genetic and antisense approaches. Dimerization of RNA molecules carrying both the palindrome and G-rich sequences was completely inhibited by an oligonucleotide complementary to the palindrome; molecules lacking the palindrome could not dimerize in the presence of oligomers that hybridize to two G-rich sequences. The results of spontaneous dimerization experiments also demonstrated that RNA molecules lacking either of the two stretches of guanines dimerized much more slowly than the full-length molecule which includes the dimer linkage structure (DLS). However, the addition of an oligonucleotide complementary to the remaining stretch of guanines restored the kinetics of dimerization to wild-type levels. The ability of this oligomer to rescue the kinetics of dimerization was dependent on the presence of the palindrome, suggesting that interactions within the G-rich regions produce changes in the palindrome that allow dimerization to proceed with maximum efficiency. Further, unsuccessful attempts to produce heterodimers between constructs lacking various combinations of these elements indicate that the G-rich regions and the palindrome do not interact directly. Finally, we demonstrate that both of these elements are important in maintaining efficient viral replication. Modified antisense oligonucleotides targeting the DLS were found to reduce the level of viral vector titer production. The reduction in viral titer is due to a decrease in the efficiency of viral genomic RNA encapsidation. Overall, our data support a dynamic model of retroviral RNA dimerization in which discrete dimerization elements act in a concerted fashion.