cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage
Creators: name: Gulnik, S.
name: Everitt, L.
name: Pettit, S. C.
name: Kaplan, A. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.
Two-bath spin-boson model: Phase diagram and critical properties
Creators: name: Bruognolo, Benedikt
name: Weichselbaum, Andreas
name: Guo, Cheng
name: von Delft, Jan
name: Schneider, Imke
name: Vojta, Matthias
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The spin-boson model, describing a two-level system coupled to a bath of harmonic oscillators, is a generic model for quantum dissipation, with manifold applications. It has also been studied as a simple example for an impurity quantum phase transition. Here we present a detailed study of a U(1)-symmetric two-bath spin-boson model, where two different components of an SU(2) spin 1/2 are coupled to separate dissipative baths. Non-trivial physics arises from the competition of the two dissipation channels, resulting in a variety of phases and quantum phase transitions. We employ a combination of analytical and numerical techniques to determine the properties of both the stable phases and the quantum critical points. In particular, we find a critical intermediate-coupling phase which is bounded by a continuous quantum phase transition which violates the quantum-to-classical correspondence.
description: 22 pages, 20 figs
Pre- Cryopreservation Umbilical Cord Blood quality: The significance of Gestational age and Birth weight
Creators: name: Fergany, Marim
Publisher: name: figshare
Year: 2022
Subjects: Biotechnology

description: The umbilical cord is a helical and tubular blood vessel that connects the fetus to the placenta. Cord blood was formerly considered a waste substance that should be discarded. According to groundbreaking data from over 130 million yearly global births in the 1980s, umbilical cord blood (UCB) is recognized as the most abundant source of cells and can regenerate in several therapeutic applications. Stem cells are a sort of undifferentiated cell that may reproduce forever (self-renewal), usually begin from a single cell (clonal), and differentiate into many different types of cells and tissues (potent). No other cell in the body can generate new cell types on its own. Stem cells offer a lot of potential for future treatments. The purpose of this research is to determine which parameters, specifically birth weight and gestational age that influence the quality of umbilical cord blood before cryopreservation and know the suitable conditions. This study has 24 participants. UCB was collected immediately post-delivery in the AXP collection bags, followed by flowcytometry assay for counting the nucleated cell and enumeration of the CD34+/CD45+ hematopoietic stem cells in addition to, evaluation of cell viability by 7amino-actinomycin D. Blood plasma isolation was done for maternal blood for determination of hemoglobin and TLC count, quantified using automated hematology analyzer (Sysmex) and finally, Excel were used for data analyses (Statistical analysis). Results: The results showed that there were no significant effects of gestational age and birth weight on the quality, quantity, TLC (pre), and TLC (post) of Umbilical Cord blood before Cryopreservation and the P-Value was more than 0.05. Also, maternal age and Type of delivery have no significant effect. Stem cells are the most important type of cells in Umbilical cord blood. There is no correlation between the gestational age and birth weight and umbilical cord blood quality and quantity. Other factors should be taken under consideration to get the best results.
Three-Dimensional Structures of the A, B, and C Capsids of Rhesus Monkey Rhadinovirus: Insights into Gammaherpesvirus Capsid Assembly, Maturation, and DNA Packaging
Creators: name: O'Connor, C. M.
name: Yu, X.-K.
name: Kedes, D. H.
name: Atanasov, I.
name: Zhou, Z. H.
name: Damania, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Rhesus monkey rhadinovirus (RRV) exhibits high levels of sequence homology to human gammaherpesviruses, such as Kaposi's sarcoma-associated herpesvirus, and grows to high titers in cell cultures, making it a good model system for studying gammaherpesvirus capsid structure and assembly. We have purified RRV A, B, and C capsids, thus for the first time allowing direct structure comparisons by electron cryomicroscopy and three-dimensional reconstruction. The results show that the shells of these capsids are identical and are each composed of 12 pentons, 150 hexons, and 320 triplexes. Structural differences were apparent inside the shells and through the penton channels. The A capsid is empty, and its penton channels are open. The B capsid contains a scaffolding core, and its penton channels are closed. The C capsid contains a DNA genome, which is closely packaged into regularly spaced density shells (25 Å apart), and its penton channels are open. The different statuses of the penton channels suggest a functional role of the channels during capsid maturation, and the overall structural similarities of RRV capsids to alphaherpesvirus capsids suggest a common assembly and maturation pathway. The RRV A capsid reconstruction at a 15-Å resolution, the best achieved for gammaherpesvirus particles, reveals overall structural similarities to alpha- and betaherpesvirus capsids. However, the outer regions of the capsid, including densities attributed to the Ta triplex and the small capsomer-interacting protein (SCIP or ORF65), exhibit prominent differences from their structural counterparts in alphaherpesviruses. This structural disparity suggests that SCIP and the triplex, together with tegument and envelope proteins, confer structural and potentially functional specificities to alpha-, beta-, and gammaherpesviruses.
Turnover of env Variable Region 1 and 2 Genotypes in Subjects with Late-Stage Human Immunodeficiency Virus Type 1 Infection
Creators: name: Nelson, J. A. E.
name: Kitrinos, K. M.
name: Swanstrom, R.
name: Hoffman, N. G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The env gene of human immunodeficiency virus type 1 (HIV-1) includes some of the most genetically diverse regions of the viral genome, which are called variable regions 1 through 5 (V1 through V5). We have developed a heteroduplex tracking assay to detect changes in variable regions 1 and 2 of env (V1/V2-HTA). Using sequences from two molecular clones as probes, we have studied the nature of longitudinal virus population changes in a cohort of HIV-1-infected subjects. Viral sequences present in 21 subjects with late-stage HIV-1 infection were initially screened for stability of the virus population by V1/V2-HTA. The virus populations at entry comprised an average of five coexisting V1/V2 genotypic variants (as identified by HTA). Eight of the 21 subjects were examined in detail because of the dynamic behavior of their env variants over an approximately 9-month period. In each of these cases we detected a single discrete transition of V1/V2 genotypes based on monthly sampling. The major V1/V2 genotypes (those present at >10% abundance) from the eight subjects were cloned and sequenced to define the nature of V1/V2 variability associated with a discrete transition. Based on a comparison of V1/V2 genotypic variants present at entry with the newly emerged variants we categorized the newly emerged variants into two groups: variants without length differences and variants with length differences. Variants without length differences had fewer nucleotide substitutions, with the changes biased to either V1 or V2, suggestive of recent evolutionary events. Variants with length differences included ones with larger numbers of changes that were distributed, suggestive of recall of older genotypes. Most length differences were located in domains where the codon motif AVT (V = A, G, C) had become enriched and fixed. Finally, recombination events were detected in two subjects, one of which resulted in the reassortment of V1 and V2 regions. We suggest that turnover in V1/V2 populations was largely driven by selection on either V1 or V2 and that escape was accomplished either through changes focused in the region under selection or by the appearance of a highly divergent variant.
Semarkona: Lessons for chondrule and chondrite formation
Creators: name: Hubbard, Alexander
name: Ebel, Denton S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We consider the evidence presented by the LL3.0 chondrite Semarkona, including its chondrule fraction, chondrule size distribution and matrix thermal history. We show that no more than a modest fraction of the ambient matrix material in the Solar Nebula could have been melted into chondrules; and that much of the unprocessed matrix material must have been filtered out at some stage of Semarkona's parent body formation process. We conclude that agglomerations of many chondrules must have formed in the Solar Nebula, which implies that chondrules and matrix grains had quite different collisional sticking parameters. Further, we note that the absence of large melted objects in Semarkona means that chondrules must have exited the melting zone rapidly, before the chondrule agglomerations could form. The simplest explanation for this rapid exit is that chondrule melting occurred in surface layers of the disk. The newly formed, compact, chondrules then settled out of those layers on short time scales.
description: 9 pages, 3 figures, accepted, Icarus
Accumulation of Cytoplasmic  -Catenin and Nuclear Glycogen Synthase Kinase 3  in Epstein-Barr Virus-Infected Cells
Creators: name: Everly, D. N.
name: Raab-Traub, N.
name: Kusano, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with cancers in immunocompromised populations. EBV establishes a latent infection and immortalizes and transforms B lymphocytes. Several latent proteins have profound effects on cellular growth, including activation of NF-κB, phosphatidylinositol 3′-OH kinase (PI3K) signaling, and notch signaling. Activation of PI3K can affect the activity of β-catenin, the target of the wnt signaling pathway. Deregulation of β-catenin is associated with a number of malignancies. To determine if β-catenin is regulated by EBV infection, EBV-infected cells were examined for β-catenin levels and localization. β-Catenin was increased in EBV-positive tumor cell lines compared to EBV-negative lines, in EBV-infected Burkitt's lymphoma cell lines, and in EBV-transformed lymphoblastoid cell lines (LCL). In contrast to wnt signaling, EBV consistently induced the accumulation of β-catenin in the cytoplasm but not the nucleus. The β-catenin regulating kinase, glycogen synthase kinase 3β (GSK3β), was shown to be phosphorylated and inactivated in EBV-infected lymphocytes. Inactivated GSK3β was localized to the nucleus of EBV-infected LCL. Neither the cytoplasmic accumulation of β-catenin nor the nuclear inactivation of GSK3β was affected by the inhibition of PI3K signaling. These data indicate that latent infection with EBV has unique effects on β-catenin signaling that are distinct from activation of wnt and independent of its effects on PI3K.
Cleavage between Replicase Proteins p28 and p65 of Mouse Hepatitis Virus Is Not Required for Virus Replication
Creators: name: Graham, R. L.
name: Brockway, S. M.
name: Baric, R. S.
name: Yount, B.
name: Sims, A. C.
name: Denison, M. R.
name: Lu, X.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The p28 and p65 proteins of mouse hepatitis virus (MHV) are the most amino-terminal protein domains of the replicase polyprotein. Cleavage between p28 and p65 has been shown to occur in vitro at cleavage site 1 (CS1), 247Gly↓Val248, in the polyprotein. Although critical residues for CS1 cleavage have been mapped in vitro, the requirements for cleavage have not been studied in infected cells. To define the determinants of CS1 cleavage and the role of processing at this site during MHV replication, mutations and deletions were engineered in the replicase polyprotein at CS1. Mutations predicted to allow cleavage at CS1 yielded viable virus that grew to wild-type MHV titers and showed normal expression and processing of p28 and p65. Mutant viruses containing predicted noncleaving mutations or a CS1 deletion were also viable but demonstrated delayed growth kinetics, reduced peak titers, decreased RNA synthesis, and small plaques compared to wild-type controls. No p28 or p65 was detected in cells infected with predicted noncleaving CS1 mutants or the CS1 deletion mutant; however, a new protein of 93 kDa was detected. All introduced mutations and the deletion were retained during repeated virus passages in culture, and no phenotypic reversion was observed. The results of this study demonstrate that cleavage between p28 and p65 at CS1 is not required for MHV replication. However, proteolytic separation of p28 from p65 is necessary for optimal RNA synthesis and virus growth, suggesting important roles for these proteins in the formation or function of viral replication complexes.
Comparison of the Rta/Orf50 Transactivator Proteins of Gamma-2-Herpesviruses
Creators: name: Bowser, B. S.
name: Dittmer, D. P.
name: Jeong, J. H.
name: Staudt, M. R.
name: DeWire, S. M.
name: Damania, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The viral immediate-early transactivator Rta/Orf50 is necessary and sufficient to initiate Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV/HHV-8) reactivation from latently infected cells. Since Rta/Orf50 is conserved among all known gamma-2-herpesviruses, we investigated whether the murine gamma-68-herpesvirus (MHV-68) and rhesus monkey rhadinovirus (RRV) homologs can functionally substitute for KSHV Rta/Orf50. (i) Our comparison of 12 KSHV promoters showed that most responded to all three Rta/Orf50proteins, but three promoters (vGPCR, K8, and gB) responded only to the KSHV Rta/Orf50 transactivator. Overall, the activation of KSHV promoters was higher with KSHV Rta than with the RRV and MHV-68 Rta. (ii) Only the primate Rta/Orf50 homologs were able to interfere with human p53-depedent transcriptional activation. (iii) Transcriptional profiling showed that the KSHV Rta/Orf50 was more efficient than it's homologs in inducing KSHV lytic transcription from the latent state. These results suggest that the core functionality of Rta/Orf50 is conserved and independent of its host, but the human protein has evolved additional, human-specific capabilities.
Phase control of squeezing in fluorescence radiation
Creators: name: Arun, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study squeezing properties of the fluorescence radiation emitted by a driven $Λ$-type atom in which the metastable lower energy levels are coupled by an additional field. We find that the relative phase of the applied fields can significantly modify the squeezing characteristics of radiation. It is shown that the additional field connecting the lower levels in the system can induce spectral squeezing in a parameter regime for which the squeezing is absent without the additional field. Moreover, the squeezing can be shifted from inner- to outer-sidebands of the spectrum by simply changing the relative phase. A dressed-state description is presented to explain these numerical results. The phase control of squeezing in the total variance of quadrature components is also examined. We show that the squeezing in total variance attains its maximal value when the system reduces to an effective two-level system.
description: 7 pages, 5 figures
Duhumbi Lexicon - Inherited Nouns
Creators: name: Bodt, Timotheus Adrianus
Publisher: name: Zenodo
Year: 2018
Subjects: Duhumbi
Proto-Western Kho-Bwa
noun prefixes
lexical-semantic categories
borrowing
linguistic reconstruction
Chug
Arunachal Pradesh

description: This file presents the preliminary analysis of the Duhumbi noun prefixes and the native Duhumbi nouns. As the reconstruction of Proto-Western Kho-Bwa is ongoing, these reconstructed roots may change. The final reconstructions will be presented in a future paper or monograph. This material is made freely available to everyone for informative or scientific purposes as long as the source (this DOI) / the collectors are properly credited. Please note that use of the material for commercial purposes of any kind, which includes conversion into commercial audio-visual media (documentaries etc.), storage and dissemination through sites that require registration & payment for access, or sites that rely on advertisement (including YouTube) is not permitted without specific written consent from the speakers and their community, obtained through the collectors of the material. By downloading our material, you agree to these restrictions. This data set falls under the Attribution-NonCommercial-ShareAlike (CC BY-NC-SA) license. This license lets you remix, tweak, and build upon this work non-commercially, as long as you credit us and license your new creations under the identical terms. License Deed on https://creativecommons.org/licenses/by-nc-sa/4.0/. Legal Code on https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode. Tim Bodt: bodttim (at) gmail (dot) com
Pre- Cryopreservation Umbilical Cord Blood quality: The significance of Gestational age and Birth weight
Creators: name: Fergany, Marim
name: Seif, Alyaa
name: Mostafa, Haidan
Publisher: name: figshare
Year: 2022
Subjects: Biotechnology

description: The umbilical cord is a helical and tubular blood vessel that connects the fetus to the placenta. Cord blood was formerly considered a waste substance that should be discarded. According to groundbreaking data from over 130 million yearly global births in the 1980s, umbilical cord blood (UCB) is recognized as the most abundant source of cells and can regenerate in several therapeutic applications. Stem cells are a sort of undifferentiated cell that may reproduce forever (self-renewal), usually begin from a single cell (clonal), and differentiate into many different types of cells and tissues (potent). No other cell in the body can generate new cell types on its own. Stem cells offer a lot of potential for future treatments. The purpose of this research is to determine which parameters, specifically birth weight and gestational age that influence the quality of umbilical cord blood before cryopreservation and know the suitable conditions. This study has 24 participants. UCB was collected immediately post-delivery in the AXP collection bags, followed by flowcytometry assay for counting the nucleated cell and enumeration of the CD34+/CD45+ hematopoietic stem cells in addition to, evaluation of cell viability by 7amino-actinomycin D. Blood plasma isolation was done for maternal blood for determination of hemoglobin and TLC count, quantified using automated hematology analyzer (Sysmex) and finally, Excel were used for data analyses (Statistical analysis). Results: The results showed that there were no significant effects of gestational age and birth weight on the quality, quantity, TLC (pre), and TLC (post) of Umbilical Cord blood before Cryopreservation and the P-Value was more than 0.05. Also, maternal age and Type of delivery have no significant effect. Stem cells are the most important type of cells in Umbilical cord blood. There is no correlation between the gestational age and birth weight and umbilical cord blood quality and quantity. Other factors should be taken under consideration to get the best results.
Correlation between env V1/V2 Region Diversification and Neutralizing Antibodies during Primary Infection by Simian Immunodeficiency Virus sm in Rhesus Macaques
Creators: name: Rybarczyk, B. J.
name: Johnston, R. E.
name: West, A.
name: Montefiori, D.
name: Johnson, P. R.
name: Swanstrom, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Evolution of the domain encoding the V1/V2 variable region of the simian immunodeficiency virus sm (SIVsm) envelope (env) gene was analyzed in relation to route of virus challenge, virus load, and neutralizing antibody (NAb) titers during primary infection of rhesus macaques with the pathogenic SIVsmE660 isolate. In this model system animals are initially infected with multiple viruses as evidenced by the presence of multiple V1/V2 genotypic variants that could be resolved by using a heteroduplex tracking assay (HTA). Overlapping subsets of the multiple variants were established in each animal. There was no selection for the establishment of specific variants in comparing intravenous- and intrarectal-challenged macaques at week 2 postinfection, suggesting that no genotypic selection occurred at the mucosal surface. There was an initial period of significant stability of the V1/V2 variants. Macaques challenged intravenously displayed subsequent V1/V2 diversification significantly earlier than macaques challenged intrarectally and well past the initial resolution of viremia. The time when SIVsmE660-specific NAbs reached a threshold titer of 100 was significantly correlated with the timing of V1/V2 diversification, even though antibodies to the Env protein could be detected much earlier. The time when NAbs reached a titer of 400 was significantly correlated with virus load late in infection. These results show that the route of infection affects the timing of V1/V2 diversification and that this diversification is correlated with the maturation of a specific NAb response. However, prior immunization capable of priming an anamnestic Env antibody response did not accelerate V1/V2 diversification. This result suggests that diversification of the SIV env V1/V2 region is the result of a type-specific antibody response.
Pre- Cryopreservation Umbilical Cord Blood quality: The significance of Gestational age and Birth weight
Creators: name: Fergany, Marim
name: Seif, Alyaa
Publisher: name: figshare
Year: 2022
Subjects: Biotechnology

description: The umbilical cord is a helical and tubular blood vessel that connects the fetus to the placenta. Cord blood was formerly considered a waste substance that should be discarded. According to groundbreaking data from over 130 million yearly global births in the 1980s, umbilical cord blood (UCB) is recognized as the most abundant source of cells and can regenerate in several therapeutic applications. Stem cells are a sort of undifferentiated cell that may reproduce forever (self-renewal), usually begin from a single cell (clonal), and differentiate into many different types of cells and tissues (potent). No other cell in the body can generate new cell types on its own. Stem cells offer a lot of potential for future treatments. The purpose of this research is to determine which parameters, specifically birth weight and gestational age that influence the quality of umbilical cord blood before cryopreservation and know the suitable conditions. This study has 24 participants. UCB was collected immediately post-delivery in the AXP collection bags, followed by flowcytometry assay for counting the nucleated cell and enumeration of the CD34+/CD45+ hematopoietic stem cells in addition to, evaluation of cell viability by 7amino-actinomycin D. Blood plasma isolation was done for maternal blood for determination of hemoglobin and TLC count, quantified using automated hematology analyzer (Sysmex) and finally, Excel were used for data analyses (Statistical analysis). Results: The results showed that there were no significant effects of gestational age and birth weight on the quality, quantity, TLC (pre), and TLC (post) of Umbilical Cord blood before Cryopreservation and the P-Value was more than 0.05. Also, maternal age and Type of delivery have no significant effect. Stem cells are the most important type of cells in Umbilical cord blood. There is no correlation between the gestational age and birth weight and umbilical cord blood quality and quantity. Other factors should be taken under consideration to get the best results.
Black hole solutions in Chern-Simons AdS supergravity
Creators: name: Giribet, Gaston
name: Merino, Nelson
name: Miskovic, Olivera
name: Zanelli, Jorge
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study charged AdS black hole solutions in five-dimensional Chern-Simons supergravity. The minimal supergroup containing such AdSxU(1) configurations is the superunitary group SU(2,2|N). For this model, we find analytic black hole solutions that asymptote to locally AdS spacetime at the boundary. A solution can carry U(1) charge provided the spacetime torsion is non-vanishing. Thus, we analyze the most general configuration consistent with the local AdS isometries in Riemann-Cartan space. The coupling of torsion in the action resembles that of the universal axion of string theory, and it is ultimately due to this field that the theory acquires propagating degrees of freedom. Through a careful analysis of the canonical structure the local degrees of freedom of the theory are identified in the static symmetric sector of phase space.
description: 45 pages, no figures
Cross-Dressing the Virion: the Transcapsidation of Adeno-Associated Virus Serotypes Functionally Defines Subgroups
Creators: name: Cunningham, S. E.
name: Bowles, D. E.
name: Samulski, R. J.
name: Ledford, J. G.
name: Rabinowitz, J. E.
name: Faust, S. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: For all adeno-associated virus (AAV) serotypes, 60 monomers of the Vp1, Vp2, and Vp3 structural proteins assemble via an unknown mechanism to form an intact capsid. In an effort to better understand the properties of the capsid monomers and their role in viral entry and infection, we evaluated whether monomers from distinct serotypes can be mixed to form infectious particles with unique phenotypes. This transcapsidation approach consisted of the transfection of pairwise combinations of AAV serotype 1 to 5 helper plasmids to produce mosaic capsid recombinant AAV (rAAV). All ratios (19:1, 3:1, 1:1, 1:3, and 1:19) of these mixtures were able to replicate the green fluorescent protein transgene and to produce capsid proteins. A high-titer rAAV was obtained with mixtures that included either serotype 1, 2, or 3, whereas an rAAV of intermediate titer was obtained from serotype 5 mixtures. Only mixtures containing the AAV4 capsid exhibited reduced packaging capacity. The binding profiles of the mixed-virus preparations to either heparin sulfate (HS) or mucin agarose revealed that only AAV3-AAV5 mixtures at the 3:1 ratio exhibited duality in binding. All other mixtures displayed either an abrupt shift or a gradual alteration in the binding profile to the respective ligand upon increase of a capsid component that conferred either HS or mucin binding. The transduction of cell lines was used to further evaluate the phenotypes of these transcapsidated virions. Three transduction profiles were observed: (i) small to no change regardless of ratio, (ii) a gradual increase in transduction consistent with titration of a second capsid component, or (iii) an abrupt increase in transduction (threshold effect) dependent on the specific ratios used. Interestingly, an unexpected synergistic effect in transduction was observed when AAV1 helper constructs were combined with type 2 or type 3 recipient helpers. Further studies determined that at least two components contributed to this observed synergy: (i) heparin-mediated binding from AAV2 and (ii) an unidentified enhancement activity from AAV1 structural proteins. Using this procedure of mixing different AAV helper plasmids to generate “cross-dressed” AAV virions, we propose an additional means of classifying new AAV serotypes into subgroups based on functional approaches to analyze AAV capsid assembly, receptor-mediated binding, and virus trafficking. Exploitation of this approach in generating custom-designed AAV vectors should be of significant value to the field of gene therapy.
Biverbal constructions and related comparative concepts: (Retro-)definitions vs. analyses
Creators: name: Haspelmath, Martin
Publisher: name: Zenodo
Year: 2022

description: This is the presentation handout for a talk at a conference on complex predicates, JGU Mainz, 2022 November 14-16: https://www.linguistik.fb05.uni-mainz.de/conference-typology-of-complex-predicates/conference-schedule/
Efficient Replication by Herpes Simplex Virus Type 1 Involves Activation of the I B Kinase-I B-p65 Pathway
Creators: name: Holmes, D.
name: Hargett, D.
name: Bachenheimer, S. L.
name: Money, E.
name: Gregory, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Infection by herpes simplex virus type 1 (HSV-1) induces a persistent nuclear translocation of NFκB. To identify upstream effectors of NFκB and their effect on virus replication, we employed mouse embryo fibroblast (MEF)-derived cell lines with deletions of either IKK1 or IKK2, the catalytic subunits of the IκB kinase (IKK) complex. Infected MEFs were assayed for virus yield, loss of IκBα, nuclear translocation of p65, and NFκB DNA-binding activity. Absence of either IKK1 or IKK2 resulted in an 86 to 94% loss of virus yield compared to that of normal MEFs, little or no loss of IκBα, and greatly reduced NFκB nuclear translocation. Consistent with reduced virus yield, accumulation of the late proteins VP16 and gC was severely depressed. Infection of normal MEFs, Hep2, or A549 cells with an adenovirus vector expressing a dominant-negative (DN) IκBα, followed by superinfection with HSV, resulted in a 98% drop in virus yield. These results indicate that the IKK-IκB-p65 pathway activates NFκB after virus infection. Analysis of NFκB activation and virus replication in control and double-stranded RNA-activated protein kinase-null MEFs indicated that this kinase plays no role in the NFκB activation pathway. Finally, in cells where NFκB was blocked because of DNIκB expression, HSV failed to suppress two markers of apoptosis, cell surface Annexin V staining and PARP cleavage. These results support a model in which activation of NFκB promotes efficient replication by HSV, at least in part by suppressing a host innate response to virus infection.
Evolution of the Fermi surface of arsenic through the rhombohedral to simple-cubic phase transition: a Wannier interpolation study
Creators: name: Silas, Patricia K.
name: Haynes, Peter D.
name: Yates, Jonathan R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The pressure dependence of the Fermi surface of arsenic is examined using the technique of Wannier interpolation, enabling a dense sampling of the Brillouin zone and the ability to capture fine features within it. Focusing primarily on the A7 to simple-cubic phase transition, we find that this semimetal to metal transition is accompanied by the folding of Fermi surfaces. The pressure dependence of the density of states (DOS) of arsenic indicates that the onset of the Peierls-type cubic to rhombohedral distortion is signified by the appearance of emerging van Hove singularities in the DOS, especially around the Fermi level. As we noted in an earlier study, high levels of convergence are consequently required for an accurate description of this transition.
description: 19 pages, 21 figures, 16 animated gif files
Epstein-Barr Virus Immediate-Early Protein BZLF1 Inhibits Tumor Necrosis Factor Alpha-Induced Signaling and Apoptosis by Downregulating Tumor Necrosis Factor Receptor 1
Creators: name: Mauser, A.
name: Klingelhutz, A.
name: Morrison, T. E.
name: Kenney, S. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Tumor necrosis factor alpha (TNF-α) is a key mediator of host immune and inflammatory responses and inhibits herpesvirus replication by cytolytic and noncytolytic mechanisms. TNF-α effects are primarily mediated through the major TNF-α receptor, TNF-R1, which is constitutively expressed in most cell types. Here we show that the Epstein-Barr virus (EBV) immediate-early protein BZLF1 prevents TNF-α activation of target genes and TNF-α-induced cell death. These effects are mediated by down-regulation of the promoter for TNF-R1. Additionally, we demonstrate that expression of TNF-R1 is downregulated during the EBV lytic replication cycle. Thus, EBV has developed a novel mechanism for evading TNF-α antiviral effects during lytic reactivation or primary infection.
Screening and Purification of Methionase Enzyme from Soil Fung
Creators: name: Fergany, Marim
name: balbool, Bassem
name: El-Henfy, Ingy
Publisher: name: figshare
Year: 2022
Subjects: subject: 60107 Enzymes
subject: FOS: Biological sciences
subject: Biotechnology

description: Fungi are valuable to humans, whether directly or indirectly. Fungi have different applications in medical, pharmaceutical, agricultural and industrial applications. Many different fungal species are utilized in the industrial synthesis of enzymes. In addition, one of the important enzymes that fungi produce is methionase. Methylation of DNA, polyamine synthesis, and protein production are all dependent on methionine. Methionine restriction is a common strategy for controlling cancer metabolism, since malignancies rely on it for survival and proliferation. In fruit flies, such restriction results in significant lifetime extension and also there are other applications for Methionase enzyme in real life. The aim of this research is to screen the ability of soil fungi to produce methionase and to purify methionase from it. To achieve this purpose, the following summarized steps will be carried out; qualitative screening of 20 soil fungi to produce methionase by using Methionine-glucose medium and phenol red as an indecator, fermentation of the selected isolate to produce methionase in a large scale, followed with purification of methionase using different chromatographic techniques. The research found that after screening the best one of the 20 fungi was Trichoderma viride. After that the production of methionase enzyme done in two types of media the first type is sold state media and the second type is submerged fermentation, the activity on sold state was 1077.23± 906.106 and the activity on submerged fermentation was 70.14 ± 0.003. The purification of the methionase enzyme was done and the estimated molecular weight is around 48kDa.
La ceramica arcaica dai contesti di Poseidonia. Produzioni, tipologie e funzioni
Creators: name: Citera, Emanuela
Publisher: name: Universita degli studi di Salerno
Year: 2012
Subjects: subject: L-ANT/07 ARCHEOLOGIA CLASSICA
subject: Poseidonia
subject: Ceramica arcaica

description: 2010 - 2011
description: Poseidonia-­‐Paestum, per l’intensa attività di ricerca svolta dalla Soprintendenza archeologica in collaborazione con Istituiti e Università italiane e straniere, è una delle colonie della Magna Grecia meglio conosciute grazie ai numerosi studi incentrati su vari aspetti della città, dall’impianto urbanistico all’organizzazione della chora, alle aree sacre, all’ideologia funeraria, alle pitture funerarie e alle emissioni monetali. Oggetto della ricerca è stato lo studio della ceramica databile fra gli inizi del VI e la metà del V sec. a.C al fine di offrirne un’analisi sistematica, finalizzata a fissare produzioni, sequenze tipologiche orientate cronologicamente, comprendere e definire forme e modi della specificità culturale di Poseidonia attraverso l’analisi dei contesti funerari e le testimonianze mobili provenienti dai santuari e dai livelli urbani. La ricerca ha avuto inizio con la messa in sistema di tutti i dati editi, il cui censimento ha consentito di delineare un primo quadro delle ceramiche di età arcaica, a cui sono stati aggiunti gli elementi ricavati dall’analisi autoptica di alcuni contesti significativi, che hanno permesso non solo di ampliare lo stato delle conoscenze, ma di puntualizzare morfologie e cronologie degli oggetti al fine di disporre di una serrata griglia cronologica di riferimento. L’analisi filologica delle forme ceramiche attestate per ogni classe, è stata affrontata separatamente per le importazioni e le produzioni locali; per queste ultime la tipologia utilizzata è stata basata su un sistema aperto, organizzato in senso gerarchico, dal generale al particolare, in cui i diversi livelli di approfondimento sono indicati da codici alfabetici e numerici. I dati sono stati organizzati e commentati in base ad una sequenza cronologica delle classi e delle forme, volta a presentare un quadro complessivo degli elementi esaminati e documentati per l’orizzonte cronologico compreso tra la fondazione della città e la metà del V sec. a.C.; infine grazie alla messa in sistema dei dati disponibili, è stato delineato il quadro delle funzioni delle principali forme ceramiche nei contesti di rinvenimento, prevalentemente necropoli e santuari. [a cura dell'Autore]
Expression and Localization of the Epstein-Barr Virus-Encoded Protein Kinase
Creators: name: Gershburg, E.
name: Hong, K.
name: Marschall, M.
name: Pagano, J. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The protein kinase (PK) encoded by the Epstein-Barr Virus (EBV) BGLF4 gene is the only EBV protein kinase. The expression pattern of EBV PK during the reactivation of the viral lytic cycle and the subcellular localization of the protein were analyzed with a polyclonal antiserum raised against a peptide corresponding to the N terminus of EBV PK. Based on previously published data (E. Gershburg and J. S. Pagano, J. Virol. 76:998-1003, 2002) and the expression pattern described here, we conclude that EBV PK is an early protein that requires viral-DNA replication for maximum expression. By biochemical fractionation, the protein could be detected mainly in the nuclear fraction 4 h after viral reactivation in Akata cells. Nuclear localization could be visualized by indirect immunofluorescence in HeLa cells transiently expressing EBV BGLF4 in the absence of other viral products. Transient expression of 3′-terminal deletion mutants of EBV BGLF4 resulted in cytoplasmic localization, confirming the presence of a nuclear localization site in the C-terminal region of the protein. In contrast to the wild-type EBV PK, all of the mutants were unable to hyperphosphorylate EA-D during coexpression or to phosphorylate ganciclovir, as measured by an in-cell activity assay. Thus, the results demonstrate that the nuclear localization, as well as the kinase activity, of BGFL4 is dependent on an intact C-terminal region.
Solving Bethe-Salpeter scattering state equation in Minkowski space
Creators: name: Carbonell, J.
name: Karmanov, V. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present a method to directly solving the Bethe-Salpeter equation in Minkowski space, both for bound and scattering states. It is based on a proper treatment of the singularities which appear in the kernel, propagators and Bethe-Salpeter amplitude itself. The off-mass shell scattering amplitude for spinless particles interacting by a one boson exchange is computed for the first time.
description: 24 pages, 12 figures, to be published in Phys. Rev. D
Heterostructured HfO2/TiO2 spherical nanoparticles for visible photocatalytic water remediation
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: 30101 Analytical Spectrometry
subject: FOS: Chemical sciences
subject: 30402 Biomolecular Modelling and Design
subject: 30301 Chemical Characterisation of Materials
subject: 30403 Characterisation of Biological Macromolecules
subject: 30401 Biologically Active Molecules

description: Photocatalytic activity of low band gap hydrogenated HfO2 doped TiO2 (H-HfO2/TiO2), HfO2 doped TiO2 (HfO2/TiO2) and TiO2 (pristine) were investigated by photocatalytic degradation of five different indus?trial dyes. The current study envisages the effect of doping hydrogen and HfO2 up on TiO2 for photocat?alytic degradation of different chemically structured dyes. Methylene Blue attains fast degradation efficiency of 90%, within 10 min of the reaction due to high photocatalytic adsorption and degradation over the rough TiO2 surface. Effect of pH on dye degradation is observed, leading to disintegration and mineralization.
Screening and Purification of Methionase Enzyme from Soil Fung
Creators: name: Fergany, Marim
name: balbool, Bassem
Publisher: name: figshare
Year: 2022
Subjects: subject: 60107 Enzymes
subject: FOS: Biological sciences
subject: Biotechnology

description: Fungi are valuable to humans, whether directly or indirectly. Fungi have different applications in medical, pharmaceutical, agricultural and industrial applications. Many different fungal species are utilized in the industrial synthesis of enzymes. In addition, one of the important enzymes that fungi produce is methionase. Methylation of DNA, polyamine synthesis, and protein production are all dependent on methionine. Methionine restriction is a common strategy for controlling cancer metabolism, since malignancies rely on it for survival and proliferation. In fruit flies, such restriction results in significant lifetime extension and also there are other applications for Methionase enzyme in real life. The aim of this research is to screen the ability of soil fungi to produce methionase and to purify methionase from it. To achieve this purpose, the following summarized steps will be carried out; qualitative screening of 20 soil fungi to produce methionase by using Methionine-glucose medium and phenol red as an indecator, fermentation of the selected isolate to produce methionase in a large scale, followed with purification of methionase using different chromatographic techniques. The research found that after screening the best one of the 20 fungi was Trichoderma viride. After that the production of methionase enzyme done in two types of media the first type is sold state media and the second type is submerged fermentation, the activity on sold state was 1077.23± 906.106 and the activity on submerged fermentation was 70.14 ± 0.003. The purification of the methionase enzyme was done and the estimated molecular weight is around 48kDa.
Fatty Acid Synthase Expression Is Induced by the Epstein-Barr Virus Immediate-Early Protein BRLF1 and Is Required for Lytic Viral Gene Expression
Creators: name: Webster-Cyriaque, J.
name: Kenney, S.
name: Yohe, M.
name: Li, Y.
name: Tomlinson, C. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The Epstein-Barr virus (EBV) immediate-early (IE) protein BRLF1 (R) is a transcription factor that induces the lytic form of EBV infection. R activates certain early viral promoters through a direct binding mechanism but induces transcription of the other EBV IE gene, BZLF1 (Z), indirectly through cellular factors binding to a CRE motif in the Z promoter (Zp). Here we demonstrate that R activates expression of the fatty acid synthase (FAS) cellular gene through a p38 stress mitogen-activated protein kinase-dependent mechanism. B-cell receptor engagement of Akata cells also increases FAS expression. The FAS gene product is required for de novo synthesis of the palmitate fatty acid, and high-level FAS expression is normally limited to liver, brain, lung, and adipose tissue. We show that human epithelial tongue cells lytically infected with EBV (from oral hairy leukoplakia lesions) express much more FAS than uninfected cells. Two specific FAS inhibitors, cerulenin and C75, prevent R activation of IE (Z) and early (BMRF1) lytic EBV proteins in Jijoye cells. In addition, cerulenin and C75 dramatically attenuate IE and early lytic gene expression after B-cell receptor engagement in Akata cells and constitutive lytic viral gene expression in EBV-positive AGS cells. However, FAS inhibitors do not reduce lytic viral gene expression induced by a vector in which the Z gene product is driven by a strong heterologous promoter. In addition, FAS inhibitors do not reduce R activation of a naked DNA reporter gene construct driven by the Z promoter (Zp). These results suggest that cellular FAS activity is important for induction of Z transcription from the intact latent EBV genome, perhaps reflecting the involvement of lipid-derived signaling pathways or palmitoylated proteins. Furthermore, using FAS inhibitors may be a completely novel approach for blocking the lytic form of EBV replication.