cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing
Creators: name: Guffey, M. B.
name: Anderson, J. A.
name: Korber, B. T. M.
name: Pham, K. T.
name: Keele, B. F.
name: Haynes, B. F.
name: Salazar-Gonzalez, J. F.
name: Manigart, O.
name: Salazar, M. G.
name: Allen, S.
name: Mulenga, J.
name: Swanstrom, R.
name: Sharp, P. M.
name: Athreya, G. S.
name: Derdeyn, C. A.
name: Hunter, E.
name: Shaw, G. M.
name: Bailes, E.
name: Hahn, B. H.
name: Farmer, P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating the transmission of human immunodeficiency virus type 1 (HIV-1) and in developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach to analyze HIV-1 env genes as intact genetic units amplified from plasma virion RNA by single-genome amplification (SGA), followed by direct sequencing of uncloned DNA amplicons. We show that this strategy precludes in vitro artifacts caused by Taq-induced nucleotide substitutions and template switching, provides an accurate representation of the env quasispecies in vivo, and has an overall error rate (including nucleotide misincorporation, insertion, and deletion) of less than 8 × 10−5. Applying this method to the analysis of virus in plasma from 12 Zambian subjects from whom samples were obtained within 3 months of seroconversion, we show that transmitted or early founder viruses can be identified and that molecular pathways and rates of early env diversification can be defined. Specifically, we show that 8 of the 12 subjects were each infected by a single virus, while 4 others acquired more than one virus; that the rate of virus evolution in one subject during an 80-day period spanning seroconversion was 1.7 × 10−5 substitutions per site per day; and that evidence of strong immunologic selection can be seen in Env and overlapping Rev sequences based on nonrandom accumulation of nonsynonymous mutations. We also compared the results of the SGA approach with those of more-conventional bulk PCR amplification methods performed on the same patient samples and found that the latter is associated with excessive rates of Taq-induced recombination, nucleotide misincorporation, template resampling, and cloning bias. These findings indicate that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately.
An Introduction to Biomolecular Simulations and Docking
Creators: name: Mura, Cameron
name: McAnany, Charles E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences

description: The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given biomolecule also samples (and is sampled by) a rapidly fluctuating local environment comprised of other biopolymers, small molecules, water, ions, etc. that diffuse to within a few nanometers, leading to inter-molecular contacts that stitch together large supramolecular assemblies. Indeed, all biological systems can be viewed as dynamic networks of molecular interactions. As a complement to experimentation, molecular simulation offers a uniquely powerful approach to analyze biomolecular structure, mechanism, and dynamics; this is possible because the molecular contacts that define a complicated biomolecular system are governed by the same physical principles (forces, energetics) that characterize individual small molecules, and these simpler systems are relatively well-understood. With modern algorithms and computing capabilities, simulations are now an indispensable tool for examining biomolecular assemblies in atomic detail, from the conformational motion in an individual protein to the diffusional dynamics and inter-molecular collisions in the early stages of formation of cellular-scale assemblies such as the ribosome. This text introduces the physicochemical foundations of molecular simulations and docking, largely from the perspective of biomolecular interactions.
description: The text is accompanied by 6 figures and 5 boxes. The text is in press at Molecular Simulation (2014), as part of a special issue on simulations in molecular biology
Ectromelia Virus Encodes a Novel Family of F-Box Proteins That Interact with the SCF Complex
Creators: name: Barry, M.
name: Couturier, B.
name: Xiong, Y.
name: van Buuren, N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Poxviruses are notorious for encoding multiple proteins that regulate cellular signaling pathways, including the ubiquitin-proteasome system. Bioinformatics indicated that ectromelia virus, the causative agent of lethal mousepox, encoded four proteins, EVM002, EVM005, EVM154, and EVM165, containing putative F-box domains. In contrast to cellular F-box proteins, the ectromelia virus proteins contain C-terminal F-box domains in conjunction with N-terminal ankyrin repeats, a combination that has not been previously reported for cellular proteins. These observations suggested that the ectromelia virus F-box proteins interact with SCF (Skp1, cullin-1, and F-box) ubiquitin ligases. We focused our studies on EVM005, since this protein had only one ortholog in cowpox virus. Using mass spectrometry, we identified cullin-1 as a binding partner for EVM005, and this interaction was confirmed by overexpression of hemagglutinin (HA)-cullin-1. During infection, Flag-EVM005 and HA-cullin-1 colocalized to distinct cellular bodies. Significantly, EVM005 coprecipitated with endogenous Skp1, cullin-1, and Roc1 and associated with conjugated ubiquitin, suggesting that EVM005 interacted with the components of a functional ubiquitin ligase. Interaction of EVM005 with cullin-1 and Skp1 was abolished upon deletion of the F-box, indicating that the F-box played a crucial role in interaction with the SCF complex. Additionally, EVM002 and EVM154 interacted with Skp1 and conjugated ubiquitin, suggesting that ectromelia virus encodes multiple F-box-containing proteins that regulate the SCF complex. Our results indicate that ectromelia virus has evolved multiple proteins that interact with the SCF complex.
Epstein-Barr Virus BART MicroRNAs Are Produced from a Large Intron prior to Splicing
Creators: name: Raab-Traub, N.
name: Marquitz, A. R.
name: Edwards, R. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Latent Epstein-Barr virus (EBV) infection is associated with several lymphoproliferative disorders, including posttransplant lymphoma, Hodgkin's disease, and Burkitt's lymphoma, as well as nasopharyngeal carcinoma (NPC). Twenty-nine microRNAs (miRNAs) have been identified that are transcribed during latent infection from three clusters in the EBV genome. Two of the three clusters of miRNAs are made from the BamHI A rightward transcripts (BARTs), a set of alternatively spliced transcripts that are highly abundant in NPC but have not been shown to produce a detectable protein. This study indicates that while the BART miRNAs are located in the first four introns of the transcripts, processing of the pre-miRNAs from the primary transcript occurs prior to completion of the splicing reaction. Additionally, production of the BART miRNAs correlates with accumulation of a spliced mRNA in which exon 1 is joined directly to exon 3, suggesting that this form of the transcript may favor production of miRNAs. Sequence variations and processing of pre-miRNAs to the mature form also may account for various differences in miRNA abundance. Importantly, residual intronic pieces that result from processing of the pre-miRNAs were detected in the nucleus. The predicted structures of these pieces suggest there is a bias or temporal pattern to the production of the individual pre-miRNAs. These findings indicate that multiple factors contribute to the production of the BART miRNAs and to the apparent differences in abundance between the individual miRNAs of the cluster.
title: La vita etica della persona nella filosofia di Max Scheler
Creators: name: Merante , Maria
Publisher: name: Roma Tre-Press
Year: 2012

description: Quella di Max Scheler è un'indagine etico-antropologico-esistenziale. Vagliando attentamente questi tre campi, l'autore tenta di comprendere quale posizione occupi l'uomo all'interno del cosmo. Per quella sua riflessione che conduce ad una concezione unitaria, quel particolare essere può porsi domande sul proprio status – quali: "Chi sono?", oppure: "Dove sono?". Scheler può pertanto essere indubbiamente considerato uno dei padri dell'antropologia filosofica.

description: B@belonline vol. 13 Chaos/Kosmos
Debris disc formation induced by planetary growth
Creators: name: Kobayashi, Hiroshi
name: Loehne, Torsten
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Several hundred stars older than 10 million years have been observed to have infrared excesses. These observations are explained by dust grains formed by the collisional fragmentation of hidden planetesimals. Such dusty planetesimal discs are known as debris discs. In a dynamically cold planetesimal disc, collisional coagulation of planetesimals produces planetary embryos which then stir the surrounding leftover planetesimals. Thus, the collisional fragmentation of planetesimals that results from planet formation forms a debris disc. We aim to determine the properties of the underlying planetesimals in debris discs by numerically modelling the coagulation and fragmentation of planetesimal populations. The brightness and temporal evolution of debris discs depend on the radial distribution of planetesimal discs, the location of their inner and outer edges, their total mass, and the size of planetesimals in the disc. We find that a radially narrow planetesimal disc is most likely to result in a debris disc that can explain the trend of observed infrared excesses of debris discs around G-type stars, for which planet formation occurs only before 100 million years. Early debris disc formation is induced by planet formation, while the later evolution is explained by the collisional decay of leftover planetesimals around planets that have already formed. Planetesimal discs with underlying planetesimals of radii $\sim 100\,$km at $\approx 30$ AU most readily explain the Spitzer Space Telescope 24 and 70$ μ$m fluxes from debris discs around G-type stars.
description: 10 pages, 11 figures; accepted for publication in MNRAS
Epstein-Barr Virus Latent Membrane Protein 1 Induces Expression of the Epidermal Growth Factor Receptor through Effects on Bcl-3 and STAT3
Creators: name: Raab-Traub, N.
name: Kung, C.-P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) activates multiple signaling pathways. Two regions, C-terminal-activating region 1 (CTAR1) and CTAR2, have been identified within the cytoplasmic carboxy terminal domain that activates NF-κB. CTAR2 activates the canonical NF-κB pathway, which includes p50/p65 complexes. CTAR1 can activate both the canonical and noncanonical pathways to produce multiple distinct NF-κB dimers, including p52/p50, p52/p65, and p50/p50. CTAR1 also uniquely upregulates the epidermal growth factor receptor (EGFR) in epithelial cells. Increased p50-Bcl-3 complexes have been detected by chromatin precipitation on the NF-κB consensus motifs within the egfr promoter in CTAR1-expressing epithelial cells and nasopharyngeal carcinoma cells. In this study, the mechanism responsible for the increase in Bcl-3 has been further investigated. The data indicate that LMP1-CTAR1 induces Bcl-3 mRNA and increases the nuclear translocation of both Bcl-3 and p50. LMP1-CTAR1 constitutively activates STAT3, and this activation was not due to the induction of interleukin 6 (IL-6). In LMP1-CTAR1-expressing cells, increased levels of activated STAT3 were detected by chromatin immunoprecipitation on STAT-binding sites located within both the promoter and the second intron of Bcl-3. A STAT3 inhibitor significantly reduced the activation of STAT3, as well as the CTAR1-mediated upregulation of Bcl-3 and EGFR. These data suggest that LMP1 activates distinct forms of NF-κB through multiple pathways. In addition to activating the canonical and noncanonical pathways, LMP1-CTAR1 constitutively activates STAT3 and increases Bcl-3. The increased nuclear Bcl-3 and p50 homodimer complexes positively regulate EGFR expression. These results indicate that LMP1 likely regulates distinct cellular genes by activating specific NF-κB pathways.
Human Parainfluenza Virus Type 1 C Proteins Are Nonessential Proteins That Inhibit the Host Interferon and Apoptotic Responses and Are Required for Efficient Replication in Nonhuman Primates
Creators: name: Hennessey, M.
name: Boonyaratanakornkit, J.
name: Schmidt, A. C.
name: Pickles, R. J.
name: Collins, P. L.
name: Cruz, A.-M.
name: Esker, J.
name: Castano, A.
name: Schomacker, H.
name: Bartlett, E. J.
name: Surman, S. R.
name: Murphy, B. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Recombinant human parainfluenza virus type 1 (rHPIV1) was modified to create rHPIV1-P(C−), a virus in which expression of the C proteins (C′, C, Y1, and Y2) was silenced without affecting the amino acid sequence of the P protein. Infectious rHPIV1-P(C−) was readily recovered from cDNA, indicating that the four C proteins were not essential for virus replication. Early during infection in vitro, rHPIV1-P(C−) replicated as efficiently as wild-type (wt) HPIV1, but its titer subsequently decreased coincident with the onset of an extensive cytopathic effect not observed with wt rHPIV1. rHPIV1-P(C−) infection, but not wt rHPIV1 infection, induced caspase 3 activation and nuclear fragmentation in LLC-MK2 cells, identifying the HPIV1 C proteins as inhibitors of apoptosis. In contrast to wt rHPIV1, rHPIV1-P(C−) and rHPIV1-CF170S, a mutant encoding an F170S substitution in C, induced interferon (IFN) and did not inhibit IFN signaling in vitro. However, only rHPIV1-P(C−) induced apoptosis. Thus, the anti-IFN and antiapoptosis activities of HPIV1 were separable: both activities are disabled in rHPIV1-P(C−), whereas only the anti-IFN activity is disabled in rHPIV1-CF170S. In African green monkeys (AGMs), rHPIV1-P(C−) was considerably more attenuated than rHPIV1-CF170S, suggesting that disabling the anti-IFN and antiapoptotic activities of HPIV1 had additive effects on attenuation in vivo. Although rHPIV1-P(C−) protected against challenge with wt HPIV1, its highly restricted replication in AGMs and in primary human airway epithelial cell cultures suggests that it might be overattenuated for use as a vaccine. Thus, the C proteins of HPIV1 are nonessential but have anti-IFN and antiapoptosis activities required for virulence in primates.
Recent advances in ultra-low temperature (sub-zero to 100 C) synthesis, mechanism and applications of titania (TiO2) nanoparticles
Creators: Laishram, Devika
Publisher: name: University of Alberta Library
Year: 2022

The development of titania (TiO2) nanomaterials for next-generation photonic, optoelectronic, and catalytic applications necessitates a facile and cost-effective synthetic methodology for precisely tuning the composition, phase, and morphology at nanometer scales. In this review, an attempt has been made to comprehend the progress of the emerging and rapidly developing synthesis methods evolved for the low-temperature synthesis of titania with a particular emphasis on sub-zero temperature. Insights and understandings of how the temperature affects the characteristic surface properties and morphology of titania, along with a detailed discussion on the material characteristics for various technological device applications are dealt with various methods of analysis. Furthermore, the temperature-dependent morphological (0D–3D) and structural changes and their impact on different energy-harvesting and storage and water remediation applications are elucidated. Thus, this review specifically opens the understanding of different TiO2 polymorph syntheses and their physiochemical comprehension for advanced technological device performance enhancement.
Comparing Dense Galaxy Cluster Redshift Surveys with Weak Lensing Maps
Creators: name: Hwang, Ho Seong
name: Geller, Margaret J.
name: Diaferio, Antonaldo
name: Rines, Kenneth J.
name: Zahid, H. Jabran
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We use dense redshift surveys of nine galaxy clusters at $z\sim0.2$ to compare the galaxy distribution in each system with the projected matter distribution from weak lensing. By combining 2087 new MMT/Hectospec redshifts and the data in the literature, we construct spectroscopic samples within the region of weak-lensing maps of high (70--89%) and uniform completeness. With these dense redshift surveys, we construct galaxy number density maps using several galaxy subsamples. The shape of the main cluster concentration in the weak-lensing maps is similar to the global morphology of the number density maps based on cluster members alone, mainly dominated by red members. We cross correlate the galaxy number density maps with the weak-lensing maps. The cross correlation signal when we include foreground and background galaxies at 0.5$z_{\rm cl}$20% for A383, A689 and A750). The fractional excess in the cross correlation signal including foreground and background structures could be a useful proxy for assessing the reliability of weak-lensing cluster mass estimates.
description: 22 pages, 19 figures, 2 tables. To appear in ApJ. Paper with high resolution figures is available at http://astro.kias.re.kr/~hshwang/ms_hwang20141014.pdf
Initial B-Cell Responses to Transmitted Human Immunodeficiency Virus Type 1: Virion-Binding Immunoglobulin M (IgM) and IgG Antibodies Followed by Plasma Anti-gp41 Antibodies with Ineffective Control of Initial Viremia
Creators: name: Haynes, B. F.
name: Lucas, J. T.
name: Tomaras, G. D.
name: Eron, J.
name: Perelson, A. S.
name: Ashley, V. C.
name: Liao, H.-X.
name: Hicks, C. B.
name: Yates, N. L.
name: Self, S. G.
name: Hahn, B. H.
name: Landucci, G.
name: Karim, S. S. A.
name: Forthal, D. N.
name: Keele, B. F.
name: Fouda, G. G.
name: Chavez, L. L.
name: Qin, L.
name: Greenberg, M. L.
name: Decamp, A. C.
name: Weinhold, K. J.
name: Parks, R. J.
name: Morris, L.
name: Liu, P.
name: Cohen, M.
name: Montefiori, D. C.
name: Shaw, G. M.
name: Blattner, W. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: A window of opportunity for immune responses to extinguish human immunodeficiency virus type 1 (HIV-1) exists from the moment of transmission through establishment of the latent pool of HIV-1-infected cells. A critical time to study the initial immune responses to the transmitted/founder virus is the eclipse phase of HIV-1 infection (time from transmission to the first appearance of plasma virus), but, to date, this period has been logistically difficult to analyze. To probe B-cell responses immediately following HIV-1 transmission, we have determined envelope-specific antibody responses to autologous and consensus Envs in plasma donors from the United States for whom frequent plasma samples were available at time points immediately before, during, and after HIV-1 plasma viral load (VL) ramp-up in acute infection, and we have modeled the antibody effect on the kinetics of plasma viremia. The first detectable B-cell response was in the form of immune complexes 8 days after plasma virus detection, whereas the first free plasma anti-HIV-1 antibody was to gp41 and appeared 13 days after the appearance of plasma virus. In contrast, envelope gp120-specific antibodies were delayed an additional 14 days. Mathematical modeling of the earliest viral dynamics was performed to determine the impact of antibody on HIV replication in vivo as assessed by plasma VL. Including the initial anti-gp41 immunoglobulin G (IgG), IgM, or both responses in the model did not significantly impact the early dynamics of plasma VL. These results demonstrate that the first IgM and IgG antibodies induced by transmitted HIV-1 are capable of binding virions but have little impact on acute-phase viremia at the timing and magnitude that they occur in natural infection.
A New Course on Creativity in an Engineering Program: Foundations and Issues
Creators: name: Morin, Sophie
name: Robert, Jean-Marc
name: Gabora, Liane
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computers and Society (cs.CY)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: The importance of innovation in the world's economy, now undeniable, draws great attention to the need to improve organizations' creative potential. In the last 60 years, hundreds of books have been written on the subject and hundreds of webpages display information on how to be more creative and achieve innovation. Several North American and European universities offer graduated programs in creativity. However, building an effective and validated creativity training program is not without challenges. Because of the nature of their work, engineers are often asked to be innovative. Without aiming for a degree in creativity, could future engineers benefit from training programs in creativity? This article presents the conceptual framework and pedagogical elements of a new course in creativity for engineering students.
description: 10 pages, Intl Conf on Innovative Design and Manufacturing (pp. 270-275). Aug 13-15, Montreal. IEEE Conference Proceedings
Analysis of the Cramer-Rao lower uncertainty bound in the joint estimation of astrometry and photometry
Creators: name: Mendez, Rene A.
name: Silva, Jorge F.
name: Orsotica, Rodrigo
name: Lobos, Rodrigo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: In this paper we use the Cramer-Rao lower uncertainty bound to estimate the maximum precision that could be achieved on the joint simultaneous (or 2D) estimation of photometry and astrometry of a point source measured by a linear CCD detector array. We develop exact expressions for the Fisher matrix elements required to compute the Cramer-Rao bound in the case of a source with a Gaussian light profile. From these expressions we predict the behavior of the Cramer-Rao astrometric and photometric precision as a function of the signal and the noise of the observations, and compare them to actual observations - finding a good correspondence between them. We show that the astrometric Cramer-Rao bound goes as $(S/N)^{-1}$ (similar to the photometric bound) but, additionally, we find that this bound is quite sensitive to the value of the background - suppressing the background can greatly enhance the astrometric accuracy. We present a systematic analysis of the elements of the Fisher matrix in the case when the detector adequately samples the source (oversampling regime), leading to closed-form analytical expressions for the Cramer-Rao bound. We show that, in this regime, the joint parametric determination of photometry and astrometry for the source become decoupled from each other, and furthermore, it is possible to write down expressions (approximate to first order in the small quantities F/B or B/F) for the expected minimum uncertainty in flux and position. These expressions are shown to be quite resilient to the oversampling condition, and become thus very valuable benchmark tools to estimate the approximate behavior of the maximum photometric and astrometric precision attainable under pre-specified observing conditions and detector properties.
description: Twenty-nine pages, three figures, two tables. Accepted by PASP
Role of Interferon in the Replication of Human Parainfluenza Virus Type 1 Wild Type and Mutant Viruses in Human Ciliated Airway Epithelium
Creators: name: Hennessey, M.
name: Bartlett, E. J.
name: Murphy, B. R.
name: Schmidt, A. C.
name: Pickles, R. J.
name: Skiadopoulos, M. H.
name: Collins, P. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Human parainfluenza virus type 1 (HPIV1) is a significant cause of pediatric respiratory disease in the upper and lower airways. An in vitro model of human ciliated airway epithelium (HAE), a useful tool for studying respiratory virus-host interactions, was used in this study to show that HPIV1 selectively infects ciliated cells within the HAE and that progeny virus is released from the apical surface with little apparent gross cytopathology. In HAE, type I interferon (IFN) is induced following infection with an HPIV1 mutant expressing defective C proteins with an F170S amino acid substitution, rHPIV1-CF170S, but not following infection with wild-type HPIV1. IFN induction coincided with a 100- to 1,000-fold reduction in virus titer, supporting the hypothesis that the HPIV1 C proteins are critical for the inhibition of the innate immune response. Two recently characterized live attenuated HPIV1 vaccine candidates expressing mutant C proteins were also evaluated in HAE. The vaccine candidates, rHPIV1-CR84G/Δ170HNT553ALY942A and rHPIV1-CR84G/Δ170HNT553ALΔ1710-11, which contain temperature-sensitive (ts) attenuating (att) and non-ts att mutations, were highly restricted in growth in HAE at permissive (32°C) and restrictive (37°C) temperatures. The viruses grew slightly better at 37°C than at 32°C, and rHPIV1-CR84G/Δ170HNT553ALY942A was less attenuated than rHPIV1-CR84G/Δ170HNT553ALΔ1710-11. The level of replication in HAE correlated with that previously observed for African green monkeys, suggesting that the HAE model has potential as a tool for the preclinical evaluation of HPIV1 vaccines, although how these in vitro data will correlate with vaccine virus replication in seronegative human subjects remains to be seen.
Forward-backward multiplicity correlations in pp collisions at high energy in Monte Carlo model with string fusion
Creators: name: Kovalenko, Vladimir
name: Vechernin, Vladimir
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The correlations between multiplicities in two separated rapidity windows, is studied in the framework of the Monte Carlo model based on the picture of string formation in elementary collisions of colour dipoles. The hardness of the elementary collisions is defined by a transverse size of the interacting dipoles. The dependencies of the forward-backward correlation strength on the width and position of the pseudorapidity windows, as well as on transverse momentum range of observed particles were studied. It is demonstrated that taking into account of the string fusion effects improves the agreement with the available experimental data.
description: 4 pages, 3 figures, proc. PANIC 2014
Suffering from the collective cult of cognition
Creators: name: Te Wildt, Bert
Publisher: name: B. te Wildt, Suffering from the collective cult of cognition, «Public history weekly», 2, 2014, n. 41
Year: 2014

description: Why is it that of all the mental diseases on record we are so preoccupied with those occurring at the beginning and at the end of life? The Attention Deficit Hyperactivity Disorder (ADHD) and dementia have both attracted the attention of the medical profession and the wider public only comparatively late in history. Many a physician has even dared to claim that these disorders were not discovered but as it were invented in the past century.
description: Wie kommt es, dass uns von allen psychischen Erkrankungen seit Jahren diejenigen am meisten beschäftigen, die den Lebensanfang und das Lebensende betreffen? Die Aufmerksamkeitsdefizit- und Hyperaktivitätsstörung (ADHS) und die Demenzerkrankungen haben miteinander gemeinsam, dass sie erst relativ spät ins Rampenlicht von Medizin und Öffentlichkeit gerückt sind. Manch ein Psychiater hat sich sogar zu der Behauptung verstiegen, dass sie nicht im vergangenen Jahrhundert entdeckt, sondern quasi erfunden wurden.
ScriptPT.txt
Creators: name: Jouault, Corentin
name: nel, andre
name: Perrichot, Vincent
name: Legendre, Frédéric
name: Condamine, Fabien
Publisher: name: figshare
Year: 2022
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Paleontology
subject: 60206 Palaeoecology

description: PyRate commands (Script.txt): it includes a command list of the Bayesian analyses used to perform analyses using PyRate
Ross River Virus Envelope Glycans Contribute to Type I Interferon Production in Myeloid Dendritic Cells
Creators: name: Shabman, R. S.
name: Heise, M. T.
name: Rogers, K. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Alphaviruses are mosquito-transmitted viruses that cause significant human disease, and understanding how these pathogens successfully transition from the mosquito vector to the vertebrate host is an important area of research. Previous studies demonstrated that mosquito and mammalian-cell-derived alphaviruses differentially induce type I interferons (alpha/beta interferon [IFN-α/β]) in myeloid dendritic cells (mDCs), where the mosquito cell-derived virus is a poor inducer of IFN-α/β compared to the mammalian-cell-derived virus. Furthermore, the reduced IFN-α/β induction by the mosquito cell-derived virus is attributed to differential N-linked glycosylation (29). To further evaluate the role of viral envelope glycans in regulating the IFN-α/β response, studies were performed to assess whether the mosquito cell-derived virus actively inhibits IFN-α/β induction or is simply a poor inducer of IFN-α/β. Coinfection studies using mammalian- and mosquito cell-derived Ross River virus (mam-RRV and mos-RRV, respectively) indicated that mos-RRV was unable to suppress IFN-α/β induction by mam-RRV in mDC cultures. Additionally, a panel of mutant viruses lacking either individual or multiple N-linked glycosylation sites was used to demonstrate that N-linked glycans were essential for high-level IFN-α/β induction by the mammalian-cell-derived virus. These results suggest that the failure of the mosquito cell-derived virus to induce IFN-α/β is due to a lack of complex carbohydrates on the virion rather than the active suppression of the DC antiviral response.
Subtype-Specific Conformational Differences within the V3 Region of Subtype B and Subtype C Human Immunodeficiency Virus Type 1 Env Proteins
Creators: name: Hoffman, N. G.
name: Patel, M. B.
name: Swanstrom, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The V3 region of the human immunodeficiency virus type 1 gp120 Env protein is a key domain in Env due to its role in interacting with the coreceptors CCR5 and CXCR4. We examined potential subtype-specific V3 region differences by comparing patterns of amino acid variability and probing for subtype-specific structures using 11 anti-V3 monoclonal antibodies (V3 MAbs). Differences between the subtypes in patterns of variability were most evident in the stem and turn regions of V3 (positions 9 to 24), with the two subtypes being very similar in the base region. The characteristics of the binding of V3 MAbs to Env proteins of the subtype B virus JR-FL and the subtype C virus BR025 suggested three patterns, as each group of MAbs recognized a specific conformation- or sequence-based epitope. Viruses pseudotyped with Env from JR-FL and BR025 were resistant to neutralization by the V3 MAbs, although the replacement of the Env V3 region of the SF162 virus with the JR-FL V3 created a pseudotyped virus that was hypersensitive to neutralization. A single mutation in V3 (H13R) made this chimeric Env selectively resistant to one group of V3 MAbs, consistent with the mAb binding properties. We hypothesize that there are intrinsic differences in V3 conformation between subtype B and subtype C that are localized to the stem and turn regions and that these differences have two important biological consequences: first, subtype B and subtype C V3 regions can have subtype-specific epitopes that will inherently limit antibody cross-reactivity, and second, V3 conformational differences may potentiate the frequent evolution of R5- into X4-tropic variants of subtype B but limit subtype C virus from using the same mechanism to evolve X4-tropic variants as efficiently.
Surface Loop Dynamics in Adeno-Associated Virus Capsid Assembly
Creators: name: Govindasamy, L.
name: DiPrimio, N.
name: Asokan, A.
name: Agbandje-McKenna, M.
name: Samulski, R. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The HI loop is a prominent domain on the adeno-associated virus (AAV) capsid surface that extends from each viral protein (VP) subunit overlapping the neighboring fivefold VP. Despite the highly conserved nature of the residues at the fivefold pore, the HI loops surrounding this critical region vary significantly in amino acid sequence between the AAV serotypes. In order to understand the role of this unique capsid domain, we ablated side chain interactions between the HI loop and the underlying EF loop in the neighboring VP subunit by generating a collection of deletion, insertion, and substitution mutants. A mutant lacking the HI loop was unable to assemble particles, while a substitution mutant (10 glycine residues) assembled particles but was unable to package viral genomes. Substitution mutants carrying corresponding regions from AAV1, AAV4, AAV5, and AAV8 yielded (i) particles with titers and infectivity identical to those of AAV2 (AAV2 HI1 and HI8), (ii) particles with a decreased virus titer (1 log) but normal infectivity (HI4), and (iii) particles that synthesized VPs but were unable to assemble into intact capsids (HI5). AAV5 HI is shorter than all other HI loops by one amino acid. Replacing the missing residue (threonine) in AAV2 HI5 resulted in a moderate particle assembly rescue. In addition, we replaced the HI loop with peptides varying in length and amino acid sequence. This region tolerated seven-amino-acid peptide substitutions unless they spanned a conserved phenylalanine at amino acid position 661. Mutation of this highly conserved phenylalanine to a glycine resulted in a modest decrease in virus titer but a substantial decrease (1 log order) in infectivity. Subsequently, confocal studies revealed that AAV2 F661G is incapable of efficiently completing a key step in the infectious pathway nuclear entry, hinting at a possible perturbation of VP1 phospholipase activity. Molecular modeling studies with the F661G mutant suggest that disruption of interactions between F661 and an underlying P373 residue in the EF loop of the neighboring subunit might adversely affect incorporation of the VP1 subunit at the fivefold axis. Western blot analysis confirmed inefficient incorporation of VP1, as well as a proteolytically processed VP1 subunit that could account for the markedly reduced infectivity. In summary, our studies show that the HI loop, while flexible in amino acid sequence, is critical for AAV capsid assembly, proper VP1 subunit incorporation, and viral genome packaging, all of which implies a potential role for this unique surface domain in viral infectivity.
The next-generation BLASTPol experiment
Creators: name: Dober, Bradley
name: Ade, Peter A. R.
name: Ashton, Peter
name: Angilè, Francesco E.
name: Beall, James A.
name: Becker, Dan
name: Bradford, Kristi J.
name: Che, George
name: Cho, Hsiao-Mei
name: Devlin, Mark J.
name: Fissel, Laura M.
name: Fukui, Yasuo
name: Galitzki, Nicholas
name: Gao, Jiansong
name: Groppi, Christopher E.
name: Hillbrand, Seth
name: Hilton, Gene C.
name: Hubmayr, Johannes
name: Irwin, Kent D.
name: Klein, Jeffrey
name: Van Lanen, Jeff
name: Li, Dale
name: Li, Zhi-Yun
name: Lourie, Nathan P.
name: Mani, Hamdi
name: Martin, Peter G.
name: Mauskopf, Philip
name: Nakamura, Fumitaka
name: Novak, Giles
name: Pappas, David P.
name: Pascale, Enzo
name: Santos, Fabio P.
name: Savini, Giorgio
name: Scott, Douglas
name: Stanchfield, Sara
name: Ullom, Joel N.
name: Underhill, Matthew
name: Vissers, Michael R.
name: Ward-Thompson, Derek
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry (BLASTPol) is a suborbital mapping experiment designed to study the role magnetic fields play in star formation. BLASTPol has had two science flights from McMurdo Station, Antarctica in 2010 and 2012. These flights have produced thousands of polarization vectors at 250, 350 and 500 microns in several molecular cloud targets. We present the design, specifications, and progress towards the next-generation BLASTPol experiment (BLAST-TNG). BLAST-TNG will fly a 40% larger diameter primary mirror, with almost 8 times the number of polarization-sensitive detectors resulting in a factor of 16 increase in mapping speed. With a spatial resolution of 22 arcseconds and four times the field of view of BLASTPol, BLAST-TNG will bridge the angular scales between Planck's low resolution all-sky maps and ALMA's ultra-high resolution narrow fields. The new receiver has a larger cryogenics volume, allowing for a 28 day hold time. BLAST-TNG employs three arrays of Microwave Kinetic Inductance Detectors (MKIDs) with 30% fractional bandwidth at 250, 350 and 500 microns. In this paper, we will present the new BLAST-TNG instrument and science objectives.
description: 12 pages, 6 figures. Presented at SPIE Ground-based and Airborne Telescopes V, June 23, 2014. To be published in Proceedings of SPIE Volume 9145
Upregulation of the TLR3 Pathway by Kaposi's Sarcoma-Associated Herpesvirus during Primary Infection
Creators: name: West, J.
name: Damania, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with several different human malignancies, including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. KSHV establishes lifelong latency in the host and modulates the host immune response. Innate immunity is critical for controlling de novo viral infection. Toll-like receptors (TLRs) are key components of the innate immune system, and they serve as pathogen recognition receptors that stimulate the host antiviral response. In particular, TLR3 has been implicated in RNA virus recognition. Currently, there is no information regarding how KSHV infection modulates any TLR pathway. We report the first evidence that KSHV upregulates TLR3 expression in human monocytes during primary infection. This is also the first demonstration of a human DNA tumor virus upregulating TLR3, a TLR that thus far has been associated with the recognition of RNA viruses. We found that KSHV upregulates the TLR3 pathway and induces TLR3-specific cytokines and chemokines, including beta 1 interferon (IFN-β1) and CXCL10 (IP-10). Small interfering RNAs directed against TLR3 greatly reduced the ability of KSHV to upregulate IFN-β1 and CXCL10 upon infection.
Robust Statistical Approach for Extraction of Moving Human Silhouettes from Videos
Creators: name: Devi, Oinam Binarani
name: Paul, Nissi S.
name: Singh, Y. Jayanta
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Human pose estimation is one of the key problems in computer vision that has been studied in the recent years. The significance of human pose estimation is in the higher level tasks of understanding human actions applications such as recognition of anomalous actions present in videos and many other related applications. The human poses can be estimated by extracting silhouettes of humans as silhouettes are robust to variations and it gives the shape information of the human body. Some common challenges include illumination changes, variation in environments, and variation in human appearances. Thus there is a need for a robust method for human pose estimation. This paper presents a study and analysis of approaches existing for silhouette extraction and proposes a robust technique for extracting human silhouettes in video sequences. Gaussian Mixture Model (GMM) A statistical approach is combined with HSV (Hue, Saturation and Value) color space model for a robust background model that is used for background subtraction to produce foreground blobs, called human silhouettes. Morphological operations are then performed on foreground blobs from background subtraction. The silhouettes obtained from this work can be used in further tasks associated with human action interpretation and activity processes like human action classification, human pose estimation and action recognition or action interpretation.
description: 10 pages, 5 figures
A Limited Group of Class I Histone Deacetylases Acts To Repress Human Immunodeficiency Virus Type 1 Expression
Creators: name: Hazuda, D. J.
name: Keedy, K. S.
name: Espeseth, A.
name: Margolis, D. M.
name: Archin, N. M.
name: Gates, A. T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Silencing of the integrated human immunodeficiency virus type 1 (HIV-1) genome in resting CD4+ T cells is a significant contributor to the persistence of infection, allowing the virus to evade both immune detection and pharmaceutical attack. Nonselective histone deacetylase (HDAC) inhibitors are capable of inducing expression of quiescent HIV-1 in latently infected cells. However, potent global HDAC inhibition can induce host toxicity. To determine the specific HDACs that regulate HIV-1 transcription, we evaluated HDAC1 to HDAC11 RNA expression and protein expression and compartmentalization in the resting CD4+ T cells of HIV-1-positive, aviremic patients. HDAC1, -3, and -7 had the highest mRNA expression levels in these cells. Although all HDACs were detected in resting CD4+ T cells by Western blot analysis, HDAC5, -8, and -11 were primarily sequestered in the cytoplasm. Using chromatin immunoprecipitation assays, we detected HDAC1, -2, and -3 at the HIV-1 promoter in Jurkat J89GFP cells. Targeted inhibition of HDACs by small interfering RNA demonstrated that HDAC2 and HDAC3 contribute to repression of HIV-1 long terminal repeat expression in the HeLa P4/R5 cell line model of latency. Together, these results suggest that HDAC inhibitors specific for a limited number of class I HDACs may offer a targeted approach to the disruption of persistent HIV-1 infection.
Is It Still Data? Scholarly Editing of Text From Early Born-Digital Heritage
Creators: name: Roeder, Torsten
Publisher: name: Zenodo
Year: 2022
Subjects: Digital Scholarly Edition
Digital Heritage
Retrocomputing
Preservation

description: Presentation slides for a long paper on preservation and digital scholarly edition of 1980's and 1990's Disk Magazines (electronic journals published on floppy) and related questions on TEI encoding practices.
A Strongly Transdominant Mutation in the Human Immunodeficiency Virus Type 1 gag Gene Defines an Achilles Heel in the Virus Life Cycle
Creators: name: Lee, S.-K.
name: Harris, J.
name: Swanstrom, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The human immunodeficiency virus type 1 (HIV-1) protease (PR) makes five obligatory cleavages in the viral Gag polyprotein precursor. The cleavage events release the virion structural proteins from the precursor and allow the virion to undergo maturation to become infectious. The protease cleavage between the matrix protein (MA) domain and the adjacent capsid protein (CA) domain releases CA from the membrane-anchored MA and allows the N terminus of CA to refold into a structure that facilitates the formation of hexamer arrays that represent the structural unit of the capsid shell. In this study, we analyzed the extent to which each of the HIV-1 Gag processing sites must be cleaved by substituting the P1-position amino acid at each processing site with Ile. A mutation that blocks cleavage at the MA/CA processing site (Y132I) displayed a strong transdominant effect when tested in a phenotypic mixing strategy, inhibiting virion infectivity with a 50% inhibitory concentration of only 4% of the mutant relative to the wild type. This mutation is 10- to 20-fold more potent in phenotypic mixing than an inactivating mutation in the viral protease, the target of many successful inhibitors, and more potent than an inactivating mutation at any of the other Gag cleavage sites. The transdominant effect is manifested as the assembly of an aberrant virion core. Virus containing 20% of the Y132I mutant and 80% of the wild type (to assess the transdominant effect on infectivity) was blocked either before reverse transcription (RT) or at an early RT step. The ability of a small amount of the MA/CA fusion protein to poison the oligomeric assembly of infectious virus identifies an essential step in the complex process of virion formation and maturation. The effect of a small-molecule inhibitor that is able to block MA/CA cleavage even partially would be amplified by this transdominant negative effect on the highly orchestrated process of virion assembly.
Alphavirus-Adjuvanted Norovirus-Like Particle Vaccines: Heterologous, Humoral, and Mucosal Immune Responses Protect against Murine Norovirus Challenge
Creators: name: Lindesmith, L.
name: Thompson, J. M.
name: Johnston, R. E.
name: LoBue, A. D.
name: Baric, R. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The development of an effective norovirus vaccine likely requires the capacity to protect against infection with multiple norovirus strains. Advanced recombinant genetic systems and the recent discovery of a mouse-tropic norovirus strain (MNV) provide robust model systems for vaccine efficacy studies. We coadministered multivalent norovirus-like particle (VLP) vaccines with alphavirus adjuvant particles to mice and evaluated homotypic and heterotypic humoral and protective immunity to human and murine norovirus strains. Multivalent VLP vaccines induced robust receptor-blocking antibody responses to heterologous human strains not included in the vaccine composition. Inclusion of alphavirus adjuvants in the inoculum significantly augmented VLP-induced systemic and mucosal immunity compared to the responses induced by low-dose CpG DNA, validating the utility of such adjuvants with VLP antigens. Furthermore, multivalent vaccination, either including or excluding MNV VLP, resulted in significantly reduced viral loads following MNV challenge. Passive transfer of sera from mice monovalently vaccinated with MNV VLP to immunodeficient or immunocompetent mice protected against MNV infection; however, adoptive transfer of purified CD4+ or CD8+ cells did not influence viral loads in murine tissues. Together, these data suggest that humoral immunity induced by multivalent norovirus vaccines may protect against heterologous norovirus challenge.