cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A low HI column density filament in NGC 2403: signature of interaction or accretion
Creators: name: de Blok, W. J. G.
name: Keating, Katie M.
name: Pisano, D. J.
name: Fraternali, F.
name: Walter, F.
name: Oosterloo, T.
name: Brinks, E.
name: Bigiel, F.
name: Leroy, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Observed HI accretion around nearby galaxies can only account for a fraction of the gas supply needed to sustain the currently observed star formation rates. It is possible that additional accretion happens in the form of low column density cold flows, as predicted by numerical simulations of galaxy formation. To contrain the presence and properties of such flows, we present deep HI observations obtained with the NRAO Green Bank Telescope of an area measuring 4 by 4 degrees around NGC 2403. These observations, with a 5 sigma detection limit of 2.4 x 10^18 cm^-2 over a 20 km/s linewidth, reveal the presence of a low-column density, extended cloud outside the main HI disk, about 17' (~16 kpc or ~2R25) to the NW of the center of the galaxy. The total HI mass of the cloud is 6.3 x 10^6 Msun, or 0.15 percent of the total HI mass of NGC 2403. The cloud is associated with an 8-kpc anomalous-velocity HI filament in the inner disk, previously observed in deep VLA observations by Fraternali et al. (2001, 2002). We discuss several scenarios for the origin of the cloud, and conclude that it is either accreting from the intergalactic medium, or is the result of a minor interaction with a neigbouring dwarf galaxy.
description: Accepted for publication in Astronomy & Astrophysics
Additional file 5 of Effect of lunch with different calorie and nutrient balances on dinner-induced postprandial glucose variability
Creators: name: Kuwahara, Mai
name: Kim, Hyeon-Ki
name: Furutani, Akiko
name: Mineshita, Yui
name: Nakaoka, Takashi
name: Shibata, Shigenobu
Publisher: name: figshare
Year: 2022
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 5. Fig. S5: Association between lunch energy intake during daily life and after-dinner blood glucose levels in the balance trial. Relationship between percentage of protein during daily life for lunch and iAUC for 2 h after dinner in the protein-rich trial (A). Relationship between the percentage of fat during daily life for lunch and iAUC for 2 h after dinner in the fat-rich trial (B). Relationship between percentage of carbohydrates during daily life for lunch and iAUC for 2 h after dinner in the carbohydrate-rich trial (C). Relationship between percentage of protein (D), fat (E), and carbohydrate (F) during daily life for lunch and peak blood glucose levels after dinner in the standard trial.
Cellular recombination pathways and viral terminal repeat hairpin structures are sufficient for adeno-associated virus integration in vivo and in vitro.
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: 1997

description: The human parvovirus adeno-associated virus (AAV) is unique in its ability to target viral integration to a specific site on chromosome 19 (ch-19). Recombinant AAV (rAAV) vectors retain the ability to integrate but have apparently lost this ability to target. In this report, we characterize the terminal-repeat-mediated integration for wild-type (wt), rAAV, and in vitro systems to gain a better understanding of these differences. Cell lines latent for either wt or rAAV were characterized by a variety of techniques, including PCR, Southern hybridization, and fluorescence in situ hybridization analysis. More than 40 AAV-rAAV integration junctions were cloned, sequenced, and then subjected to comparison and analysis. In both immortalized and normal diploid human cells, wt AAV targeted integration to ch-19. Integrated provirus structures consisted of head-to-tail tandem arrays with the majority of the junction sequences involving the AAV inverted terminal repeats (ITRs). No complete viral ITRs were directly observed. In some examples, the AAV p5 promoter sequence was found to be fused at the virus-cell junction. Data from dot blot analysis of PCR products were consistent with the occurrence of inversions of genomic and/or viral DNA sequences at the wt integration site. Unlike wt provirus junctions, rAAV provirus junctions mapped to a subset of non-ch-19 sequences. Southern analysis supported the integration of proviruses from two independent cell lines at the same locus on ch-2. In addition, provirus terminal repeat sequences existed in both the flip and flop orientations, with microhomology evident at the junctions. In all cases with the exception of the ITRs, the vector integrated intact. rAAV junction sequence data were consistent with the occurrence of genomic rearrangement by deletion and/or rearrangement-translocation at the integration locus. Finally, junctions formed in an in vitro system between several AAV substrates and the ch-19 target site were isolated and characterized. Linear AAV substrates typically utilized the end of the virus DNA substrate as the point of integration, whereas products derived from AAV terminal repeat hairpin structures in the presence or absence of Rep protein resembled AAV-ch-19 junctions generated in vivo. These results describing wt AAV, rAAV, and in vitro integration junctions suggest that the viral integration event itself is mediated by terminal repeat hairpin structures via nonviral cellular recombination pathways, with specificity for ch-19 in vivo requiring additional viral components. These studies should have an important impact on the use of rAAV vectors in human gene therapy.
Cross-clade human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte responses in HIV-infected Zambians.
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: 1997

description: We have examined cross-clade HIV-specific cytotoxic T-lymphocyte (CTL) activity in peripheral blood of eight Zambian individuals infected with non-B-clade human immunodeficiency virus type 1 (HIV-1). Heteroduplex mobility assay and partial sequence analysis of env and gag genes strongly suggests that all the HIV-infected subjects were infected with clade C HIV-1. Six of eight C-clade HIV-infected individuals elicited CTL activity specific for recombinant vaccinia virus-infected autologous targets expressing HIV gag-pol-env derived from B-clade HIV-1 (IIIB). Recognition of individual recombinant HIV-1 B-clade vaccinia virus-infected targets expressing gag, pol, or env was variable among the patients tested, indicating that cross-clade CTL activity is not limited to a single HIV protein. These data demonstrate that HIV clade C-infected individuals can mount vigorous HIV clade B-reactive CTL responses.
Giovani e gioventù tra ‘forma’ e ‘omologazione’: Gombrowicz e Pasolini intorno al ’68
Creators: name: Marinelli, Luigi
Publisher: name: Universita' degli Studi di Salerno
Year: 2019
Subjects: Pier Paolo Pasolini
Witold Gombrowicz
Youth
Form
Homologation
Year 1968

description: The article is a parallel reading of some literary and nonfictional works of Witold Gombrowicz and Pier Paolo Pasolini, concerning ‘youth’ and ‘young people’ in the 1960s, particularly around 1968. In spite of the substantial difference between the youth movements in the West and in Eastern Europe, as well as despite the immense diversity between the ways of life and world views of the two authors, it is still possible to notice astonishing similarities in their ideas. Their analyses of the contemporary mass-society, of the relationship between the individual (notably, the young person), Power and the community also reveal surprising points in common. All things considered, the pessimistic vision of both authors is based on general concepts, like Gombrowicz’s ‘Form’ and Pasolini’s ‘Homologation’, of different origin (i.e. psychosociological and socio-political), but apparently not so distant from each other from today’s standpoint. The article stresses other surprising similarities, such as the constant interest in Dante in the whole production of both writers, especially in the mid-60s, as well as a kind of ‘thematic intertextuality’ in some of their major texts from that period, as the novel Pornografia and the drama Fabrication on the one side, and the tragicomedy History (An Operetta) and the play Calderon on the other one: these works all centre on the relationship between grown-ups and young people.
Quasi-exactly-solvable confining solutions for spin-1 and spin-0 bosons in (1+1)-dimensions with a scalar linear potential
Creators: name: Castro, Luis B.
name: de Castro, Antonio S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We point out a misleading treatment in the recent literature regarding confining solutions for a scalar potential in the context of the Duffin-Kemmer-Petiau theory. We further present the proper bound-state solutions in terms of the generalized Laguerre polynomials and show that the eigenvalues and eigenfunctions depend on the solutions of algebraic equations involving the potential parameter and the quantum number.
description: 8 pages, 1 figure
Determinants of the human immunodeficiency virus type 1 p15NC-RNA interaction that affect enhanced cleavage by the viral protease.
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: 1997

description: During human immunodeficiency virus type 1 (HIV-1) virion assembly, cleavage of the Gag precursor by the viral protease results in the transient appearance of a nucleocapsid-p1-p6 intermediate product designated p15NC. Utilizing the p15NC precursor protein produced with an in vitro transcription-translation system or purified after expression in Escherichia coli, we have demonstrated that RNA is required for efficient cleavage of HIV p15NC. Gel mobility shift and nitrocellulose filter binding experiments indicate that purified p15NC protein specifically binds its corresponding mRNA with an estimated Kd of 1.5 nM. Binding was not affected by the presence or absence of zinc or EDTA. Moreover, mutagenesis of the cysteine residues within either of the two Cys-His arrays had no effect on RNA binding or on RNA-dependent cleavage by the viral protease. In contrast, decreased binding of RNA and diminished susceptibility to cleavage in vitro were observed with p15NC-containing mutations in one or more residues within the triplet of basic amino acids present in the region between the two zinc fingers. In addition, we found that 21- to 24-base DNA and RNA oligonucleotides of a particular sequence and secondary structure could substitute for p15 RNA in the enhancement of p15NC cleavage. Virus particles carrying a mutation in the triplet of NC basic residues (P3BE) show delayed cleavage of p15NC and a defect in core formation despite the eventual appearance of fully processed virion protein. These results define determinants of the p15NC-RNA interaction that lead to enhanced protease-mediated cleavage and demonstrate the importance of the triplet of basic residues in formation of the virus core.
Epstein-Barr virus LMP1 induction of the epidermal growth factor receptor is mediated through a TRAF signaling pathway distinct from NF-kappaB activation.
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: 1997

description: The Epstein-Barr virus (EBV)-encoded LMP1 protein induces several cellular changes including induction of epidermal growth factor receptor (EGFR) expression and activation of the NF-kappaB transcription factor. Two domains within the carboxy terminus have been identified that activate NF-kappaB. In this study, mutational analysis of the LMP1 protein indicated that the proximal NF-kappaB activation domain, which is identical to the TRAF interaction domain (amino acids 187 to 231), is essential for induction of the EGFR. The distal NF-kappaB activation domain (amino acids 352 to 386) did not induce expression of the EGFR. In contrast, the two domains both independently activated a kappaB-CAT reporter gene and induced expression of the NF-kappaB-regulated A20 gene in C33A epithelial cells. These results indicate that induction of the EGFR by LMP1 involves the TRAF interaction domain and that activation of NF-kappaB alone is not sufficient. Northern blot analysis revealed that induction of EGFR and A20 expression is likely to be at the transcriptional level. Interestingly expression of CD40 in the C33A cells also induced expression of the EGFR. Overexpression of either TRAF3 or an amino-terminal-truncated form of TRAF3 (TRAF3-C) inhibited signaling from the LMP1 TRAF interaction domain but did not affect signaling from the distal NF-kappaB activation domain. These data further define the mechanism by which LMP1 induces expression of the EGFR and indicate that TRAF signaling from LMP1 and CD40 activates a downstream transcription pathway distinct from NF-kappaB that induces expression of the EGFR.
Evolutionary variants of the human immunodeficiency virus type 1 V3 region characterized by using a heteroduplex tracking assay.
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: 1997

description: Syncytium-inducing (SI) variants of human immunodeficiency virus type 1 (HIV-1) are evolutionary variants that are associated with rapid CD4+ cell loss and rapid disease progression. The heteroduplex tracking assay (HTA) was used to detect evolutionary V3 variants by amplifying the V3 sequences from viral RNA derived from 50 samples of patient plasma. For this V3-specific HTA (V3-HTA), heteroduplexes were formed between the patient V3 sequences and a probe with the subtype B consensus V3 sequence. Evolution was then measured by divergence from the consensus. The presence of evolutionary variants was correlated with SI detection data on the same samples from the MT-2 cell culture assay. Evolutionary variants were correlated with the SI phenotype in 88% of the samples, and 96% of the SI samples contained evolutionary variants. In most cases the evolutionary V3 variants represented discrete clonal outgrowths of virus. Sequence analysis of the six discordant samples that did not show this correlation indicated that three non-syncytium-inducing (NSI) samples had V3 sequences that had evolved away from the consensus sequence but not toward an SI genotype. A fourth sample showed little evolution away from the consensus but was SI, which indicates that not all SI variants require basic substitutions in V3. The other two samples had SI-like genotypes and NSI phenotypes, suggesting that V3-HTA was able to detect SI emergence in these samples in the absence of their detection in vitro. V3-HTA was also used to confirm SI variant selection in MT-2 cells and to examine the possibility of variant selection during virus culture in peripheral blood cells.
Spectroscopy of heavy baryons with breaking of heavy-quark symmetry
Creators: name: Yasui, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Transition decay widths by one-pion emissions for excited heavy-baryons with a single heavy (charm and bottom) quark are investigated by following the heavy-quark symmetry and its breaking effects at ${\cal O}(1/M)$ for a heavy-baryon mass $M$. Based on the heavy-baryon effective theory, interaction Lagrangian for the heavy baryons with axial-vector current induced by a pion is constructed. It is presented that the transition decay widths up to ${\cal O}(1/M)$ in several channels are constrained. The results will be useful in experimental study of excited heavy-baryons.
description: 11 pages
Additional file 1 of Glut1 deficiency syndrome throughout life: clinical phenotypes, intelligence, life achievements and quality of life in familial cases
Creators: name: Olivotto, Sara
name: Duse, Alessandra
name: Bova, Stefania Maria
name: Leonardi, Valeria
name: Biganzoli, Elia
name: Milanese, Alberto
name: Cereda, Cristina
name: Bertoli, Simona
name: Previtali, Roberto
name: Veggiotti, Pierangelo
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Geology
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Interview. Description: Ad hoc interview used to study life achievements, investigating educational aspects, employment status, autonomy, and social condition.
Humoral, mucosal, and cellular immunity in response to a human immunodeficiency virus type 1 immunogen expressed by a Venezuelan equine encephalitis virus vaccine vector.
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: 1997

description: A molecularly cloned attenuated strain of Venezuelan equine encephalitis virus (VEE) has been genetically configured as a replication-competent vaccine vector for the expression of heterologous viral proteins (N. L. Davis, K. W. Brown, and R. E. Johnston, J. Virol. 70:3781-3787, 1996). The matrix/capsid (MA/CA) coding domain of human immunodeficiency virus type 1 (HIV-1) was cloned into the VEE vector to determine the ability of a VEE vector to stimulate an anti-HIV immune response in mice. The VEE-MA/CA vector replicated rapidly in the cytoplasm of baby hamster kidney (BHK) cells and expressed large quantities of antigenically identifiable MA/CA protein. When injected subcutaneously into BALB/c mice, the vector invaded and replicated in the draining lymphoid tissues, expressing HIV-1 MA/CA at a site of potent immune activity. Anti-MA/CA immunoglobulin G (IgG) and IgA antibodies were present in serum of all immunized mice, and titers increased after a second booster inoculation. IgA antibodies specific for MA/CA were detected in vaginal washes of mice that received two subcutaneous immunizations. Cytotoxic T-lymphocyte responses specific for MA/CA were detected following immunization with the MA/CA-expressing VEE vector. These findings demonstrate the ability of a VEE-based vaccine vector system to stimulate a comprehensive humoral and cellular immune response. The multifaceted nature of this response makes VEE an attractive vaccine for immunization against virus infections such as HIV-1, for which the correlates of protective immunity remain unclear, but may include multiple components of the immune system.
Identification of a novel protein encoded by the BamHI A region of the Epstein-Barr 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: 1997

description: An unusual set of 3' coterminal, spliced mRNAs transcribed through the BamHI A fragment have been previously identified in nasopharyngeal carcinoma (NPC) tissues. These RNAs have also been detected at low levels in Burkitt's lymphoma (BL) cell lines and Epstein-Barr virus (EBV)-transformed lymphocytes. Sequence analyses of clones from a cDNA library derived from the C15 NPC tumor indicated that the primary transcripts are differentially spliced, giving rise to a family of related transcripts, all of which encompass the BARF0 open reading frame (ORF) at the 3' end of the transcripts. One cDNA was identified that extended the BARF0 ORF at the 5' end, forming the RK-BARF0 ORF. In this study, a rabbit antiserum to a synthetic peptide representing an amino acid sequence encoded by the BARF0 ORF was prepared. This antiserum detected a glutathione S-transferase-BARF0 fusion protein and both BARF0 and RK-BARF0 proteins expressed from transfected constructs in H1299 cells. The serum also immunoprecipitated the 20-kDa BARF0 and 30-kDa RK-BARF0 in vitro-translated proteins. Immunoblot analyses identified a protein doublet of 30 and 35 kDa in all of the EBV-infected cell lines tested. Cellular fractionation studies revealed that the proteins were membrane associated. The sizes of the proteins detected in cell lines and their association with membranes suggests that they are likely encoded by the RK-BARF0 transcript, which is predicted to contain a membrane localization signal. The proteins were also detected in protein extracts prepared from NPC biopsies and a BL biopsy but not from hairy leukoplakia, a permissive EBV infection. These results reveal that the rightward RNA transcripts from the BamHI A region of EBV encode one or more proteins that are expressed in latently infected cells and in tumor tissue.
Some Trigonometric Polynomials with Extremely Small Uniform Norm
Creators: name: Grigoriev, Pavel G.
name: Radomskii, Artyom O.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: An example of trigonometric polynomials with extremely small uniform norm is given. This example demonstrates the potential limits for extension of Sidon's inequality for lacunary polynomials in a certain direction.
Additional file 3 of Glut1 deficiency syndrome throughout life: clinical phenotypes, intelligence, life achievements and quality of life in familial cases
Creators: name: Olivotto, Sara
name: Duse, Alessandra
name: Bova, Stefania Maria
name: Leonardi, Valeria
name: Biganzoli, Elia
name: Milanese, Alberto
name: Cereda, Cristina
name: Bertoli, Simona
name: Previtali, Roberto
name: Veggiotti, Pierangelo
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Geology
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3. Pearson’s correlation coefficients matrix relative to PCA performed on 9 adult patients. Description: Correlations across the 6 QoL domains are shown here. The Pearson’s correlation coefficients ranging from 0.38 up to 0.96.
Magnetic and dielectric behavior of the spin-chain compound Er2BaNiO5 well below its Néel temperature
Creators: name: Basu, Tathamay
name: Singh, Kiran
name: Mohapatra, N.
name: Sampathkumaran, E. V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We have recently reported that the Haldane spin-chain system, Er2BaNiO5, undergoing antiferromagnetic order below 32 K, is characterized by the onset of ferroelectricity near 60K due to magnetoelectric coupling induced by short-range magnetic-order within spin-chains. We have carried out additional magnetic and dielectric studies to understand the properties well below antiferromagnetic ordering temperature. We emphasize here on the following: (i) A strong frequency dependent behaviors of ac magnetic susceptibility and complex dielectric properties have been observed at much lower temperatures (below 8 K), that is, reentrant multiglass-like phenomenon, naturally suggesting the existence of an additional transition well below Neel temperature; ii) Magnetoelectric phase coexistence is observed at very low temperature (e.g., T =2K), where the high-field magnetoelectric phase is partially arrested on returning to zero magnetic field after a cycling through metamagnetic transition.
description: J. Applied Physics, in press
Induction of the transcription factor Sp1 during human cytomegalovirus infection mediates upregulation of the p65 and p105/p50 NF-kappaB promoters.
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: 1997

description: During human cytomegalovirus (HCMV) infection, the promoters for the classical NF-kappaB subunits (p65 and p105/p50) are transactivated. Previously, we demonstrated that the viral immediate-early (IE) proteins (IE1-72, IE2-55, and IE2-86) were involved in this upregulation. These viral factors alone, however, could not account for the entirety of the increased levels of transcription. Because one of the hallmarks of HCMV infection is the induction of cellular transcription factors, we hypothesized that one or more of these induced factors was also critical to the regulation of NF-kappaB during infection. Sp1 was one such factor that might be involved because p65 promoter activity was upregulated by Sp1 and both of the NF-kappaB subunit promoters are GC rich and contain Sp1 binding sites. Therefore, to detail the role that Sp1 plays in the regulation of NF-kappaB during infection, we initially examined Sp1 levels for changes during infection. HCMV infection resulted in increased Sp1 mRNA expression, protein levels, and DNA binding activity. Because both promoters were transactivated by Sp1, we reasoned that the upregulation of Sp1 played a role in p65 and p105/p50 promoter activity during infection. To address the specific role of Sp1 in p65 and p105/p50 promoter transactivation by HCMV, we mutated both promoters. These results demonstrated that the Sp1-specific DNA binding sites were involved in the virus-mediated transactivation. Last, to further dissect the role of HCMV in the Sp1-mediated induction of NF-kappaB, we examined the role that the viral IE genes played in Sp1 regulation. The IE gene products (IE1-72, IE2-55, and IE2-86) cooperated with Sp1 to increase promoter transactivation and physically interacted with Sp1. In addition, the IE2-86 product increased Sp1 DNA binding by possibly freeing up inactive Sp1. These data supported our hypothesis that Sp1 was involved in the upregulation of NF-kappaB during HCMV infection through the Sp1 binding sites in the p65 and p105/p50 promoters and additionally demonstrated a potential viral mechanism that might be responsible for the upregulation of Sp1 activity.
Role for highly regulated rep gene expression in adeno-associated virus vector production.
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: 1997

description: Recent success achieving long-term in vivo gene transfer without a significant immune response by using adeno-associated virus (AAV) vectors (X. Xiao, J. Li, and R. J. Samulski, J. Virol. 70:8098-8108, 1996) has encouraged further development of this vector for human gene therapy. Currently, studies focus on the generation of high-titer vectors by using the two-plasmid helper-vector system in adenovirus (Ad)-infected cells. To examine the effects of the AAV replication (rep) genes on recombinant AAV (rAAV) vector production, we have constructed a series of AAV helper plasmids that contain strong heterologous promoters in place of the endogenous p5 promoter. Although high-level rep gene expression was achieved, rAAV DNA failed to replicate in the absence of Ad infection. Moreover, unregulated overexpression of Rep78/68 led to substantially lower rAAV yields in the presence of Ad (10(4-5) versus 10(7-8)). In contrast, under similar conditions, reduced Rep78/68 expression resulted in much higher rAAV yields (10(9)). Molecular characterization showed that overexpression of the rep gene decreased rAAV DNA replication and severely inhibited capsid (cap) gene expression. Interestingly, a reduced rep level enhanced cap gene expression and supported normal rAAV DNA replication. These studies suggest a critical role for regulated rep gene expression in rAAV production and have facilitated the development of a new AAV helper plasmid that increases vector production eightfold over currently used constructs.
Particle multiplicity-dependent charmonia production in p+p collisions by the PHENIX experiment
Creators: name: Lim, Sanghoon
Publisher: name: Zenodo
Year: 2023
Subjects: pic23
phenix
p+p
charmonium
heavy flavor
multiplicity
muon
dimuon
nuclear
modification
raa
J/Ψ
p+al
p+au
3he+au

description: Talk presented at the Physics in Collision 2023 conference
Robust Consensus in the Presence of Impulsive Channel Noise
Creators: name: Dasarathan, Sivaraman
name: Tepedelenlioglu, Cihan
name: Banavar, Mahesh
name: Spanias, Andreas
Publisher: name: arXiv
Year: 2014
Subjects: subject: Systems and Control (eess.SY)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: A distributed average consensus algorithm robust to a wide range of impulsive channel noise distributions is proposed. This work is the first of its kind in the literature to propose a consensus algorithm which relaxes the requirement of finite moments on the communication noise. It is shown that the nodes reach consensus asymptotically to a finite random variable whose expectation is the desired sample average of the initial observations with a variance that depends on the step size of the algorithm and the receiver nonlinear function. The asymptotic performance is characterized by deriving the asymptotic covariance matrix using results from stochastic approximation theory. Simulations corroborate our analytical findings and highlight the robustness of the proposed algorithm.
description: 24 pages, 7 figures, Submitted to Transactions on Signal Processing, Apr 2014 (Submitted, currently in review)
The cellular YY1 transcription factor binds a cis-acting, negatively regulating element in the Epstein-Barr virus BRLF1 promoter.
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: 1997

description: Disruption of Epstein-Barr virus latency is induced by expression of either the BZLF1 (in B cells and epithelial cells) or BRLF1 (in epithelial cells only) immediate-early protein. Regulation of BZLF1 and BRLF1 transcription may therefore modulate the stringency of viral latency. The cellular transcription factor YY1 negatively regulates BZLF1 transcription. Here we show that the BRLF1 promoter (Rp) sequences from -206 to -227 (relative to the mRNA start site) and from -7 to +6 are directly bound by YY1. Mutation of the upstream YY1 binding site increases constitutive Rp activity in epithelial cells and B cells, while mutation of the downstream YY1 binding site does not significantly affect Rp activity. Negative regulation of BZLF1 and BRLF1 transcription by YY1 may act to maintain viral latency.
The human cytomegalovirus UL55 (gB) and UL75 (gH) glycoprotein ligands initiate the rapid activation of Sp1 and NF-kappaB during infection.
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: 1997

description: The cellular transcription factors Sp1 and NF-kappaB were upregulated shortly after the binding of purified live or UV-inactivated human cytomegalovirus (HCMV) to the cell surface. The rapid time frame of transcription factor induction is similar to that seen in other systems in which cellular factors are induced following receptor-ligand engagement. This similarity suggested that a cellular receptor-viral ligand interaction might be involved in Sp1 and NF-kappaB activation during the earliest stages of HCMV infection. To focus on the possible role viral ligands play in initiating cellular events following infection, we first used purified viral membrane extracts to demonstrate that constituents on the membrane are responsible for cellular activation. Additionally, these studies showed, through the use of neutralizing antibodies, that the viral membrane mediators of this activation are the major envelope glycoproteins gB (UL55) and gH (UL75). To confirm these results, neutralizing anti-gB and -gH antibodies were used to block the interactions of these glycoproteins on whole purified virus with their cell surface receptors. In so doing, we found that Sp1 and NF-kappaB induction was inhibited. Lastly, through the use of purified viral gB protein and an anti-idiotypic antibody that mimics the image of the viral gH protein, it was found that the engagement of individual viral ligands with their appropriate cell surface receptors was sufficient to activate cellular Sp1 and NF-kappaB. These results support our hypothesis that HCMV glycoproteins mediate an initial signal transduction pathway which leads to the upregulation of host cell transcription factors and suggests a model wherein the orderly sequence of virus-mediated changes in cellular activation initiates with viral binding via envelope glycoproteins to the cognate cellular receptor(s).
Study of Some Parameters of Modified Chaplygin Gas in Galileon Gravity Theory from Observational Perspective
Creators: name: Ranjit, Chayan
name: Rudra, Prabir
name: Debnath, Ujjal
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: We have assumed the FRW model of the universe in Galileon gravity, which is filled with dark matter and Modified Chaplygin gas (MCG) type dark energy. We present the Hubble parameter in terms of some unknown parameters and observational parameters with the redshift $z$. Some cosmological parameters are reconstructed and plots are generated to study the nature of the model and its viability. It is seen that the model is perfectly consistent with the present cosmic acceleration. From \textit{observed Hubble data (OHD) set or Stern data set} of 12 points, we have obtained the bounds of the arbitrary parameters ($A,B$) & ($A,C$) by minimizing the $χ^{2}$ test. Next due to joint analysis of \textit{Stern+BAO} and \textit{Stern+BAO+CMB} observations, we have also obtained the best fit values and the bounds of the parameters ($A,B$) & ($A,C$) by fixing some other parameters. The best-fit values and bounds of the parameters are obtained with 66%, 90% and 99% confidence levels for \textit{Stern, Stern+BAO and Stern+BAO+CMB} joint analysis. Next we have also taken type Ia supernovae data set (union 2 data set with 557 data points). The distance modulus $μ(z)$ against redshift $z$ for our theoretical MCG model in Galileon gravity have been tested for the best fit values of the parameters and the observed \textit{SNe Ia union 2 data} sample and from this, we have concluded that our model is in agreement with the union 2 sample data.
description: 14 pages, 12 figures, Accepted for Publication in Can. J. Phys. arXiv admin note: substantial text overlap with arXiv:1304.6713, arXiv:1206.0507, arXiv:1310.2144
Additional file 10 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 10: Figure S9. Genomic prediction accuracy and bias when preselection of variants and training of the predictive equation are performed in two mutually exclusive subsets.
Virus-specific, CD8+ major histocompatibility complex class I-restricted cytotoxic T lymphocytes in lymphocytic choriomeningitis virus-infected beta2-microglobulin-deficient mice.
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: 1997

description: Following infection with lymphocytic choriomeningitis virus (LCMV), normal adult mice generate virus-specific, major histocompatibility complex (MHC) class I-restricted cytotoxic T lymphocytes (CTL) which clear the virus after intraperitoneal infection or cause death following intracranial (i.c.) infection. We have investigated the response of beta2-microglobulin-deficient (beta2m-) mice of the H-2d haplotype (KOD mice) to LCMV infection. Unlike H-2b beta2m- mice, which generate CD4+ MHC class II-restricted CTL in response to LCMV, KOD mice generate high levels of CD8+ MHC class I-restricted, virus-specific CTL. These CTL are specific for the LCMV nucleoprotein epitope (residues 118 to 126) in association with the Ld class I molecule, analogous to the CTL response in wild-type mice. KOD mice are also susceptible to lethal LCM disease, with 75 to 80% of the mice dying 7 to 9 days following i.c. infection with virus. Similar to results with normal mice, lethal LCM disease in KOD mice is prevented by in vivo depletion of CD8+ T cells prior to i.c. infection. In contrast to wild-type mice, however, KOD mice cannot control LCMV and become persistently infected. Overall, these results demonstrate that beta2m is not an absolute requirement for presentation of endogenous antigen on Ld or for induction of virus-specific Ld-restricted CTL in vivo.
Absence of Macrophage Inflammatory Protein-1α Prevents the Development of Blinding Herpes Stromal Keratitis
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: 1998

description: Prior studies in our laboratory have suggested that the CC chemokine macrophage inflammatory protein-1α (MIP-1α) may be an important mediator in the blinding ocular inflammation which develops following herpes simplex virus type 1 (HSV-1) infection of the murine cornea. To directly test this hypothesis, MIP-1α-deficient (−/−) mice and their wild-type (+/+) counterparts were infected topically on the scarified cornea with 2.5 × 105 PFU of HSV-1 strain RE and subsequently graded for corneal opacity. Four weeks postinfection (p.i.), the mean corneal opacity score of −/− mice was 1.1 ± 0.3 while that of the +/+ mice was 3.7 ± 0.5. No detectable infiltrating CD4+ T cells were seen histologically at 14 or 21 days p.i. in −/− animals, whereas the mean CD4+ T-cell count per field (36 fields counted) in +/+ hosts was 26 ± 2 (P < 0.001). In addition, neutrophil counts in the −/− mouse corneas were reduced by >80% in comparison to the wild-type controls. At 2 weeks p.i., no interleukin-2 or gamma interferon could be detected in six of seven −/− mice, whereas both T-cell cytokines were readily demonstrable in +/+ mouse corneas. Also, MIP-2 and monocyte chemoattractant protein-1 protein levels were significantly lower in MIP-1α −/− mouse corneas than in +/+ host corneas, suggesting that MIP-1α directly, or more likely indirectly, influences the expression of other chemokines. Interestingly, despite the paucity of infiltrating cells, HSV-1 clearance from the eyes of −/− mice was not significantly different from that observed in +/+ hosts. We conclude that MIP-1α is not needed to control virus growth in the cornea but is essential for the development of severe stromal keratitis.
Additional file 11 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 11: Figure S10. Genome-wide association study on backfat thickness with marker array or whole-genome sequence data in line A.
Quantum Google Algorithm: Construction and Application to Complex Networks
Creators: name: Paparo, G. D.
name: Müller, M.
name: Comellas, F.
name: Martin-Delgado, M. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: We review the main findings on the ranking capabilities of the recently proposed Quantum PageRank algorithm (G.D. Paparo et al., Sci. Rep. 2, 444 (2012) and G.D. Paparo et al., Sci. Rep. 3, 2773 (2013)) applied to large complex networks. The algorithm has been shown to identify unambiguously the underlying topology of the network and to be capable of clearly highlighting the structure of secondary hubs of networks. Furthermore, it can resolve the degeneracy in importance of the low-lying part of the list of rankings. Examples of applications include real-world instances from the WWW, which typically display a scale-free network structure and models of hierarchical networks. The quantum algorithm has been shown to display an increased stability with respect to a variation of the damping parameter, present in the Google algorithm, and a more clearly pronounced power-law behaviour in the distribution of importance among the nodes, as compared to the classical algorithm.
Adaptation of Sindbis Virus to BHK Cells Selects for Use of Heparan Sulfate as an Attachment Receptor
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: 1998

description: Attachment of Sindbis virus to the cell surface glycosaminoglycan heparan sulfate (HS) and the selection of this phenotype by cell culture adaptation were investigated. Virus (TR339) was derived from a cDNA clone representing the consensus sequence of strain AR339 (K. L. McKnight, D. A. Simpson, S. C. Lin, T. A. Knott, J. M. Polo, D. F. Pence, D. B. Johannsen, H. W. Heidner, N. L. Davis, and R. E. Johnston, J. Virol. 70:1981–1989, 1996) and from mutant clones containing either one or two dominant cell culture adaptations in the E2 structural glycoprotein (Arg instead of Ser at E2 position 1 [designated TRSB]) or this mutation plus Arg for Ser at E2 114 [designated TRSB-R114]). The consensus virus, TR339, bound to baby hamster kidney (BHK) cells very poorly. The mutation in TRSB increased binding 10- to 50-fold, and the additional mutation in TRSB-R114 increased binding 3- to 5-fold over TRSB. The magnitude of binding was positively correlated with the degree of cell culture adaptation and with attenuation of these viruses in neonatal mice. HS was identified as the attachment receptor for the mutant viruses by the following experimental results. (i) Low concentrations of soluble heparin inhibited plaque formation on and binding of mutant viruses to BHK cells by >95%. In contrast, TR339 showed minimal inhibition at high concentrations. (ii) Binding and infectivity of TRSB-R114 was sensitive to digestion of cell surface HS with heparinase III, and TRSB was sensitive to both heparinase I and heparinase III. TR339 infectivity was only slightly affected by either digestion. (iii) Radiolabeled TRSB and TRSB-R114 attached efficiently to heparin-agarose beads in binding assays, while TR339 showed virtually no binding. (iv) Binding and infectivity of TRSB and TRSB-R114, but not TR339, were greatly reduced on Chinese hamster ovary cells deficient in HS specifically or all glycosaminoglycans. (v) High-multiplicity-of-infection passage of TR339 on BHK cell cultures resulted in rapid coselection of high-affinity binding to BHK cells and attachment to heparin-agarose beads. Sequencing of the passaged virus population revealed a mutation from Glu to Lys at E2 70, a mutation common to many laboratory strains of Sindbis virus. These results suggest that TR339, the most virulent virus tested, attaches to cells through a low-affinity, primarily HS-independent mechanism. Adaptive mutations, selected during cell culture growth of Sindbis virus, enhance binding and infectivity by allowing the virus to attach by an alternative mechanism that is dependent on the presence of cell surface HS.
Exclusive and Persistent Use of the Entry Coreceptor CXCR4 by Human Immunodeficiency Virus Type 1 from a Subject Homozygous for CCR5 Δ32
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: 1998

description: Individuals who are homozygous for the 32-bp deletion in the gene coding for the chemokine receptor and major human immunodeficiency virus type 1 (HIV-1) coreceptor CCR5 (CCR5 −/−) lack functional cell surface CCR5 molecules and are relatively resistant to HIV-1 infection. HIV-1 infection in CCR5 −/− individuals, although rare, has been increasingly documented. We now report that the viral quasispecies from one such individual throughout disease is homogenous, T cell line tropic, and phenotypically syncytium inducing (SI); exclusively uses CXCR4; and replicates well in CCR5 −/− primary T cells. The recently discovered coreceptors BOB and Bonzo are not used. Although early and persistent SI variants have been described in longitudinal studies, this is the first demonstration of exclusive and persistent CXCR4 usage. With the caveat that the earliest viruses available from this subject were from approximately 4 years following primary infection, these data suggest that HIV-1 infection can be mediated and persistently maintained by viruses which exclusively utilize CXCR4. The lack of evolution toward the available minor coreceptors in this subject underscores the dominant biological roles of the major coreceptors CCR5 and CXCR4. This and two similar subjects (R. Biti, R. Ffrench, J. Young, B. Bennetts, G. Stewart, and T. Liang, Nat. Med. 3:252–253, 1997; I. Theodoreu, L. Meyer, M. Magierowska, C. Katlama, and C. Rouzioux, Lancet 349:1219–1220, 1997) showed relatively rapid CD4+ T-cell declines despite average or low initial viral RNA load. Since viruses which use CXCR4 exclusively cannot infect macrophages, these data have implications for the relative infection of the T-cell compartment versus the macrophage compartment in vivo and for the development of CCR5-based therapeutics.