cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
About a Stationary Schrödinger-Poisson System with Kohn-Sham potential in Nanoelectronics
Creators: name: Kaiser, Hans-Christoph
name: Rehberg, Joachim
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: stationary Schrödinger-Poisson system
subject: Kohn-Sham system
subject: Schrödinger operator with mixed boundary conditions
subject: quantum mechanical particle density operator
subject: nonlinear Poisson equations
subject: simulation of electronic devices
subject: electron gas with reduced dimension
subject: nanoelectronics
subject: 35B45
subject: 35D05
subject: 35D10
subject: 35J05
subject: 35J10
subject: 35J20
subject: 35J60
subject: 35J65
subject: 35Q40
subject: 47A55
subject: 47A60
subject: 47A75
subject: 47H05
subject: 47H10
subject: 47H15

description: The stationary Schrödinger-Poisson system with a self-consistent effective Kohn-Sham potential is a system of PDEs for the electrostatic potential and the envelopes of wave functions defining the quantum mechanical carrier densities in a semiconductor nanostructure. We regard both Poisson's and Schrödinger's equation with mixed boundary conditions and discontinuous coefficients. Without an exchange-correlation potential the Schrödinger-Poisson system is a nonlinear Poisson equation in the dual of a Sobolev space which is determined by the boundary conditions imposed on the electrostatic potential. The nonlinear Poisson operator involved is strongly monotone and boundedly Lipschitz continuous, hence the operator equation has a unique solution. The proof rests upon the following property: the quantum mechanical carrier density operator depending on the potential of the defining Schrödinger operator is anti-monotone and boundedly Lipschitz continuous. The solution of the Schrödinger-Poisson system without an exchange-correlation potential depends boundedly Lipschitz continuous on the reference potential in Schrödinger's operator. By means of this relation a fixed point mapping for the vector of quantum mechanical carrier densities is set up which meets the conditions in Schauder's fixed point theorem. Hence, the Kohn-Sham system has at least one solution. If the exchange-correlation potential is sufficiently small, then the solution of the Kohn-Sham system is unique. Moreover, properties of the solution as bounds for its values and its oscillation can be expressed in terms of the data of the problem.
Charge-to-Alanine Mutagenesis of the Adeno-Associated Virus Type 2 Rep78/68 Proteins Yields Temperature-Sensitive and Magnesium-Dependent Variants
Creators: name: Gavin, Denise
name: Young, Samuel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: The adeno-associated virus type 2 (AAV) replication (Rep) proteins Rep78 and 68 (Rep78/68) exhibit a number of biochemical activities required for AAV replication, including specific binding to a 22-bp region of the terminal repeat, site-specific endonuclease activity, and helicase activity. Individual and clusters of charged amino acids were converted to alanines in an effort to generate a collection of conditionally defective Rep78/68 proteins. Rep78 variants were expressed in human 293 cells and analyzed for their ability to mediate replication of recombinant AAV vectors at various temperatures. The biochemical activities of Rep variants were further characterized in vitro by using Rep68 His-tagged proteins purified from bacteria. The results of these analyses identified a temperature-sensitive (ts) Rep protein (D40,42,44A-78) that exhibited a delayed replication phenotype at 32°C, which exceeded wild-type activity by 48 h. Replication activity was reduced by more than threefold at 37°C and was undetectable at 39°C. Stability of the Rep78 protein paralleled replication levels at each temperature, further supporting a ts phenotype. Replication differences resulted in a 3-log-unit difference in virus yields between the permissive and nonpermissive temperatures (2.2 × 106 and 3 × 103, respectively), demonstrating that this is a relatively tight mutant. In addition to the ts Rep mutant, we identified a nonconditional mutant with a reduced ability to support viral replication in vivo. Additional characterization of this mutant demonstrated an Mg2+-dependent phenotype that was specific to Rep endonuclease activity and did not affect helicase activity. The two mutants described here are unique, in that Rep ts mutants have not previously been described and the D412A Rep mutant represents the first mutant in which the helicase and endonuclease functions can be distinguished biochemically. Further understanding of these mutants should facilitate our understanding of AAV replication and integration, as well as provide novel strategies for production of viral vectors.
Il ‘percorso speciale’ della Nuova Turchia: dalla corsa agli standard europei alle nuove ambizioni internazionali
Creators: name: Pasculli, Pietro
Publisher: name: Universita' degli Studi di Salerno
Year: 2020
Subjects: European standards
Sonderweg
New Turkey

description: Despite the last 18 years of single-coloured government led by AKP (Justice and Development Party), over the last five years Turkey seems to have redefined its political and strategic objectives. At first with its eyes turned to the West, Turkey is now a solitary power. The failure of the ceasefire with the Kurds in 2015 and the attempted coup in 2016, have launched a domestic propaganda on the need for a strong and autonomous state. Turkey no longer seems willing to subcontract its policy to the constraints of transatlantic institutions or to EU standards. A «New Turkey», as defined by President Recep Tayyip Erdoğan, able to cope with internal and external enemies, and with a strong leader who aims at restoring its lost international greatness and role. In this constantly evolving scenario, this contribution is therefore intended to look through the fundamental stages of this special path, and with its possible future scenarios.
Metastates in the Hopfield model in the replica symmetric regime
Creators: name: Bovier, Anton
name: Gayrard, Véronique
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Hopfield model
subject: neural networks
subject: metastates
subject: replica symmetry
subject: Brascamp-Lieb inequalities
subject: 82B44
subject: 60K35
subject: 82C32

description: We study the finite dimensional marginals of the Gibbs measure in the Hopfield model at low temperature when the number of patterns, M, is proportional to the volume with a sufficiently small proportionality constant ɑ > 0. It is shown that even when a single pattern is selected (by a magnetic field or by conditioning), the marginals do not converge almost surely, but only in law. The corresponding limiting law is constructed explicitly. We fit our result in the recently proposed language of "metastates" which we discuss in some length. As a byproduct, in a certain regime of the parameters ɑ and β (the inverse temperature), we also give a simple proof of Talagrand's [T1] recent result that the replica symmetric solution found by Amit, Gutfreund, and Sompolinsky [AGS] can be rigorously justified.
Additional file 7 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 7: Figure S6. Genomic prediction accuracy of ML-Top40k.
Parallel-Tempering Monte-Carlo Simulation with Feedback-Optimized Algorithm Applied to a Coil-to-Globule Transition of a Lattice Homopolymer
Creators: name: Lewandowski, Krzysztof
name: Knychala, Piotr
name: Banaszak, Michal
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedback-optimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is applied to a lattice simulation of a homopolymer chain undergoing a coil-to-globule transition upon cooling. We select the optimal number of replicas for different chain lengths, N = 25, 50 and 75, using replica's round-trip time in temperature space, in order to determine energy, specific heat, and squared end-to-end distance of the hopolymer chain for the selected temperatures. We also evaluate relative merits of this optimization method.
Epithelial Cell Adhesion to Extracellular Matrix Proteins Induces Tyrosine Phosphorylation of the Epstein-Barr Virus Latent Membrane Protein 2: a Role for C-Terminal Src 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: The Epstein-Barr virus (EBV) latent membrane protein 2 (LMP2) is expressed in latently EBV-infected B cells, where it forms patches in the plasma membrane and interferes with B-cell receptor signal transduction through dominant-negative effects on protein kinases. LMP2 transcripts are detected in nasopharyngeal carcinoma, an epithelial-cell malignancy. In this study the function of LMP2A in epithelial cells was investigated. LMP2A was found to coprecipitate with protein kinase activities and to become phosphorylated in in vitro kinase assays. Analysis of LMP2A deletion mutants demonstrated that tyrosines implicated in interacting with Src family kinase SH2 domains and the SH2 domain of Csk, as well as the LMP2A immunoreceptor tyrosine-based activation motif, are important for its phosphorylation in epithelial cells. LMP2A tyrosine phosphorylation was triggered by cell adhesion to extracellular-matrix (ECM) proteins. Src family kinases, whose involvement in cell-ECM signaling and LMP2A phosphorylation in B lymphocytes has been well established, were found not to be responsible for LMP2A phosphorylation in epithelial cells. Instead, coexpression of Csk, a negative Src regulator, and LMP2A led to an increase in LMP2A phosphorylation both in nonadherent cells and upon cell adhesion. Csk also phosphorylated LMP2A in vitro. These results suggest that LMP2A has a different role in epithelial cells, where it interacts with cell adhesion-initiated signaling pathways. Although tyrosine phosphorylation of LMP2A occurs in both cell types, different protein kinases seem to be used: Src family kinases in B lymphocytes and Csk in epithelial cells.
A new model for electrostatic MEMS 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, 35J57, 35B30, 74F15, 74M05

description: A moving boundary problem with two free boundaries modeling a two-dimensional idealized MEMS device with pull-in instability is discussed. We use a fixed point argument to show that the model possesses stationary solutions for small source voltages. We also give a rigorous evidence that solutions of the model converge towards solutions of the associated small aspect ratio equation in the vanishing aspect ratio limit.
description: 17 pages
Expression of EBNA-1 mRNA Is Regulated by Cell Cycle during Epstein-Barr Virus Type I Latency
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: Expression of EBNA-1 protein is required for the establishment and maintenance of the Epstein-Barr virus (EBV) genome during latent infection. During type I latency, the BamHI Q promoter (Qp) gives rise to EBNA-1 expression. The dominant regulatory mechanism for Qp appears to be mediated through the Q locus, located immediately downstream of the transcription start site. Binding of EBNA-1 to the Q locus represses Qp constitutive activity, and repression has been reported to be overcome by an E2F family member that binds to the Q locus and displaces EBNA-1 (N. S. Sung, J. Wilson, M. Davenport, N. D. Sista, and J. S. Pagano, Mol. Cell. Biol. 14:7144–7152, 1994). These data suggest that the final outcome of Qp activity is reciprocally controlled by EBNA-1 and E2F. Since E2F activity is cell cycle regulated, Qp activity and EBNA-1 expression are predicted to be regulated in a cell cycle-dependent manner. Proliferation of the type I latently infected cell line, Akata, was synchronized with the use of the G2/M blocking agent nocodazole. From 65 to 75% of cells could be made to peak in S phase without evidence of viral reactivation. Following release from G2/M block, EBNA-1 mRNA levels declined as the synchronized cells entered the G1 phase of the cell cycle. As cells proceeded into S phase, EBNA-1 mRNA levels increased parallel to the peak in cell numbers in S phase. However, EBNA-1 protein levels showed no detectable change during the cell cycle, most likely due to the protein’s long half-life as estimated by inhibition of protein synthesis by cycloheximide. Finally, in Qp luciferase reporter assays, the activity of Qp was shown to be regulated by cell cycle and to be dependent on the E2F sites within the Q locus. These findings demonstrate that transcriptional activity of Qp is cell cycle regulated and indicated that E2F serves as the stimulus for this regulation.
Additional file 8 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 8. Genomic prediction and genome-wide association study using simulated traits.
Infection of Neonatal Mice with Sindbis Virus Results in a Systemic Inflammatory Response Syndrome
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: Laboratory strains of viruses may contain cell culture-adaptive mutations which result in significant quantitative and qualitative alterations in pathogenesis compared to natural virus isolates. This report suggests that this is the case with Sindbis virus strain AR339. A cDNA clone comprising a consensus sequence of Sindbis virus strain AR339 has been constructed (W. B. Klimstra, K. D. Ryman, and R. E. Johnston, J. Virol. 72:7357–7366, 1998). This clone (pTR339) regenerates a sequence predicted to be very close to that of the original AR339 isolate by eliminating several cell culture-adaptive mutations present in individual laboratory strains of the virus (K. L. McKnight et al., J. Virol. 70:1981–1989, 1996). It thus provides a unique reagent for study of the pathogenesis of Sindbis virus strain AR339 in mice. Neonatal mouse pathogenesis of virus (TR339) generated from the pTR339 clone was compared with that of virus from a cDNA clone of the cell culture-passaged laboratory AR339 strain, TRSB, and virus from a clone of a more highly cell culture-adapted strain, HRsp (Toto 50). The sequence of TRSB differs from the consensus at three coding positions, while Toto 50 differs at eight codons and one nucleotide in the 5′ nontranslated region. Both cell culture-adapted strains contain mutations associated with heparan sulfate (HS)-dependent attachment to cells (W. B. Klimstra, K. D. Ryman, and R. E. Johnston, J. Virol. 72:7357–7366, 1998). TR339 caused 100% mortality with an average survival time (AST) of 1.7 ± 0.25 days. While TRSB also caused 100% mortality, the AST was extended to 2.9 ± 0.52 days. The more extensively cell culture-adapted virus Toto 50 caused only 30% mortality with an AST extended to 11.0 ± 4.8 days. TRSB and TR339 induced high serum levels of alpha/beta interferon, gamma interferon, tumor necrosis factor alpha, interleukin-6, and corticosterone and induced pathology reminiscent of lipopolysaccharide-induced endotoxic shock, a type of systemic inflammatory response syndrome. However, the reduced intensity of this response in TRSB-infected mice correlated with the increased AST. Toto 50 failed to induce the shock-like cytokine cascade. In situ hybridization studies indicated that TR339 and TRSB replicated in identical tissues, but the TRSB signal was less widespread at early times postinfection. While Toto 50 also replicated in similar tissues, the extent of replication was severely restricted and mice developed lesions characteristic of encephalitis. A single mutation in TRSB at E2 position 1 (Arg) conferred HS-dependent attachment to cells and was associated with reduced cytokine induction and extended AST in vivo.
On Performance Measures for Infinite Swapping Monte Carlo Methods
Creators: name: Doll, J. D.
name: Dupuis, Paul
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We introduce and illustrate a number of performance measures for rare-event sampling methods. These measures are designed to be of use in a variety of expanded ensemble techniques including parallel tempering as well as infinite and partial infinite swapping approaches. Using a variety of selected applications we address questions concerning the variation of sampling performance with respect to key computational ensemble parameters.
description: 52 pages, 19 figures
Inhibition of Epstein-Barr Virus Replication by a Benzimidazole l-Riboside: Novel Antiviral Mechanism of 5,6-Dichloro-2-(Isopropylamino)-1-β-l-Ribofuranosyl-1H-Benzimidazole
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: Although a number of antiviral drugs inhibit replication of Epstein-Barr virus (EBV) in cell culture, and acyclovir (ACV) suppresses replication in vivo, currently available drugs have not proven effective for treatment of EBV-associated diseases other than oral hairy leukoplakia. Benzimidazole riboside compounds represent a new class of antiviral compounds that are potent inhibitors of human cytomegalovirus (HCMV) replication but not of other herpesviruses. Here we characterize the effects of two compounds in this class against lytic replication of EBV induced in a Burkitt lymphoma cell line latently infected with EBV. We analyzed linear forms of EBV genomes, indicative of lytic replication, and episomal forms present in latently infected cells by terminal probe analysis followed by Southern blot hybridization as well as the high-molecular-weight unprocessed viral DNA by pulsed-field gel electrophoresis. d-Ribofuranosyl benzimidazole compounds that act as inhibitors of HCMV DNA maturation, including BDCRB (5,6-dichloro-2-bromo-1-β-d-ribofuranosyl-1H-benzimidazole), did not affect the accumulation of high-molecular-weight or monomeric forms of EBV DNA in the induced cells. In contrast, the generation of linear EBV DNA as well as precursor viral DNA was sensitive to the l-riboside 1263W94 [5,6-dichloro-2-(isopropylamino)-1-β-l-ribofuranosyl-1H-benzimidazole]. The 50% inhibitory concentration range for 1263W94 was 0.15 to 1.1 μM, compared with 10 μM for ACV. Thus, 1263W94 is a potent inhibitor of EBV. In addition, 1263W94 inhibited the phosphorylation and the accumulation of the essential EBV replicative cofactor, early antigen D.
Matrix Metalloproteinase 9 Expression Is Induced by Epstein-Barr Virus Latent Membrane Protein 1 C-Terminal Activation Regions 1 and 2
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: Nasopharyngeal carcinoma (NPC), which is closely associated with the Epstein-Barr virus (EBV), is a highly metastatic malignant tumor. An important activity in tumor invasion and metastasis is that of the 92-kDa type IV collagenase or gelatinase, matrix metalloproteinase 9 (MMP-9), which mediates the degradation of the basement membrane and extracellular matrix. The expression of MMP-9 has been shown to be enhanced by the EBV oncoprotein, latent membrane protein 1 (LMP-1). LMP-1, which is expressed in NPC, has two essential signaling domains within the carboxy terminus, termed C-terminal activation regions 1 (CTAR-1) and CTAR-2. This study reveals that either signaling domain can activate the MMP-9 promoter and induce MMP-9 activity; however, LMP-1 deletion mutants lacking either CTAR-1 or CTAR-2 had a decreased ability to induce MMP-9 expression. The deletion of both activation regions completely abolished the induction of MMP-9 activity, while the cotransfection of both the CTAR-1 and CTAR-2 deletion mutants restored MMP-9 activity to levels produced by wild-type LMP-1. The NF-κB and activator protein 1 (AP-1) binding sites in the MMP-9 promoter were essential for the activation of MMP-9 gene expression by both CTAR-1 and CTAR-2. The induction of MMP-9 expression by LMP-1 and both CTAR-1 and CTAR-2 mutants was blocked by the overexpression of IκB. The tumor necrosis factor receptor-associated factor (TRAF) pathway also contributed to the activation of the MMP-9 promoter as shown by the use of TRAF-2 and TRAF-3 dominant-negative constructs. These data indicate that the activation of both the NF-κB and AP-1 pathways by LMP-1, CTAR-1, and CTAR-2 is necessary for the activation of MMP-9 expression. In NPC, LMP-1 may contribute to invasiveness and metastasis through the induction of MMP-9 transcription and enzymatic activity.
Mammals, Bajo Caguan, Camera Trap Data set
Creators: name: Lizcano, Diego J.
name: Niño-Reyes, Alejandra
name: Parra, Juan Pablo
name: Bonell, William
name: Garay, Miguel
Publisher: name: Zenodo
Year: 2018
Subjects: Camera trap
mammal
bird
vertebrates
Caguan
Caqueta
Colombia
Amazon

description: Camera trap data set for Field Museum Rapid Inventory 30 (IR30) Restiction: None. Cite as Lizcano et al 2019. IR-30/WCS Colombia/Field Museum/Resguardo Indigena Huitora
Additional file 9 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9: Figures S7 and S8. Genomic prediction results using simulated traits.
Moloney Murine Sarcoma Virus Genomic RNAs Dimerize via a Two-Step Process: a Concentration-Dependent Kissing-Loop Interaction Is Driven by Initial Contact between Consecutive Guanines
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: Retroviruses contain two plus-strand genomic RNAs, which are stably but noncovalently joined in their 5′ regions by a dimer linkage structure (DLS). Two models have been put forward to explain the mechanisms by which the RNAs dimerize; each model emphasizes the role of specific molecular determinants. The kissing-loop model implicates interactions between palindromic sequences in the DLS region. The second model proposes that purine-rich stretches in the region form purine quartet structures. Here, we present an examination of the in vitro dimerization of Moloney murine sarcoma virus (MuSV) RNA in the context of these two models. Dimers were found to form spontaneously in a temperature-, time-, concentration-, and salt-dependent manner. In contrast to earlier reports, we found that deletion of neither the palindrome nor the consensus purine motifs (PuGGAPuA) affected the level of dimer formation at low concentrations of RNA. Rather, different purine-rich sequences, i.e., consecutive stretches of guanines, were found to enhance both in vitro RNA dimerization and in vivo viral replication. Biochemical evidence further suggests that these guanine-rich (G-rich) stretches form guanine quartet structures. We also found that the palindromic sequences could support dimerization at significantly higher RNA concentrations. In addition, the G-rich stretches were as important as the palindromic sequence for maintaining efficient viral replication. Overall, our data support a model that entails contributions from both of the previously proposed mechanisms of retroviral RNA dimerization.
Chemical probes of turbulence in the diffuse medium: the TDR model
Creators: name: Godard, Benjamin
name: Falgarone, Edith
name: Forêts, Guillaume Pineau Des
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Context. Tens of light hydrides and small molecules have now been detected over several hundreds sight lines sampling the diffuse interstellar medium (ISM) in both the Solar neighbourhood and the inner Galactic disk. They provide unprecedented statistics on the first steps of chemistry in the diffuse gas. Aims. These new data confirm the limitations of the traditional chemical pathways driven by the UV photons and the cosmic rays (CR) and the need for additional energy sources, such as turbulent dissipation, to open highly endoenergetic formation routes. The goal of the present paper is to further investigate the link between specific species and the properties of the turbulent cascade in particular its space-time intermittency. Methods. We have analysed ten different atomic and molecular species in the framework of the updated model of turbulent dissipation regions (TDR). We study the influence on the abundances of these species of parameters specific to chemistry (density, UV field, and CR ionisation rate) and those linked to turbulence (the average turbulent dissipation rate, the dissipation timescale, and the ion neutral velocity drift in the regions of dissipation). Results. The most sensitive tracers of turbulent dissipation are the abundances of CH+ and SH+, and the column densities of the J = 3, 4, 5 rotational levels of H2 . The abundances of CO, HCO+, and the intensity of the 158 $μ$m [CII] emission line are significantly enhanced by turbulent dissipation. The vast diversity of chemical pathways allows the independent determinations of free parameters never estimated before: an upper limit to the average turbulent dissipation rate, $\overline{\varepsilon}$ < 10$^{-23}$ erg cm$^{-3}$ s$^{-1}$ for $n_H$=20 cm$^{-3}$, from the CH+ abundance; an upper limit to the ion-neutral velocity drift, $u_{in}$ < 3.5 km s$^{-1}$, from the SH+ to CH+ abundance ratio; and a range of dissipation timescales, 100 < $τ_V$ < 1000 yr, from the CO to HCO+ abundance ratio. For the first time, we reproduce the large abundances of CO observed on diffuse lines of sight, and we show that CO may be abundant even in regions with UV-shieldings as low as $5 \times 10^{-3}$ mag. The best range of parameters also reproduces the abundance ratios of OH, C2H, and H2O to HCO+ and are consistent with the known properties of the turbulent cascade in the Galactic diffuse ISM. Conclusions. Our results disclose an unexpected link between the dissipation of turbulence and the emergence of molecular richness in the diffuse ISM. Some species, such as CH+ or SH+, turn out to be unique tracers of the energy trail in the ISM. In spite of some degeneracy, the properties of the turbulent cascade, down to dissipation, can be captured through specific molecular abundances.
Mutant Cells Selected during Persistent Reovirus Infection Do Not Express Mature Cathepsin L and Do Not Support Reovirus Disassembly
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: Persistent reovirus infections of murine L929 cells select cellular mutations that inhibit viral disassembly within the endocytic pathway. Mutant cells support reovirus growth when infection is initiated with infectious subvirion particles (ISVPs), which are intermediates in reovirus disassembly formed following proteolysis of viral outer-capsid proteins. However, mutant cells do not support growth of virions, indicating that these cells have a defect in virion-to-ISVP processing. To better understand mechanisms by which viruses use the endocytic pathway to enter cells, we defined steps in reovirus replication blocked in mutant cells selected during persistent infection. Subcellular localization of reovirus after adsorption to parental and mutant cells was assessed using confocal microscopy and virions conjugated to a fluorescent probe. Parental and mutant cells did not differ in the capacity to internalize virions or distribute them to perinuclear compartments. Using pH-sensitive probes, the intravesicular pH was determined and found to be equivalent in parental and mutant cells. In both cell types, virions localized to acidified intracellular organelles. The capacity of parental and mutant cells to support proteolysis of reovirus virions was assessed by monitoring the appearance of disassembly intermediates following adsorption of radiolabeled viral particles. Within 2 h after adsorption to parental cells, proteolysis of viral outer-capsid proteins was observed, consistent with formation of ISVPs. However, in mutant cells, no proteolysis of viral proteins was detected up to 8 h postadsorption. Since treatment of cells with E64, an inhibitor of cysteine-containing proteases, blocks reovirus disassembly, we used immunoblot analysis to assess the expression of cathepsin L, a lysosomal cysteine protease. In contrast to parental cells, mutant cells did not express the mature, proteolytically active form of the enzyme. The defect in cathepsin L maturation was not associated with mutations in procathepsin L mRNA, was not complemented by procathepsin L overexpression, and did not affect the maturation of cathepsin B, another lysosomal cysteine protease. These findings indicate that persistent reovirus infections select cellular mutations that affect the maturation of cathepsin L and suggest that alterations in the expression of lysosomal proteases can modulate viral cytopathicity.
Multi-gap absorption in CaCu$_{3}$Ti$_{4}$O$_{12}$ and the predictivity of ab initio methods
Creators: name: Ricci, Francesco
name: Alippi, Paola
name: Filippetti, Alessio
name: Fiorentini, Vincenzo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the electronic properties of the quadruple perovskite CaCu$_{3}$Ti$_{4}$O$_{12}$ as obtained via several density-functional based methods, and propose a new interpretation of optical experiments to the effect that four distinct transitions (centered around 0.7, 1.5, 2.5, and 3.5 eV) contribute to the spectrum. The comparison with experiment is satisfactory, especially after we account for the effects of spin disorder, which does not close the fundamental gap but suppresses the transition intensity. We find that some of the methods we employ tend to overestimate considerably the gaps for standard values of the respective adjustable parameters.
description: 10 pages, 13 figures, 1 table
Natural Variation in Translational Activities of the 5′ Nontranslated RNAs of Hepatitis C Virus Genotypes 1a and 1b: Evidence for a Long-Range RNA-RNA Interaction outside of the Internal Ribosomal Entry Site
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: The 5′ nontranslated RNA (5′NTR) of a genotype 1b hepatitis C virus (HCV-N) directs cap-independent translation of the HCV-N polyprotein with about twofold less efficiency than the 5′NTR of a genotype 1a virus under physiologic conditions (Hutchinson strain, or HCV-H) (M. Honda et al., Virology 222:31–42, 1996). Here, we show by mutational analysis that substitution of the AG dinucleotide sequence at nucleotides (nt) 34 and 35 of HCV-N with GA (present in HCV-H) restores the translational activity to that of the HCV-H 5′NTR both in vitro and in vivo. These nucleotides are located upstream of the minimal essential internal ribosome entry site (IRES), as a 6-nt deletion spanning nt 32 to 37 also increased the translational activity of the HCV-N 5′NTR to that of HCV-H. Thus, the upstream AG dinucleotide sequence has an inhibitory effect on IRES-directed translation. Surprisingly, however, this inhibitory effect was observed only when the translated, downstream RNA sequence contained nt 408 to 929 of HCV (capsid-coding RNA). Further analysis of RNA transcripts containing frameshift mutations demonstrated that the nucleotide sequence of the transcript, and not the amino acid sequence of the expressed capsid protein, determines this difference in translation efficiency. The difference between the translational activities of the HCV-N and HCV-H transcripts was increased when translation was carried out in reticulocyte lysates containing high K+ concentrations, with a sevenfold difference evident at 130 to 150 mM K+. These results suggest that there is an RNA-RNA interaction involving 5′NTR and capsid-coding sequences flanking the IRES and that this is responsible for the reduced IRES activity of the genotype 1b virus, HCV-N.
The AGN Population in X-ray Selected Galaxy Groups at $0.5 < z < 1.1$
Creators: name: Oh, Semyeong
name: Mulchaey, John S.
name: Woo, Jong-Hak
name: Finoguenov, Alexis
name: Tanaka, Masayuki
name: Cooper, Michael C.
name: Ziparo, Felicia
name: Bauer, Franz E.
name: Matsuoka, Kenta
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: We use Chandra data to study the incidence and properties of Active Galactic Nuclei (AGN) in 16 intermediate redshift ($0.5 < z < 1.1$) X-ray-selected galaxy groups in the Chandra Deep Field-South. We measure an AGN fraction of $f(L_{X,H} > 10^{42}; M_R 10^{41}$ erg/s) = 25), we find only 4 emission-line AGN, 3 of which are also X-ray bright. Furthermore, most of the X-ray AGN in our groups are optically-dull (i.e. lack strong emission-lines) similar to those found in low redshift X-ray groups and clusters of galaxies. This contrasts with the AGN population found in low redshift optically-selected groups which are dominated by emission-line AGN. The differences between the optically and X-ray-selected AGN populations in groups are consistent with a scenario where most AGN in the densest environments are currently in a low accretion state.
description: 8 pages, 4 figures, accepted for publication in ApJ
Persistent Infection Promotes Cross-Species Transmissibility of Mouse Hepatitis Virus
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: Persistent infection with mouse hepatitis virus (MHV) strain A59 in murine DBT (delayed brain tumor) cells resulted in the emergence of host range variants, designated V51A and V51B, at 210 days postinfection. These host range mutants replicated efficiently in normally nonpermissive Chinese hamster ovary (CHO), in human hepatocarcinoma (HepG2), and to a lesser extent in human breast carcinoma (MCF7) cell lines. Little if any replication was noted in baby hamster kidney (BHK), green African monkey kidney (COS-7), feline kidney (CRFK), and swine testicular (ST) cell lines. By fluorescent antibody (FA) staining, persistent viruses V10B and V30B, isolated at days 38 and 119 days postinfection, also demonstrated very low levels of replication in human HepG2 cells. These data suggest that persistence may rapidly select for host range expansion of animal viruses. Pretreatment of HepG2 cells with a polyclonal antibody directed against human carcinoembryonic antigens (CEA) or with some monoclonal antibodies (Col-1, Col-4, Col-12, and Col-14) that bind human CEA significantly inhibited V51B infection. Under identical conditions, little or no blockade was evident with other monoclonal antibodies (kat4c or Col-6) which also bind the human CEA glycoproteins. In addition, an antibody (EDDA) directed against irrelevant antigens did not block V51B replication. Pretreatment with the Col-4 and Col-14 antibodies did not block Sindbis virus replication in HepG2 cells or MHV infection in DBT cells, suggesting that one or more CEA glycoproteins likely functioned as receptors for V51B entry into human cell lines. To test this hypothesis, the human biliary glycoprotein (Bgp) and CEA genes were cloned and expressed in normally nonpermissive BHK cell lines by using noncytopathic Sindbis virus replicons (pSinRep19). By growth curves and FA staining, human CEA and to a much lesser extent human Bgp functioned as receptors for V51B entry. Furthermore, V51B replication was blocked with polyclonal antiserum directed against human CEA and Bgp. Under identical conditions, the parental MHV strain A59 failed to replicate in BHK cells expressing human Bgp or CEA. These data suggest that MHV persistence may promote virus cross-species transmissibility by selecting for virus variants that recognize phylogenetic homologues of the normal receptor.
The Epstein-Barr Virus BZLF1 Protein Interacts Physically and Functionally with the Histone Acetylase CREB-Binding Protein
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: The Epstein-Barr virus (EBV) immediate-early protein BZLF1 (Z) is a key regulator of the EBV latent-to-lytic switch. Z is a transcriptional activator which induces EBV early gene expression. We demonstrate here that Z interacts with CREB-binding protein (CBP), a histone acetylase and transcriptional coactivator. This interaction requires the amino-terminal region of CBP as well as the transactivation and leucine zipper domains of Z. We show that CBP enhances Z-mediated transactivation of EBV early promoters, in reporter gene assays and in the context of the endogenous genome. We also demonstrate that Z decreases CREB transactivation function and that this inhibitory effect is reversed by overexpression of CBP. We show that Z also interacts directly with CREB. However, mutational analysis indicates that Z inhibition of CREB activity requires the direct interaction between Z and CBP but not the direct interaction between Z and CREB. We propose that Z interacts with CBP to enhance viral early gene transcription. In addition, the Z-CBP interaction may control host cellular transcription factor activity through competition for limiting amounts of cellular CBP.
The Epstein-Barr Virus Protein BRLF1 Activates S Phase Entry through E2F1 Induction
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: The Epstein-Barr Virus (EBV) immediate-early protein BRLF1 is one of two transactivators which mediate the switch from latent to lytic replication in EBV-infected cells. DNA viruses often modulate the function of critical cell cycle proteins to maximize the efficiency of virus replication. Here we have examined the effect of BRLF1 on cell cycle progression. A replication-deficient adenovirus expressing BRLF1 (AdBRLF1) was used to infect normal human fibroblasts and various epithelial cell lines. BRLF1 expression induced S phase entry in contact-inhibited fibroblasts and in the human osteosarcoma cell line U-2 OS. AdBRLF1 infection produced a dramatic increase in the level of E2F1 but not E2F4. In contrast, the levels of Rb, p107, and p130 were decreased in AdBRLF1-infected cells. Electrophoretic mobility shift assays confirmed an increased level of free E2F1 in the AdBRLF1-infected human fibroblasts. Consistent with the previously described effect of E2F1, AdBRLF1-infected fibroblasts had increased levels of p53 and p21 and died by apoptosis. BRLF1-induced activation of E2F1 may be required for efficient EBV lytic replication, since at least one critical viral replication gene (the viral DNA polymerase) is activated by E2F (C. Liu, N. D. Sista, and J. S. Pagano, J. Virol. 70:2545–2555, 1996).
The Furin Protease Cleavage Recognition Sequence of Sindbis Virus PE2 Can Mediate Virion Attachment to Cell Surface Heparan Sulfate
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: Cell culture-adapted Sindbis virus strains attach to heparan sulfate (HS) receptors during infection of cultured cells (W. B. Klimstra, K. D. Ryman, and R. E. Johnston, J. Virol. 72:7357–7366, 1998). At least three E2 glycoprotein mutations (E2 Arg 1, E2 Lys 70, and E2 Arg 114) can independently confer HS attachment in the background of the consensus sequence Sindbis virus (TR339). In the studies reported here, we have investigated the mechanism by which the E2 Arg 1 mutation confers HS-dependent binding. Substitution of Arg for Ser at E2 1 resulted in a significant reduction in the efficiency of PE2 cleavage, yielding virus particles containing a mixture of PE2 and mature E2. Presence of PE2 was associated with an increase in HS-dependent attachment to cells and efficient attachment to heparin-agarose beads, presumably because the furin recognition site for PE2 cleavage also represents a candidate HS binding sequence. A comparison of mutants with partially or completely inhibited PE2 cleavage demonstrated that efficiency of cell binding was correlated with the amount of PE2 in virus particles. Viruses rendered cleavage defective due to deletions of portions or all of the furin cleavage sequence attached very poorly to cells, indicating that an intact furin cleavage sequence was specifically required for PE2-mediated attachment to cells. In contrast, a virus containing a partial deletion was capable of efficient binding to heparin-agarose beads, suggesting different requirements for heparin bead and cell surface HS binding. Furthermore, virus produced in C6/36 mosquito cells, which cleave PE2 more efficiently than BHK cells, exhibited a reduction in cell attachment efficiency correlated with reduced content of PE2 in particles. Taken together, these results strongly argue that the XBXBBX (B, basic; X, hydrophobic) furin protease recognition sequence of PE2 can mediate the binding of PE2-containing Sindbis viruses to HS. This sequence is very similar to an XBBXBX heparin-HS interaction consensus sequence. The attachment of furin protease cleavage sequences to HS may have relevance to other viruses whose attachment proteins are cleaved during maturation at positively charged recognition sequences.
Generalization of Lorentz-Poincare ether theory to quantum gravity
Creators: name: Schmelzer, Ilja
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: quantum grivuty
subject: 81P05
subject: 83D05
subject: 83C45

description: We present a quantum theory of gravity which is in agreement with observation in the relativistic domain. The theory is not relativistic, but a Galilean invariant generalization of Lorentz-Poincare ether theory to quantum gravity. If we apply the methodological rule that the best available theory has to be preferred, we have to reject the relativistic paradigm and return to Galilean invariant ether theory.
Engineered nano-bio cellular interfaces: Vertically aligned silicon nanowire arrays for human cell manipulation and neuronal progenitor cell differentiation
Creators: name: FIRKIN, ESTHER SUSANNE
Publisher: name: Monash University
Year: 2023
Subjects: Neural networks
Cellular interactions (incl. adhesion, matrix, cell wall)
Nanobiotechnology

description: This thesis uses a nanostructured platform to characterise how nanoscale topography influences human cell behaviour, with a specific focus on human neural stem cells. Later chapters explore in detail the impact of different vertically-aligned silicon nanowire topographies on human neural stem cell behaviour and cell fate determination. The data presented emphasise that the impact of a certain nanotopography is likely to vary for different human cell types and developmental states. The direct and controllable influence of nanotopographies on human cells may prove this platform useful in disease modelling.
An inverse problem from the 2D-groundwater modelling
Creators: name: Bruckner, Gottfried
name: Handrock-Meyer, Sybille
name: Langmach, Hartmut
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Inverse problems
subject: direct methods
subject: finite elements
subject: linear boundary value problem
subject: 35R30
subject: 86A05
subject: 76S05
subject: 65N30

description: The paper is devoted to the inverse problem of identifying the coefficient in the main term of a quasilinear elliptic differential equation describing the filtration of groundwater. Experience suggests that the gradient of the piezometric head, i.e., Darcy's velocity, may have discontinuities and the transmissivity coefficient is a piecewise constant function.
 For solving this problem we use a modification of a direct method of G. Vainikko. Starting with a weak formulation of the problem a suitable discretization is obtained by the method of minimal error. If necessary this method can be combined with Tikhonov regularization.
 The main difficulty consists in generating distributed state observations from measurements of the ground-water level. For this step we propose an optimized data preparation procedure using additional information such as knowledge of the sought parameter values at some points and lower and upper bounds for the parameter.
 Numerical tests show that locally sufficiently many measurements provide locally satisfactory results. Two numerical examples, one with simulated data and the other with real life data, are given.