cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Liquid refractive index sensing independent of opacity using an optofluidic sensor based on diffraction
Creators: name: Xu, Zhida
name: Liu, Logan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We have implemented a multi-functional optofluidic sensor that can monitor changes in the refractive index and pressure of biofluid simultaneously and can detect free-solution molecular interaction in-situ. In this paper, we demonstrate two major improvements of this sensor proven by both simulation and experiments. One improvement is the broader measurement range of refractive index by making the diffraction grating with high-index polymer. The other improvement is the separation of refractive index sensing from opacity sensing by using the relative power ratio of diffraction orders. This simple, compact and low-cost multi-functional optofluidic sensor has the potential to be used for in-situ biofluid monitoring.
description: 4 figures
title: OECD GD 239 Honey bee larvae in vitro testing and solvents: on the job training
Creators: name: Kimmel, Stefan
name: Cornement, Magdaléna
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Julius-Kühn-Archiv, 462 (Hazards of pesticides to bees : 13th International Symposium of the ICP-PR Bee Protection Group ; 18. - 20. October 2017, València (Spain) - Proceedings -)
Mutagenesis of Adeno-Associated Virus Type 2 Capsid Protein VP1 Uncovers New Roles for Basic Amino Acids in Trafficking and Cell-Specific Transduction
Creators: name: DiPrimio, N.
name: Samulski, R. J.
name: Johnson, J. S.
name: McCown, T. J.
name: Li, C.
name: Weinberg, M. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The N termini of the capsid proteins VP1 and VP2 of adeno-associated virus (AAV) play important roles in subcellular steps of infection and contain motifs that are highly homologous to a phospholipase A2 (PLA2) domain and nuclear localization signals (NLSs). To more clearly understand how virion components influence infection, we have generated mutations in these regions and examined their effects on subcellular trafficking, capsid stability, transduction, and sensitivity to pharmacological enhancement. All mutants tested assembled into capsids; retained the correct ratio of VP1, VP2, and VP3; packaged DNA similarly to recombinant AAV2 (rAAV2); and displayed similar stability profiles when heat denatured. Confocal microscopy demonstrated that these mutants trafficked through a perinuclear region in the vicinity of the Golgi apparatus, with a subset of mutants displaying more-diffuse localization consistent with an NLS-deficient phenotype. When tested for viral transduction, two mutant classes emerged. Class I (BR1−, BR2−, and BR2+K) displayed partial transduction, whereas class II (VP3only, 75HD/AN, BR3−, and BR3+K) were severely defective. Surprisingly, one class II mutant (BR3+K) trafficked identically to rAAV2 and accumulated in the nucleolus, a step recently described by our laboratory that occurs with wild-type infection. The BR3+K mutant, containing an alanine-to-lysine substitution in the third basic region of VP1, was 10- to 100-fold-less infectious than rAAV2 in transformed cell lines (such as HEK-293, HeLa, and CV1-T cells), but in contrast, it was indistinguishable from rAAV2 in several nontransformed cell lines, as well as in tissues (liver, brain, and muscle) in vivo. Complementation studies with pharmacological adjuvants or adenovirus coinfection suggested that additional positive charges in NLS regions restrict mobilization in the nucleus and limit transduction in a transformed-cell-specific fashion. Remarkably, besides displaying cell-type-specific transduction, this is the first description of a capsid mutant indicating that nuclear entry is not sufficient for AAV-mediated transduction and suggests that additional steps (i.e., subnuclear mobilization or uncoating) limit successful AAV infection.
Conformal Newton-Hooke algebras, Niederer's transformation and Pais-Uhlenbeck oscillator
Creators: name: Andrzejewski, K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Dynamical systems invariant under the action of the l-conformal Newton-Hooke algebras are constructed by the method of nonlinear realizations. The relevant first order Lagrangians together with the corresponding Hamiltonians are found. The relation to the Galajinsky and Masterov [Phys. Lett. B 723 (2013) 190] approach as well as the higher derivatives formulation is discussed. The generalized Niederer's transformation are presented which relate the systems under consideration to those invariant under the action of the l-conformal Galilei algebra [Nucl. Phys. B 876 (2013) 309]. As a nice application of these results an analogue of Niederer's transformation, on the Hamiltonian level, for the Pais-Uhlenbeck oscillator is constructed.
Excluded-Volume Approximation for Supernova Matter
Creators: name: Yudin, A. V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: A general scheme of the excluded-volume approximation as applied to multicomponent systems with an arbitrary degree of degeneracy has been developed. This scheme also admits an allowance for additional interactions between the components of a system. A specific form of the excluded-volume approximation for investigating supernova matter at subnuclear densities has been found from comparison with the hard-sphere model. The possibility of describing the phase transition to uniform nuclear matter in terms of the formalism under consideration is discussed.
description: 21 pages, 9 figures
Kepler Eclipsing Binary Stars. V. Identification of 31 Eclipsing Binaries in the K2 Engineering Data-set
Creators: name: Conroy, Kyle E.
name: Prša, Andrej
name: Stassun, Keivan G.
name: Bloemen, Steven
name: Parvizi, Mahmoud
name: Quarles, Billy
name: Boyajian, Tabetha
name: Barclay, Thomas
name: Shporer, Avi
name: Latham, David W.
name: Abdul-Masih, Michael
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Over 2500 eclipsing binaries were identified and characterized from the ultra-precise photometric data provided by the Kepler space telescope. Kepler is now beginning its second mission, K2, which is proving to again provide ultra-precise photometry for a large sample of eclipsing binary stars. In the 1951 light curves covering 12 days in the K2 engineering data-set, we have identified and determined the ephemerides for 31 eclipsing binaries that demonstrate the capabilities for eclipsing binary science in the upcoming campaigns in K2. Of those, 20 are new discoveries. We describe both manual and automated approaches to harvesting the complete set of eclipsing binaries in the K2 data, provide identifications and details for the full set of eclipsing binaries present in the engineering data-set, and discuss the prospects for application of eclipsing binary searches in the K2 mission.
description: 12 pages, 2 figures, submitted to PASP
Creation of magnetic spots at the neutron star surface
Creators: name: Geppert, U.
name: Viganò, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: According to the partially screened gap scenario, an efficient electron-positron pair creation, a general precondition of radio-pulsar activity, relies on the existence of magnetic spots, i.e., local concentrations of strong and small scale magnetic field structures at the surface of neutron stars. They have a strong impact on the surface temperature, which is potentially observable. Here we reinforce the idea that such magnetic spots can be formed by extracting magnetic energy from the toroidal field that resides in deep crustal layers, via Hall drift. We study and discuss the magneto-thermal evolution of qualitatively different neutron star models and initial magnetic field configurations that lead to the creation of magnetic spots. We find that magnetic spots can be created on a timescale of $10^4$ years with magnetic field strengths $\gtrsim 5\times 10^{13}$ G, provided almost the whole magnetic energy is stored in its toroidal component, and that the conductivity in the inner crust is not too large. The lifetime of the magnetic spots is at least $\sim$one million of years, being longer if the initial field permeates both core and crust.
description: Accepted by M.N.R.A.S
A Cascade Neural Network Architecture investigating Surface Plasmon Polaritons propagation for thin metals in OpenMP
Creators: name: Bonanno, Francesco
name: Capizzi, Giacomo
name: Sciuto, Grazia Lo
name: Napoli, Christian
name: Pappalardo, Giuseppe
name: Tramontana, Emiliano
Publisher: name: arXiv
Year: 2014
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: I.2.6; I.5.1; I.2.11
subject: 68T05

description: Surface plasmon polaritons (SPPs) confined along metal-dielectric interface have attracted a relevant interest in the area of ultracompact photonic circuits, photovoltaic devices and other applications due to their strong field confinement and enhancement. This paper investigates a novel cascade neural network (NN) architecture to find the dependance of metal thickness on the SPP propagation. Additionally, a novel training procedure for the proposed cascade NN has been developed using an OpenMP-based framework, thus greatly reducing training time. The performed experiments confirm the effectiveness of the proposed NN architecture for the problem at hand.
Respiratory Syncytial Virus Engineered To Express the Cystic Fibrosis Transmembrane Conductance Regulator Corrects the Bioelectric Phenotype of Human Cystic Fibrosis Airway Epithelium In Vitro
Creators: name: Kwilas, A. R.
name: Peeples, M. E.
name: Zhang, L.
name: Yednak, M. A.
name: Pickles, R. J.
name: Collins, P. L.
name: Liesman, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Cystic fibrosis (CF) is the most common lethal recessive genetic disease in the Caucasian population. It is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene that is normally expressed in ciliated airway epithelial cells and the submucosal glands of the lung. Since the CFTR gene was first characterized in 1989, a major goal has been to develop an effective gene therapy for CF lung disease, which has the potential to ameliorate morbidity and mortality. Respiratory syncytial virus (RSV) naturally infects the ciliated cells in the human airway epithelium. In addition, the immune response mounted against an RSV infection does not prevent subsequent infections, suggesting that an RSV-based vector might be effectively readministered. To test whether the large 4.5-kb CFTR gene could be expressed by a recombinant RSV and whether infectious virus could be used to deliver CFTR to ciliated airway epithelium derived from CF patients, we inserted the CFTR gene into four sites in a recombinant green fluorescent protein-expressing RSV (rgRSV) genome to generate virus expressing four different levels of CFTR protein. Two of these four rgRSV-CFTR vectors were capable of expressing CFTR with little effect on viral replication. rgRSV-CFTR infection of primary human airway epithelial cultures derived from CF patients resulted in expression of CFTR protein that was properly localized at the luminal surface and corrected the chloride ion channel defect in these cells.
Phosphorene oxides: bandgap engineering of phosphorene by oxidation
Creators: name: Ziletti, A.
name: Carvalho, A.
name: Trevisanutto, P. E.
name: Campbell, D. K.
name: Coker, D. F.
name: Neto, A. H. Castro
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We show that oxidation of phosphorene can lead to the formation of a new family of planar (2D) and tubular (1D) oxides and sub-oxides, most of them insulating. This confers to black phosphorus a native oxide that can be used as barrier material and protective layer. Further, the bandgap of phosphorene oxides depends on the oxygen concentration, suggesting that controlled oxidation can be used as a means to engineer the bandgap. For the oxygen saturated composition, P$_2$O$_5$, both the planar and tubular phases have a large bandgap energy of about 8.5eV, and are transparent in the near UV. These two forms of phosphorene oxides are predicted to have the same formation enthalpy as o$^\prime$-P$_2$O$_5$, the most stable of the previously known forms of phosphorus pentoxide.
description: 10 pages, 12 figures
RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1
Creators: name: Martin, D. P.
name: Negroni, M.
name: Simon-Loriere, E.
name: Weeks, K. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Many viruses, including retroviruses, undergo frequent recombination, a process which can increase their rate of adaptive evolution. In the case of HIV, recombination has been responsible for the generation of numerous intersubtype recombinant variants with epidemiological importance in the AIDS pandemic. Although it is known that fragments of genetic material do not combine randomly during the generation of recombinant viruses, the mechanisms that lead to preferential recombination at specific sites are not fully understood. Here we reanalyze recent independent data defining (i) the structure of a complete HIV-1 RNA genome and (ii) favorable sites for recombination. We show that in the absence of selection acting on recombinant genomes, regions harboring RNA structures in the NL4-3 model strain are strongly predictive of recombination breakpoints in the HIV-1 env genes of primary isolates. In addition, we found that breakpoints within recombinant HIV-1 genomes sampled from human populations, which have been acted upon extensively by natural selection, also colocalize with RNA structures. Critically, junctions between genes are enriched in structured RNA elements and are also preferred sites for generating functional recombinant forms. These data suggest that RNA structure-mediated recombination allows the virus to exchange intact genes rather than arbitrary subgene fragments, which is likely to increase the overall viability and replication success of the recombinant HIV progeny.
Secondary Structure of the Mature Ex Virio Moloney Murine Leukemia Virus Genomic RNA Dimerization Domain
Creators: name: Gherghe, C.
name: Gorelick, R. J.
name: Weeks, K. M.
name: Leonard, C. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Retroviral genomes are dimeric, comprised of two sense-strand RNAs linked at their 5′ ends by noncovalent base pairing and tertiary interactions. Viral maturation involves large-scale morphological changes in viral proteins and in genomic RNA dimer structures to yield infectious virions. Structural studies have largely focused on simplified in vitro models of genomic RNA dimers even though the relationship between these models and authentic viral RNA is unknown. We evaluate the secondary structure of the minimal dimerization domain in genomes isolated from Moloney murine leukemia virions using a quantitative and single nucleotide resolution RNA structure analysis technology (selective 2′-hydroxyl acylation analyzed by primer extension, or SHAPE). Results are consistent with an architecture in which the RNA dimer is stabilized by four primary interactions involving two sets of intermolecular base pairs and two loop-loop interactions. The dimerization domain can independently direct its own folding since heating and refolding reproduce the same structure as visualized in genomic RNA isolated from virions. Authentic ex virio RNA has a SHAPE reactivity profile similar to that of a simplified transcript dimer generated in vitro, with the important exception of a region that appears to form a compact stem-loop only in the virion-isolated RNA. Finally, we analyze the conformational changes that accompany folding of monomers into dimers in vitro. These experiments support well-defined structural models for an authentic dimerization domain and also emphasize that many features of mature genomic RNA dimers can be reproduced in vitro using properly designed, simplified RNAs.
title: Epigenetic variation in lingonberries
Creators: name: Sikdar, Arindam
Publisher: name: Memorial University of Newfoundland
Year: 2021

description: Epigenetic variation plays a role in developmental gene regulation, response to the environment, and in natural variation of gene expression levels. The purpose of the study is to investigate cytosine methylation and secondary compounds of lingonberry (Vaccinium vitis-idaea) among cutting-propagated cultivar Erntedank (ED) and its tissue-culture plants (NC, LC). This was analyzed by using Methylation Sensitive Amplified Polymorphism (MSAP) where the primers were cleaved in cytosine residues at 5'-CCGG-3' sites in CpG-islands. In leaf regenerants (LC1), we observed highest methylated sites from all primer combinations (108 bands), with their highest variation in secondary metabolites. We measured that tissue-cultured plants showed higher methylation bands than maternal plants. For instance, we identified the mother plant ED exhibited 79 bands of methylation, which is comparatively low. On the other hand, we observed the highest total phenolic content in (NC3) but LC1 represents low phenolic content. Our study showed more methylation in micropropagated plants (NC1, NC2, NC3 and LC1) than those derived from ED cutting cultivar where methylation was not present. On the contrary, we observed higher secondary metabolites in cutting cultivar ED but comparatively less in micropropagated plants (NC1, NC2, NC3 LC1). Hence, our study confirmed that higher methylation sites observed in micropropagated plants and less amount of secondary metabolites appears.
Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6
Creators: name: Govindasamy, L.
name: Parent, K. N.
name: Baker, T. S.
name: Gurda, B. L.
name: Ng, R.
name: Agbandje-McKenna, M.
name: McKenna, R.
name: Kozyreva, O. G.
name: Samulski, R. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The three-dimensional structure of adeno-associated virus (AAV) serotype 6 (AAV6) was determined using cryo-electron microscopy and image reconstruction and using X-ray crystallography to 9.7- and 3.0-Å resolution, respectively. The AAV6 capsid contains a highly conserved, eight-stranded (βB to βI) β-barrel core and large loop regions between the strands which form the capsid surface, as observed in other AAV structures. The loops show conformational variation compared to other AAVs, consistent with previous reports that amino acids in these loop regions are involved in differentiating AAV receptor binding, transduction efficiency, and antigenicity properties. Toward structure-function annotation of AAV6 with respect to its unique dual glycan receptor (heparan sulfate and sialic acid) utilization for cellular recognition, and its enhanced lung epithelial transduction compared to other AAVs, the capsid structure was compared to that of AAV1, which binds sialic acid and differs from AAV6 in only 6 out of 736 amino acids. Five of these residues are located at or close to the icosahedral 3-fold axis of the capsid, thereby identifying this region as imparting important functions, such as receptor attachment and transduction phenotype. Two of the five observed amino acids are located in the capsid interior, suggesting that differential AAV infection properties are also controlled by postentry intracellular events. Density ordered inside the capsid, under the 3-fold axis in a previously reported, conserved AAV DNA binding pocket, was modeled as a nucleotide and a base, further implicating this capsid region in AAV genome recognition and/or stabilization.
COVID-19 in China. The Great Wall of Technology
Creators: name: Gatti, Emanuele
name: Strizzolo, Nicola
Publisher: name: Universita' degli Studi di Salerno
Year: 2020
Subjects: COVID-19
New media
Space
Time
Chinese media
WeChat

description: China is the first country to have faced an extensive contagion of Covid-19. The response it has given, in terms of prevention and control measures, has been effective in eradicating the virus, even though not completely. Those measures were based on an extensive and widespread use of technologies. The strategies adopted were not the result of improvisation: the social, cultural and technological structures were already in place well before the epidemic took place. In light of the news and the media theory, the present contribution draws upon the anecdotal experience of one of the two authors, who lives in China and has been there during the epidemic. Though the Chinese approach was, indeed successful, we argue that it is doubtful that such a model can be exported to countries with different history, culture and socio-political background.
Weighted Aggregated Sum Product Assessment
Creators: name: Ale Ebrahim, Nader
name: Sorooshian, Shahryar
name: Azizan, Noor Azlinna
Publisher: name: figshare
Year: 2022
Subjects: subject: 91099 Manufacturing Engineering not elsewhere classified
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: 100306 Industrial Molecular Engineering of Nucleic Acids and Proteins
subject: FOS: Industrial biotechnology
subject: 170202 Decision Making
subject: FOS: Psychology
subject: 80605 Decision Support and Group Support Systems
subject: FOS: Computer and information sciences
subject: 220302 Decision Theory
subject: FOS: Philosophy, ethics and religion

description: Multiple Criteria decision-making (MCDM) approaches are required for complex issue resolution. However, it is debatable whether MCDMs applicability will be able to stay within the analytical possibilities for dealing with divorce issues. As a result, one of the newly introduced MCDMs Weighted aggregated sum product assessment (WASPAS), is chosen for evaluation. Therefore, this study examined 388 documents from archive of the Scopus database. To evaluate the diversity of the technique's application, the data analysis looked at a few bibliometrics measures. So, the publishing hosts and their influence patterns are displayed, the vast majority of the documents were in the fields of engineering and computer science. According to the findings, the WASPAS can deal with variety of problem-solving scenarios. Hence, this work is summed up with the aim of lowering uncertainty among decision-makers and scholars.
The existence of the Lambda effect in the solar convection zone indicated by SDO observations
Creators: name: Ruediger, Guenther
name: Kueker, Manfred
name: Tereshin, Ilya
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The empirical finding with data from the Solar Dynamics Observatory (SDO) of positive (negative) horizontal Reynolds stress at the northern (southern) hemisphere for solar giant cells (Hathaway et al. 2013) is discussed for its consequences for the theory of the solar/stellar differential rotation. Solving the nonlinear Reynolds equation for the angular velocity under neglect of the meridional circulation we show that the horizontal Reynolds stress of the northern hemisphere is always negative at the surface but it is positive in the bulk of the solar convection zone by the action of the Lambda effect. The Lambda effect, which describes the angular momentum transport of rigidly rotating anisotropic turbulence and which avoids a rigid-body rotation of the convection zones, is in horizontal direction of cubic power in the rotation rate $Ω$ and it is always equatorwards directed. Theories without Lambda effect which may also provide the observed solar rotation law only by the action of a meridional circulation lead to a horizontal Reynolds stress with the opposite sign as observed.
description: 4 pages, 6 figures
T Cells Facilitate Recovery from Venezuelan Equine Encephalitis Virus-Induced Encephalomyelitis in the Absence of Antibody
Creators: name: Brooke, C. B.
name: Whitmore, A. C.
name: Johnston, R. E.
name: White, L. J.
name: Deming, D. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne RNA virus of the genus Alphavirus that is responsible for a significant disease burden in Central and South America through sporadic outbreaks into human and equid populations. For humans, 2 to 4% of cases are associated with encephalitis, and there is an overall case mortality rate of approximately 1%. In mice, replication of the virus within neurons of the central nervous system (CNS) leads to paralyzing, invariably lethal encephalomyelitis. However, mice infected with certain attenuated mutants of the virus are able to control the infection within the CNS and recover. To better define what role T cell responses might be playing in this process, we infected B cell-deficient μMT mice with a VEEV mutant that induces mild, sublethal illness in immune competent mice. Infected μMT mice rapidly developed the clinical signs of severe paralyzing encephalomyelitis but were eventually able to control the infection and recover fully from clinical illness. Recovery in this system was T cell dependent and associated with a dramatic reduction in viral titers within the CNS, followed by viral persistence in the brain. Further comparison of the relative roles of T cell subpopulations within this system revealed that CD4+ T cells were better producers of gamma interferon (IFN-γ) than CD8+ T cells and were more effective at controlling VEEV within the CNS. Overall, these results suggest that T cells, especially CD4+ T cells, can successfully control VEEV infection within the CNS and facilitate recovery from a severe viral encephalomyelitis.
The A20 Deubiquitinase Activity Negatively Regulates LMP1 Activation of IRF7
Creators: name: Pagano, J. S.
name: Ning, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: A20 possesses both deubiquitinase (DUB) and ubiquitin E3 ligase activities that are required for termination of Toll-like receptor (TLR) signaling leading to NF-κB activation and for blockage of tumor necrosis factor (TNF)-induced cytotoxicity and apoptosis. A20 is induced by the Epstein-Barr virus (EBV) oncoprotein LMP1. However, its dual ubiquitin-editing activities have not been investigated in the context of either EBV infection or IRF7 responses. Both A20 and IRF7 have oncogenic properties. We have recently shown that LMP1 activates IRF7 through K63-linked ubiquitination which requires RIP1 and TRAF6, but how this ubiquitination event is regulated has not been studied. Here, we show that A20 negatively regulates IRF7 transcriptional activity induced by LMP1. Deletion or mutation of A20 C-terminal zinc finger motifs had no effect on the inhibition of IRF7 activity, whereas DUB-deficient truncation or point mutation ablated the ability of A20 to inhibit IRF7. Correspondingly, the A20 N-terminal DUB domain, but not the C-terminal E3 ligase domain, interacts physically with IRF7. Transient expression of A20 reduced K63-linked ubiquitination of IRF7 in vivo, but an in vitro deubiquitination assay with purified constituents shows that IRF7 did not act as a substrate for A20 DUB activity. Moreover, A20 interacts with IRF7 endogenously in latently EBV-infected type 3 Raji cells, in which expression of both A20 and IRF7 is constitutively induced by the considerable level of endogenous LMP1. Knockdown of endogenous A20 in Raji cells by expression of A20 short hairpin RNA (shRNA) vectors increases endogenous IRF7 activity and ubiquitination, as well as the protein level of LMP1, a target of IRF7. Thus, A20 negatively regulates LMP1-stimulated IRF7 ubiquitination and activity in EBV latency, and its DUB activity is indispensable for this function. Finally, we discussed the regulation and function of IRFs in EBV latency.
Simple structured illumination microscope setup with high acquisition speed by using a spatial light modulator
Creators: name: Förster, Ronny
name: Lu-Walther, Hui-Wen
name: Jost, Aurélie
name: Kielhorn, Martin
name: Wicker, Kai
name: Heintzmann, Rainer
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We describe a two-beam interference structured illumination fluorescence microscope. The novelty of the presented system lies in its simplicity. A programmable electro-optical spatial light modulator in an intermediate image plane enables precise and rapid control of the excitation pattern in the specimen. The contrast of the projected light pattern is strongly influenced by the polarization state of the light entering the high NA objective. To achieve high contrast, we use a segmented polarizer. Furthermore, a mask with six holes blocks unwanted components in the spatial frequency spectrum of the illumination grating. Both these passive components serve their purpose in a simpler and almost as efficient way as active components. We demonstrate a lateral resolution of 114.2 +- 9.5 nm at a frame rate of 7.6 fps per reconstructed 2D slice.
The Epstein-Barr Virus (EBV)-Encoded Protein Kinase, EBV-PK, but Not the Thymidine Kinase (EBV-TK), Is Required for Ganciclovir and Acyclovir Inhibition of Lytic Viral Production
Creators: name: Pagano, J. S.
name: Gershburg, E.
name: Kenney, S. C.
name: Fingeroth, J. D.
name: Hagemeier, S. R.
name: Meng, Q.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Ganciclovir (GCV) and acyclovir (ACV) are guanine nucleoside analogues that inhibit lytic herpesvirus replication. GCV and ACV must be monophosphorylated by virally encoded enzymes to be converted into nucleotides and incorporated into viral DNA. However, whether GCV and/or ACV phosphorylation in Epstein-Barr virus (EBV)-infected cells is mediated primarily by the EBV-encoded protein kinase (EBV-PK), the EBV-encoded thymidine kinase (EBV-TK), or both is controversial. To examine this question, we constructed EBV mutants containing stop codons in either the EBV-PK or EBV-TK open reading frame and selected for stable 293T clones latently infected with wild-type EBV or each of the mutant viruses. Cells were induced to the lytic form of viral replication with a BZLF1 expression vector in the presence and absence of various doses of GCV and ACV, and infectious viral titers were determined by a green Raji cell assay. As expected, virus production in wild-type EBV-infected 293T cells was inhibited by both GCV (50% inhibitory concentration [IC50] = 1.5 μM) and ACV (IC50 = 4.1 μM). However, the EBV-PK mutant (which replicates as well as the wild-type (WT) virus in 293T cells) was resistant to both GCV (IC50 = 19.6 μM) and ACV (IC50 = 36.4 μM). Expression of the EBV-PK protein in trans restored GCV and ACV sensitivity in cells infected with the PK mutant virus. In contrast, in 293T cells infected with the TK mutant virus, viral replication remained sensitive to both GCV (IC50 = 1.2 μM) and ACV (IC50 = 2.8 μM), although susceptibility to the thymine nucleoside analogue, bromodeoxyuridine, was reduced. Thus, EBV-PK but not EBV-TK mediates ACV and GCV susceptibilities.
The Viral Latency-Associated Nuclear Antigen Augments the B-Cell Response to Antigen In Vivo
Creators: name: Sin, Sang-Hoon
name: Dittmer, Dirk P.
name: Fakhari, Farnaz D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Gammaherpesviruses, including Kaposi sarcoma-associated herpesvirus (KSHV), establish latency in B cells. We hypothesized that the KSHV latency-associated nuclear antigen (LANA/orf73) provides a selective advantage to infected B cells by driving proliferation in response to antigen. To test this, we used LANA B-cell transgenic mice. Eight days after immunization with antigen without adjuvant, LANA mice had significantly more activated germinal center (GC) B cells (CD19 + PNA + CD71 + ) than controls. This was dependent upon B-cell receptor since LANA did not restore the GC defect of CD19 knockout mice. However, LANA was able to restore the marginal zone defect in CD19 knockout mice.
What do I do with my data? Visualizing a transparent author workflow for data sharing and open research publishing
Creators: name: Burrows, Kay E.
name: Grant, Rebecca
name: Milligan, Amy Flanders
Publisher: name: F1000 Research Limited
Year: 2023

description: Data sharing is an important part of open research, but it can be a challenge for authors, particularly in subject areas where data sharing is not already established practice. We have developed this novel, visual workflow to help authors navigate the process of identifying their data ahead of article submission. With a view to reaching authors across the disciplines and around the world, the workflow is designed to make it easier for authors to publish in open research journals by clarifying general guidelines and specific submission requirements. The aim is to distil a complex data policy into a set of practical steps displayed in a visually engaging way. This innovative tool improves transparency in two ways: by clarifying publisher expectations around data sharing and by facilitating the open sharing of data by researchers.
Activation of Plasmacytoid Dendritic Cells by Kaposi's Sarcoma-Associated Herpesvirus
Creators: name: Su, L.
name: Sivaraman, V.
name: Gregory, S. M.
name: West, J. A.
name: Damania, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with multiple human malignancies, including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. Following primary infection, KSHV typically goes through a brief period of lytic replication prior to the establishment of latency. Plasmacytoid dendritic cells (pDCs) are the major producers of type 1 interferon (IFN), primarily in response to virus 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. pDCs express exclusively TLR7 and TLR9, and it is through these TLRs that the type 1 interferon response is activated in pDCs. Currently, it is not known whether KSHV is recognized by pDCs and whether activation of pDCs occurs in response to KSHV infection. We now report evidence that KSHV can infect human pDCs and that pDCs are activated upon KSHV infection, as measured by upregulation of CD83 and CD86 and by IFN-α secretion. We further show that induction of IFN-α occurs through activation of TLR9 signaling and that a TLR9 inhibitor diminishes the production and secretion of IFN-α by KSHV-infected pDCs.
Characterization of Glycosylation Profiles of HIV-1 Transmitted/Founder Envelopes by Mass Spectrometry
Creators: name: Hua, D. C.
name: Chen, H.
name: Desaire, H.
name: Go, E. P.
name: Hewawasam, G.
name: Liao, H.-X.
name: Haynes, B. F.
name: Anderson, J. A.
name: Ping, L.-H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The analysis of HIV-1 envelope carbohydrates is critical to understanding their roles in HIV-1 transmission as well as in binding of envelope to HIV-1 antibodies. However, direct analysis of protein glycosylation by glycopeptide-based mass mapping approaches involves structural simplification of proteins with the use of a protease followed by an isolation and/or enrichment step before mass analysis. The successful completion of glycosylation analysis is still a major analytical challenge due to the complexity of samples, wide dynamic range of glycopeptide concentrations, and glycosylation heterogeneity. Here, we use a novel experimental workflow that includes an up-front complete or partial enzymatic deglycosylation step before trypsin digestion to characterize the glycosylation patterns and maximize the glycosylation coverage of two recombinant HIV-1 transmitted/founder envelope oligomers derived from clade B and C viruses isolated from acute infection and expressed in 293T cells. Our results show that both transmitted/founder Envs had similar degrees of glycosylation site occupancy as well as similar glycan profiles. Compared to 293T-derived recombinant Envs from viruses isolated from chronic HIV-1, transmitted/founder Envs displayed marked differences in their glycosylation site occupancies and in their amounts of complex glycans. Our analysis reveals that the glycosylation patterns of transmitted/founder Envs from two different clades (B and C) are more similar to each other than they are to the glycosylation patterns of chronic HIV-1 Envs derived from their own clades.
The Emergence of Topological Nodal Points in Photonic Crystal with Mirror Symmetry
Creators: name: He, Wen-Yu
name: Chan, C. T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We show that topological nodal points can emerge in photonic crystal possessing mirror symmetry. The mechanism of generating topological nodal points is discussed in a two-dimensional photonic square lattice, in which four topological nodal points split out naturally after the touching of two bands with different parity. The emergence of such nodal points, characterized by vortex structure in momentum space, is attributed to the unavoidable band crossing protected by mirror symmetry. The topological nodes can be unbuckled through breaking the mirror symmetry and a photonic Chern insulator can be achieved through time reversal symmetry breaking. The joint effect of breaking time reversal symmetry and breaking inversion symmetry is further found to strengthen the finite size effect, providing ways to engineer helical edge states.
Clonal Sequences Recovered from Plasma from Patients with Residual HIV-1 Viremia and on Intensified Antiretroviral Therapy Are Identical to Replicating Viral RNAs Recovered from Circulating Resting CD4+ T Cells
Creators: name: Swanstrom, R.
name: Wiegand, A.
name: Ince, W.
name: Parker, D.
name: Archin, N. M.
name: Anderson, J. A.
name: Coffin, J. M.
name: Kuruc, J.
name: Margolis, D. M.
name: Eron, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Despite successful antiretroviral therapy (ART), low-level viremia (LLV) may be intermittently detected in most HIV-infected patients. Longitudinal blood plasma and resting CD4+ T cells were obtained from two patients on suppressive ART to investigate the source of LLV. Single-genome sequencing of HIV-1 env from LLV plasma was performed, and the sequences were compared to sequences recovered from limiting-dilution outgrowth assays of resting CD4+ T cells. The circulating LLV virus clone was identical to virus recovered from outgrowth assays from pools of millions of resting CD4+ T cells. Understanding the sources of LLV requires evaluation of all possible reservoirs of persistent HIV infection.
Differences in HIV-Specific T Cell Responses between HIV-Exposed and -Unexposed HIV-Seronegative Individuals
Creators: name: McMichael, A. J.
name: Wang, Z. M.
name: Brackenridge, S.
name: Moodie, Z.
name: Legg, K.
name: Ritchie, A. J.
name: Haynes, B. F.
name: Kopycinski, J.
name: Campion, S. L.
name: Pandya, K.
name: Fidler, S.
name: Liu, M. K. P.
name: Delwart, E. L.
name: Cohen, M. S.
name: Moore, S.
name: Kuldanek, K.
name: Goonetilleke, N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: HIV-1-specific T lymphocyte responses in individuals exposed to HIV-1 but who remain persistently seronegative (HESNs) have been reported in some but not all previous studies. This study was designed to resolve unequivocally the question of whether HESNs make HIV-1-specific T cell responses. We performed a blind investigation to measure HIV-1-specific T cell responses in both HIV-1-serodiscordant couples and HIV-1-unexposed seronegative controls (HUSNs). We found low-frequency HIV-1-specific T cells in both HESNs and HUSNs but show that the response rates were higher over time in the former (P = 0.01). Furthermore, the magnitudes of the HIV-1-specific T cell responses were significantly higher among responding HESNs than among HUSNs over time (P = 0.002). In both groups, responses were mediated by CD4 T cells. The responses were mapped to single peptides, which often corresponded to epitopes restricted by multiple HLA-DR types that have previously been detected in HIV-1-infected patients. HIV-1-specific T cell responses in HUSNs and some HESNs likely represent cross-reactivity to self or foreign non-HIV-1 antigens. The significantly greater T cell responses in HESNs, including in two who were homozygous for CCR5Δ32, demonstrates that HIV-1-specific T cell responses can be induced or augmented by exposure to HIV-1 without infection.
Biographische Parameter auf Doppelinschriften
Creators: name: Ilgner, Bastian
Publisher: name: Zenodo
Year: 2023

description: Das Poster stellt kontrastiv anhand von Doppelepitaphien für Ehepartner dar, welche biographischen Parameter jeweils für Männer und Frauen im 17. Jahrhundert als relevant angesehen wurden.
description: Posterpräsentation der X-Student Research Group "Berliner Inschriften als Quelle für die historische Registerforschung" (Gohar Schnelle, Dina Serova, finanziert durch die Berlin University Alliance) am 03.04.2023.
Different Regions of HIV-1 Subtype C env Are Associated with Placental Localization and In Utero Mother-to-Child Transmission
Creators: name: Meshnick, S. R.
name: Kumar, S. B.
name: Handelman, S. K.
name: Mwapasa, V.
name: Kwiek, J. J.
name: Janies, D.
name: Rogerson, S. J.
name: Voronkin, I.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: HIV infections are initiated by a limited number of variants that diverge into a diverse quasispecies swarm. During in utero mother-to-child transmission (IU MTCT), transmitted viral variants must pass through multiple unique environments, and our previously published data suggest a nonstochastic model of transmission. As an alternative to a stochastic model of viral transmission, we hypothesize that viral selection in the placental environment influences the character of the viral quasispecies when HIV-1 is transmitted in utero. To test this hypothesis, we used single-template amplification to isolate HIV-1 envelope gene (env) sequences from both peripheral plasma and the placentas of eight nontransmitting (NT) and nine IU-transmitting participants. Statistically significant compartmentalization between peripheral and placental HIV-1 env was detected in one of the eight NT cases and six of the nine IU MTCT cases. In addition, viral sequences isolated from IU MTCT placental tissue showed variation in env V1 loop lengths compared to matched maternal sequences, while NT placental env sequences did not. Finally, comparison of env sequences from NT and IU MTCT participants indicated statistically significant differences in Kyte-Doolittle hydropathy in the signal peptide, C2, V3, and C3 regions. Our working hypothesis is that the hydropathy differences in Env associated with IU MTCT alter viral cellular tropism or affinity, allowing HIV-1 to efficiently infect placentally localized cells.
Supersymmetry from Typicality
Creators: name: Nomura, Yasunori
name: Shirai, Satoshi
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We argue that under a set of simple assumptions the multiverse leads to low energy supersymmetry with the spectrum often called spread or mini-split supersymmetry: the gauginos are in the TeV region with the other superpartners two or three orders of magnitude heavier. We present a particularly simple realization of supersymmetric grand unified theory using this idea.
description: 6 pages, 1 figure
Impromptu Deployment of Wireless Relay Networks: Experiences Along a Forest Trail
Creators: name: Chattopadhyay, Arpan
name: Ghosh, Avishek
name: Rao, Akhila S.
name: Dwivedi, Bharat
name: Anand, S. V. R.
name: Coupechoux, Marceau
name: Kumar, Anurag
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: We are motivated by the problem of impromptu or as- you-go deployment of wireless sensor networks. As an application example, a person, starting from a sink node, walks along a forest trail, makes link quality measurements (with the previously placed nodes) at equally spaced locations, and deploys relays at some of these locations, so as to connect a sensor placed at some a priori unknown point on the trail with the sink node. In this paper, we report our experimental experiences with some as-you-go deployment algorithms. Two algorithms are based on Markov decision process (MDP) formulations; these require a radio propagation model. We also study purely measurement based strategies: one heuristic that is motivated by our MDP formulations, one asymptotically optimal learning algorithm, and one inspired by a popular heuristic. We extract a statistical model of the propagation along a forest trail from raw measurement data, implement the algorithms experimentally in the forest, and compare them. The results provide useful insights regarding the choice of the deployment algorithm and its parameters, and also demonstrate the necessity of a proper theoretical formulation.
description: 7 pages, accepted in IEEE MASS 2014
title: Questionable suitability of OECD 237 protocol in risk assessment scheme?
Creators: name: Sabo, R.
name: Staroň, M.
name: Sobekova, A.
name: Sabova, L.
name: Legáth, J.
name: Javorsky, P.
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Persistent xenobiotics are potentially hazardous for the bee larvae despite that they are not directly exposed in contrary to adult foraging bees. The crucial phase of larval development is the first six days after hatching when young larva grows exponentially and during this phase larvae are potentially exposed to xenobiotics via diet. That is why the life cycle of honeybee is still a great challenge for scientists. OECD reflected “this need” and adopted the OECD 237 protocol (Honey bee (Apis mellifera) larval toxicity test, single exposure) on 26th July 2013. The protocol addresses the requirements formulated by the United States, Canada, and Europe to test the toxicity of chemicals compounds on larvae fed with spiked food under laboratory conditions in a tier1 strategy.
description: Julius-Kühn-Archiv, Nr. 462 (2018): Hazards of pesticides to bees 13th International Symposium of the ICP-PR Bee Protection Group 18. - 20. October 2017, València (Spain) - Proceedings -