cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Recent advances in ultra-low temperature (sub-zero to 100 C) synthesis, mechanism and applications of titania (TiO2) nanoparticles
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: 30201 Bioinorganic Chemistry
subject: FOS: Chemical sciences
subject: 30199 Analytical Chemistry not elsewhere classified
subject: 30401 Biologically Active Molecules
subject: 30101 Analytical Spectrometry
subject: 30402 Biomolecular Modelling and Design
subject: 30601 Catalysis and Mechanisms of Reactions
subject: 30403 Characterisation of Biological Macromolecules

description: 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.
Role of Low CD4 Levels in the Influence of Human Immunodeficiency Virus Type 1 Envelope V1 and V2 Regions on Entry and Spread in Macrophages
Creators: name: Walter, B. L.
name: Swanstrom, R.
name: Kabat, D.
name: Wehrly, K.
name: Platt, E.
name: Chesebro, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Human immunodeficiency virus type 1 (HIV-1) isolates vary in their ability to infect macrophages. Previous experiments have mapped viral determinants of macrophage infectivity to the V3 hypervariable region of the HIV-1 envelope glycoprotein. In our earlier studies, V1 and V2 sequences of HIV-1 were also shown to alter the ability of virus to spread in macrophage cultures, whereas no effect was seen in lymphocyte cultures. In the present study, determinants that allowed certain HIV-1 clones to infect and spread in macrophages were primarily mapped to the V2 region and were found to act by influencing early events of viral infection. By an assay of viral entry into macrophages, it was shown that viruses with the V2 region from the Ba-L strain of HIV-1 had >10-fold-higher entry efficiency than viruses with the V2 region derived from the NL4-3 strain. V1 region differences between these groups caused a twofold difference in entry. The known low expression of CD4 on macrophages appeared to be important in this process. In entry assays conducted with HeLa cell lines expressing various levels of CD4 and CCR5, low levels of CD4 influenced the efficiency of entry and fusion which were dependent on viral V1 and V2 envelope sequences. In contrast, no effect of V1 or V2 was seen in HeLa cells expressing high levels of CD4. Thus, the limited expression of CD4 on macrophages or other cell types could serve as a selective factor for V1 and V2 envelope sequences, and this selection could in turn influence many aspects of AIDS pathogenesis in vivo.
An Approach to Reducing Annotation Costs for BioNLP
Creators: name: Bloodgood, Michael
name: Vijay-Shanker, K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computation and Language (cs.CL)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: I.2.7; I.2.6; I.5.1; I.5.4

description: There is a broad range of BioNLP tasks for which active learning (AL) can significantly reduce annotation costs and a specific AL algorithm we have developed is particularly effective in reducing annotation costs for these tasks. We have previously developed an AL algorithm called ClosestInitPA that works best with tasks that have the following characteristics: redundancy in training material, burdensome annotation costs, Support Vector Machines (SVMs) work well for the task, and imbalanced datasets (i.e. when set up as a binary classification problem, one class is substantially rarer than the other). Many BioNLP tasks have these characteristics and thus our AL algorithm is a natural approach to apply to BioNLP tasks.
description: 2 pages, 1 figure, 5 tables; appeared in Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing at ACL (Association for Computational Linguistics) 2008
Role of Notch Signal Transduction in Kaposi's Sarcoma-Associated Herpesvirus Gene Expression
Creators: name: Hong, Y.
name: Dittmer, D. P.
name: Jung, J. U.
name: Chul, S.-Y.
name: Chang, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Kaposi's sarcoma-associated herpesvirus (KSHV) RTA transcription factor is recruited to its responsive elements through interaction with a Notch-mediated transcription factor, RBP-Jκ, indicating that RTA mimics cellular Notch signal transduction to activate viral lytic gene expression. To test whether cellular Notch signal transduction and RTA are functionally exchangeable for viral gene expression, human Notch intracellular (hNIC) domain that constitutively activates RBP-Jκ transcription factor activity was expressed in KSHV-infected primary effusion lymphoma BCBL1 cells (TRExBCBL1-hNIC) in a tetracycline-inducible manner. Gene expression profiling showed that like RTA, hNIC robustly induced expression of a number of viral genes, including viral interleukin 6 (vIL-6), K3, and K5. Unlike RTA, however, hNIC was not capable of evoking the full repertoire of lytic viral gene expression and thereby lytic replication. To further understand the role of Notch signal transduction in KSHV gene expression, vIL-6 growth factor and K5 immune modulator genes were selected for detailed analysis. Despite the presence of multiple RBP-Jκ binding sites, hNIC targeted the specific RBP-Jκ binding sites of vIL-6 and K5 promoter regions to regulate their gene expression. These results indicate that cellular Notch signal transduction not only is partially exchangeable with RTA in regard to activation of viral lytic gene expression but also provides a novel expression profile of KSHV growth and immune deregulatory genes that is likely different from that of RTA-independent standard latency program as well as RTA-dependent lytic reproduction program.
Order estimates of the best orthogonal trigonometric approximations of classes of convolutions of periodic functions of not high smoothness
Creators: name: Serdyuk, A. S.
name: Stepaniuk, T. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: We obtain order estimates for the best uniform orthogonal trigonometric approximations of $2π$-periodic functions, whose $(ψ,β)$-derivatives belong to unit balls of spaces $L_{p}, \ 1\leq p
description: 21 pages, in Ukrainian
Engineered ZnO‐TiO2 Nanospheres for High Performing Membrane Assimilated Photocatalytic Water Remediation and Energy Harvesting
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: 30101 Analytical Spectrometry
subject: FOS: Chemical sciences
subject: 30401 Biologically Active Molecules
subject: 30402 Biomolecular Modelling and Design
subject: Biochemistry
subject: 30199 Analytical Chemistry not elsewhere classified
subject: 30603 Colloid and Surface Chemistry
subject: Cheminformatics

description: A highly efficient, reusable ZnO-TiO2 heterojunction nanoparticle-based photocatalyst has been successfully demonstrated as a simple and inexpensive way for water remediation. The highly porous membrane integrated with ZnO-TiO2 nanospheres showed significant improvement for removal of specific industrial wastewater contaminates like methyl orange and Cr(VI). Additionally, the ZnO-TiO2 heterojunction nanospheres as DSSC photoanode showed a substantial photo conversion efficiency with graphene counter electrode.
Writing historical fiction about the ancient past: the challenges of portraying Hatshepsut, the first female pharaoh
Creators: name: Green, Kate K.
Publisher: name: Macquarie University
Year: 2023
Subjects: classificationCode: 399999
subject: Other education not elsewhere classified

description: This thesis explores the issues involved when attempting to write a work of historical fiction that is based in the ancient past. It focuses on the use of a modern identity to supplement what little is known about a similar personality from the past.Specifically, this work considers the life of a female pharaoh of ancient Egypt, Hatshepsut, and uses Hillary Clinton as a modern model on which to build the ancient story. The theories of historical fiction explored within the exegesis are applied to the accompanying novel, Of the Sedge and the Bee.Observations of Clinton over the last fifty years, with particular focus on 2016, when she was the Democratic nominee for the American Presidency, provided the basis for an analysis of her character. These traits were subsequently transposed to Hatshepsut to develop her characterisation within the novel. Clinton’s experiences were also used for the purposes of emplotment in Of the Sedge and the Bee. This worked on a wholistic level, framing the story within the short period leading up to Hatshepsut’s ultimate ascendance. It also functioned more specifically, with particular incidents from Clinton’s life appearing in the book as events occurring around Hatshepsut.The thesis foregrounds the gender barriers which helped prevent Clinton from achieving the presidency. These barriers form the core conflict driving Hatshepsut’s story in the novel. The thesis also considers self-reflexivity as a specific aspect of historiographical metafiction, wherein the work both questions the nature of truth and purports to the tell the truth about historical events.As a whole, this thesis is an inquiry into how a modern model can be used to illuminate the ancient past within an historical novel. It explores concepts of emplotment and characterisation, and. exposes issues of gender, media and politics which have persisted for over three and a half millennia.
HfO 2 nanodots incorporated in TiO 2 and its hydrogenation for high performance dye sensitized solar cells
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: 30199 Analytical Chemistry not elsewhere classified
subject: FOS: Chemical sciences
subject: 30101 Analytical Spectrometry
subject: 30401 Biologically Active Molecules
subject: 30601 Catalysis and Mechanisms of Reactions
subject: 30403 Characterisation of Biological Macromolecules
subject: 30602 Chemical Thermodynamics and Energetics

description: Black titania (H-TiO2) as a photoanode material has attracted huge attention due to its extremely high optical absorption in the visible region. Herein, black TiO2 doped with HfO2 shows ∼45.7% higher photo-conversion efficiency than H-TiO2 under identically similar conditions. The incorporation of HfO2 nanodots increased the optical scattering in H-TiO2 only when it underwent hydrogenation along with TiO2. Hafnia-doped TiO2 (HfO2/TiO2) is synthesized by a combination of simple sol–gel and hydrothermal method followed by thermal annealing under controlled hydrogen atmosphere. The hydrogenated H-(TiO2/HfO2) exhibited very high optical absorption but slightly lower than H-TiO2 due to light scattering by HfO2 nanodots. We observed a sharp decrease in optical band gap of TiO2/HfO2 from 3.2 to 2.4 eV up on hydrogen annealing, which is important in solar applications as demonstrated by the fabrication of high efficiency dye sensitized solar cells (DSSC).
Protein folding and binding can emerge as evolutionary spandrels through structural coupling
Creators: name: Manhart, Michael
name: Morozov, Alexandre V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences

description: Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or physical environment (such as the addition of an antibiotic), or when genes duplicate and diverge. Several recent studies have shown the importance of folding stability in constraining protein evolution. Here we investigate how structural coupling between protein folding and binding -- the fact that most proteins can only bind their targets when folded -- gives rise to evolutionary coupling between the traits of folding stability and binding strength. Using biophysical and evolutionary modeling, we show how these protein traits can emerge as evolutionary "spandrels" even if they do not confer an intrinsic fitness advantage. In particular, proteins can evolve strong binding interactions that have no functional role but merely serve to stabilize the protein if misfolding is deleterious. Furthermore, such proteins may have divergent fates, evolving to bind or not bind their targets depending on random mutation events. These observations may explain the abundance of apparently nonfunctional interactions among proteins observed in high-throughput assays. In contrast, for proteins with both functional binding and deleterious misfolding, evolution may be highly predictable at the level of biophysical traits: adaptive paths are tightly constrained to first gain extra folding stability and then partially lose it as the new binding function is developed. These findings have important consequences for our understanding of fundamental evolutionary principles of both natural and engineered proteins.
Experimental Realization of a One-way Quantum Computer Algorithm Solving Simon's Problem
Creators: name: Tame, M. S.
name: Bell, B. A.
name: Di Franco, C.
name: Wadsworth, W. J.
name: Rarity, J. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report an experimental demonstration of a one-way implementation of a quantum algorithm solving Simon's Problem - a black box period-finding problem which has an exponential gap between the classical and quantum runtime. Using an all-optical setup and modifying the bases of single-qubit measurements on a five-qubit cluster state, key representative functions of the logical two-qubit version's black box can be queried and solved. To the best of our knowledge, this work represents the first experimental realization of the quantum algorithm solving Simon's Problem. The experimental results are in excellent agreement with the theoretical model, demonstrating the successful performance of the algorithm. With a view to scaling up to larger numbers of qubits, we analyze the resource requirements for an n-qubit version. This work helps highlight how one-way quantum computing provides a practical route to experimentally investigating the quantum-classical gap in the query complexity model.
description: 9 pages, 5 figures
Roles of the ITAM and PY Motifs of Epstein-Barr Virus Latent Membrane Protein 2A in the Inhibition of Epithelial Cell Differentiation and Activation of  -Catenin Signaling
Creators: name: Morrison, J. A.
name: Raab-Traub, N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Epstein-Barr virus (EBV) latent membrane protein 2A (LMP2A) is important for maintenance of latency in infected B lymphocytes. Through its immunoreceptor tyrosine-based activation motif (ITAM) and PY motifs, LMP2A is able to block B-cell receptor (BCR) signaling, bind BCR-associated kinases, and manipulate the turnover of itself and these kinases via a PY-mediated interaction with the Nedd4 family of ubiquitin ligases. In epithelial cells, LMP2A has been shown to activate the phosphatidylinositol 3′-OH kinase/Akt and β-catenin signaling pathways. In the present study, the biological consequences of LMP2A expression in the normal human foreskin keratinocyte (HFK) cell line were investigated and the importance of the ITAM and PY motifs for LMP2A signaling effects in HFK cells was ascertained. The ITAM was essential for the activation of Akt by LMP2A in HFK cells, while both the ITAM and PY motifs contributed to LMP2A-mediated accumulation and nuclear translocation of the oncoprotein β-catenin. LMP2A inhibited induction of differentiation in an assay conducted with semisolid methylcellulose medium, and the PY motifs were critical for this inhibition. LMP2A is expressed in the EBV-associated epithelial malignancies nasopharyngeal carcinoma and gastric carcinoma, and these data indicate that LMP2A affects cellular processes that likely contribute to carcinogenesis.
Pulsar-black hole binaries: prospects for new gravity tests with future radio telescopes
Creators: name: Liu, K.
name: Eatough, R. P.
name: Wex, N.
name: Kramer, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The anticipated discovery of a pulsar in orbit with a black hole is expected to provide a unique laboratory for black hole physics and gravity. In this context, the next generation of radio telescopes, like the Five-hundred-metre Aperture Spherical radio Telescope (FAST) and the Square Kilometre Array (SKA), with their unprecedented sensitivity, will play a key role. In this paper, we investigate the capability of future radio telescopes to probe the spacetime of a black hole and test gravity theories, by timing a pulsar orbiting a stellar-mass-black-hole (SBH). Based on mock data simulations, we show that a few years of timing observations of a sufficiently compact pulsar-SBH (PSR-SBH) system with future radio telescopes would allow precise measurements of the black hole mass and spin. A measurement precision of one per cent can be expected for the spin. Measuring the quadrupole moment of the black hole, needed to test GR's no-hair theorem, requires extreme system configurations with compact orbits and a large SBH mass. Additionally, we show that a PSR-SBH system can lead to greatly improved constraints on alternative gravity theories even if they predict black holes (practically) identical to GR's. This is demonstrated for a specific class of scalar-tensor theories. Finally, we investigate the requirements for searching for PSR-SBH systems. It is shown that the high sensitivity of the next generation of radio telescopes is key for discovering compact PSR-SBH systems, as it will allow for sufficiently short survey integration times.
description: 20 pages, 11 figures, 1 table, accepted for publication in MNRAS
The Epstein-Barr Virus Protein BMRF1 Activates Gastrin Transcription
Creators: name: Kenney, S. C.
name: Bhende, P.
name: Holley-Guthrie, E. A.
name: Seaman, W. T.
name: Merchant, J. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The Epstein-Barr virus (EBV) BMRF1 gene encodes an early lytic protein that functions not only as the viral DNA polymerase processivity factor but also as a transcriptional activator. BMRF1 has been previously shown to activate transcription of an EBV early promoter, BHLF1, though a GC-rich motif which binds to SP1 and ZBP-89, although the exact mechanism for this effect is not known (D. J. Law, S. A. Tarle, and J. L. Merchant, Mamm. Genome 9:165-167, 1998). Here we demonstrate that BMRF1 activates transcription of the cellular gastrin gene in telomerase-immortalized keratinocytes. Furthermore, BMRF1 activated a reporter gene construct driven by the gastrin promoter in a variety of cell types, and this effect was mediated by two SP1/ZBP-89 binding sites in the gastrin promoter. ZBP-89 has been previously shown to negatively regulate the gastrin promoter. However, ZBP-89 can function as either a negative or positive regulator of transcription, depending upon the promoter and perhaps other, as-yet-unidentified factors. BMRF1 increased the binding of ZBP-89 to the gastrin promoter, and a ZBP-89-GAL4 fusion protein was converted into a positive transcriptional regulator by cotransfection with BMRF1. BMRF1 also enhanced the transcriptional activity of an SP1-GAL4 fusion protein. These results suggest that BMRF1 activates target promoters through its effect on both the SP1 and ZBP-89 transcription factors. Furthermore, as the EBV genome is present in up to 10% of gastric cancers, and the different forms of gastrin are growth factors for gastrointestinal epithelium, our results suggest a mechanism by which lytic EBV infection could promote the growth of gastric cells.
Multiscale mechanics of macromolecular materials with unfolding domains
Creators: name: De Tommasi, Domenico
name: Puglisi, Giuseppe
name: Saccomandi, Giuseppe
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule unfolding strategy, we obtain a three-dimensional continuum model with variable natural configuration and an energy function analytically deduced from the microscale material parameters. The comparison with the experiments shows the ability of the model to describe the complex behavior, with residual stretches and unfolding effects, observed in different biological materials.
Whole-Genome Transcription Profiling of Rhesus Monkey Rhadinovirus
Creators: name: Vahrson, W.
name: Damania, B.
name: Dittmer, D. P.
name: DeWire, S. M.
name: Gonzalez, C. M.
name: Hines-Boykin, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Rhesus monkey rhadinovirus (RRV) and Kaposi's sarcoma-associated herpesvirus (KSHV; also called human herpesvirus 8) belong to the gamma-2 grouping of herpesviruses. RRV and KSHV share a high degree of sequence similarity, and their genomes are organized in a similar fashion. RRV serves as an excellent animal model system to study the gamma herpesvirus life cycle both in vitro and in vivo. We have developed a high-sensitivity, high-throughput, high-specificity real-time quantitative reverse transcriptase-based PCR assay for RRV and have used this assay to profile transcription from the whole RRV genome during de novo productive infection of rhesus fibroblasts. Using this assay, we demonstrate that the genome-wide transcription profile for RRV closely parallels the genome-wide transcription profile for KSHV.
Measurement of net electric charge and dipole moment of dust aggregates in a complex plasma
Creators: name: Yousefi, Razieh
name: Davis, Allen B.
name: Carmona-Reyes, Jorge
name: Matthews, Lorin S.
name: Hyde, Truell W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Understanding the agglomeration of dust particles in complex plasmas requires a knowledge of the basic properties such as the net electrostatic charge and dipole moment of the dust. In this study, dust aggregates are formed from gold coated mono-disperse spherical melamine-formaldehyde monomers in a radio-frequency (rf) argon discharge plasma. The behavior of observed dust aggregates is analyzed both by studying the particle trajectories and by employing computer models examining 3D structures of aggregates and their interactions and rotations as induced by torques arising from their dipole moments. These allow the basic characteristics of the dust aggregates, such as the electrostatic charge and dipole moment, to be determined. It is shown that the experimental results support the predicted values from computer models for aggregates in these environments.
description: 6 pages, 7 figures
2,3 and  2,6 N-Linked Sialic Acids Facilitate Efficient Binding and Transduction by Adeno-Associated Virus Types 1 and 6
Creators: name: Samulski, R. J.
name: Wu, Z.
name: Agbandje-McKenna, M.
name: Miller, E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Recombinant adeno-associated viruses (AAVs) are promising vectors in the field of gene therapy. Different AAV serotypes display distinct tissue tropism, believed to be related to the distribution of their receptors on target cells. Of the 11 well-characterized AAV serotypes, heparan sulfate proteoglycan and sialic acid have been suggested to be the attachment receptors for AAV type 2 and types 4 and 5, respectively. In this report, we identify the receptor for the two closely related serotypes, AAV1 and AAV6. First, we demonstrate using coinfection experiments and luciferase reporter analysis that AAV1 and AAV6 compete for similar receptors. Unlike heparin sulfate, enzymatic or genetic removal of sialic acid markedly reduced AAV1 and AAV6 binding and transduction. Further analysis using lectin staining and lectin competition assays identified that AAV1 and AAV6 use either α2,3-linked or α2,6-linked sialic acid when transducing numerous cell types (HepG2, Pro-5, and Cos-7). Treatment of cells with proteinase K but not glycolipid inhibitor reduced AAV1 and AAV6 infection, supporting the hypothesis that the sialic acid that facilitates infection is associated with glycoproteins rather than glycolipids. In addition, we determined by inhibitor (N-benzyl GalNAc)- and cell line-specific (Lec-1) studies that AAV1 and AAV6 require N-linked and not O-linked sialic acid. Furthermore, a resialylation experiment on a deficient Lec-2 cell line confirmed a 2,3 and 2,6 N-linked sialic acid requirement, while studies of mucin with O-linked sialic acid showed no inhibition effect for AAV1 and AAV6 transduction on Cos-7 cells. Finally, using a glycan array binding assay we determined that AAV1 efficiently binds to NeuAcα2-3GalNAcβ1-4GlcNAc, as well as two glycoproteins with α2,3 and α2,6 N-linked sialic acids. Taken together, competition, genetic, inhibitor, enzymatic reconstitution, and glycan array experiments support α2,3 and α2,6 sialic acids that are present on N-linked glycoproteins as primary receptors for efficient AAV1 and AAV6 viral infection.
Adeno-Associated Virus Type 2 Contains an Integrin  5 1 Binding Domain Essential for Viral Cell Entry
Creators: name: Samulski, R. J.
name: Govindasamy, L.
name: Asokan, A.
name: Agbandje-McKenna, M.
name: Hamra, J. B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Integrins have been implicated as coreceptors in the infectious pathways of several nonenveloped viruses. For example, adenoviruses are known to interact with αV integrins by virtue of a high-affinity arginine-glycine-aspartate (RGD) domain present in the penton bases of the capsids. In the case of adeno-associated virus type 2 (AAV2), which lacks this RGD motif, integrin αVβ5 has been identified as a coreceptor for cellular entry. However, the molecular determinants of AAV2 capsid-integrin interactions and the potential exploitation of alternative integrins as coreceptors by AAV2 have not been established thus far. In this report, we demonstrate that integrin α5β1 serves as an alternative coreceptor for AAV2 infection in human embryonic kidney 293 cells. Such interactions appear to be mediated by a highly conserved domain that contains an asparagine-glycine-arginine (NGR) motif known to bind α5β1 integrin with moderate affinity. The mutation of this domain reduces transduction efficiency by an order of magnitude relative to that of wild-type AAV2 vectors in vitro and in vivo. Further characterization of mutant and wild-type AAV2 capsids through transduction assays in cell lines lacking specific integrins, cell adhesion studies, and cell surface/solid-phase binding assays confirmed the role of the NGR domain in promoting AAV2-integrin interactions. Molecular modeling studies suggest that NGR residues form a surface loop close to the threefold axis of symmetry adjacent to residues previously implicated in binding heparan sulfate, the primary receptor for AAV2. The aforementioned results suggest that the internalization of AAV2 in 293 cells might follow a “click-to-fit” mechanism that involves the cooperative binding of heparan sulfate and α5β1 integrin by the AAV2 capsids.
The ConsenCUS project: Carbon neutral clusters by electricity-based innovations in capture, utilisation and storage.
Creators: name: Andrianov, Nikolai
Publisher: name: Zenodo
Year: 2022
Subjects: Carbon Capture Demonstration, Utilisation, Storage, H2020 EU projects, Carbon Neutral Clusters, CCUS Demonstration Projects

description: This poster presents presents the ConsenCUS project in General and the potential for CO2 storage in the North-Western European cluster in particular. Specifically, the possible storage sites in Denmark (Stenlille and Havnso) are showed and CO2-storage modelling and results of the first sensitivity study on CO2 recovery during temporary storage is presented.
High-performance dye-sensitized solar cell using dimensionally controlled titania synthesized at sub-zero temperatures
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: 30199 Analytical Chemistry not elsewhere classified
subject: FOS: Chemical sciences
subject: 30101 Analytical Spectrometry
subject: 30402 Biomolecular Modelling and Design
subject: 30403 Characterisation of Biological Macromolecules
subject: 30601 Catalysis and Mechanisms of Reactions

description: The subject of the current study is a concoct of anatase and rutile mixed phase titania synthesized at −40 °C and −10 °C. At these sub-zero temperatures, highly crystalline, phase-oriented nanostructured titania were formed. At −40 °C, nanocrystals of TiO2 consist of the anatase phase while nanorods dominated by the rutile phase form at −10 °C. These samples are remarkable photoanode materials with excellent photon scattering ability in dye-sensitized solar cells (DSSCs). On performance optimization of DSSCs, a composition of 0.5 wt% TiO2 (prepared at −40 °C) and P25 improved the photon harvesting by providing a large number of sites for interaction, resulting in a high photocurrent of 18.46 mA cm−2 and 8.6% photoconversion efficiency.
Integrating Nature into Risk Science and Insurance: A Coastal Resilience Symposium
Creators: name: Kelso, Megan
name: Beck, Michael
name: Bibby, Kiya
name: Travis, Kevin
Publisher: name: Zenodo
Year: 2023
Subjects: nature-based solutions
insurance
risk science
risk modeling
coastal resilience
risk management
coastal ecosystems

description: Summary of a symosium held in 2023 on integrating nature better into risk science and insurance, with the aim of improving risk management to better protect people and support conservation and restoration of coastal ecosystems.
cdc2/Cyclin B1-Dependent Phosphorylation of EBNA2 at Ser243 Regulates Its Function in Mitosis
Creators: name: Shackelford, J.
name: Pagano, J. S.
name: Yue, W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA2) transactivates EBV genes in latently infected B cells. We have shown that mitotic hyperphosphorylation of EBNA2 suppresses its ability to transactivate the latent membrane protein 1 (LMP1) promoter. In this follow-up study, we identify EBNA2 Ser243 as a phosphorylation site for mitotic cdc2/cyclin B1 kinase. Mutation at Ser243, which mimics constitutive phosphorylation of the protein, decreases endogenous levels of both LMP1 and EBNA2. Moreover, mutation at Ser243 reduces the ability of EBNA2 to transactivate Cp, the promoter for all six EBV EBNA genes. Our data implicate EBNA2 Ser243 as a cdc2/cyclin B1 site of phosphorylation important for EBNA2's cotranscriptional function in mitosis.
Experimental implementation of adiabatic passage between different topological orders
Creators: name: Peng, Xinhua
name: Luo, Zhihuang
name: Kou, Supeng
name: Suter, Dieter
name: Du, Jiangfeng
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Topological orders are exotic phases of matter existing in strongly correlated quantum systems, which are beyond the usual symmetry description and cannot be distinguished by local order parameters. Here we report an experimental quantum simulation of the Wen-plaquette spin model with different topological orders in a nuclear magnetic resonance system, and observe the adiabatic transition between two $Z_2$ topological orders through a spin-polarized phase by measuring the nonlocal closed-string (Wilson loop) operator. Moreover, we also measure the entanglement properties of the topological orders. This work confirms the adiabatic method for preparing topologically ordered states and provides an experimental tool for further studies of complex quantum systems.
description: 5 pages, 4 figures + Supplementary Materials; Accepted in Phys. Rev. Lett. (2014)
Recent Progress in Synthesis of Nano-and Atomic-Sized Catalysts
Creators: name: Laishram, Devika
Publisher: name: figshare
Year: 2022
Subjects: subject: 30201 Bioinorganic Chemistry
subject: FOS: Chemical sciences
subject: 30101 Analytical Spectrometry
subject: 30402 Biomolecular Modelling and Design
subject: 30403 Characterisation of Biological Macromolecules
subject: 30601 Catalysis and Mechanisms of Reactions

description: Well-defined nano- and atomic-sized heterogeneous catalysts with extremely high catalytic activities and unique selectivities show promise in addressing the critical energy- and environment-related challenges of this century. The exceptional properties of these catalysts, such as their electronic and geometric structures and the effective interactions between metals and supports, give rise to unprecedented catalytic efficiency over that of conventional catalysts. The facile prospects for tuning the active sites of these catalysts pave the way to optimizing their activities, selectivities, and stabilities, thus offering extensive application possibilities in significant industry-related catalytic reactions. A prerequisite for synthesizing nano- and atomic-sized catalyst is to prepare extremely disperse nano- and subnanoscale atoms on suitable supports. This book chapter summarizes various synthesis methods employed to synthesize nano- and atomic-scale catalysts.
Presence-absence reasoning for evolutionary phenotypes
Creators: name: Balhoff, James P.
name: Dececchi, T. Alexander
name: Mabee, Paula M.
name: Lapp, Hilmar
Publisher: name: arXiv
Year: 2014
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Nearly invariably, phenotypes are reported in the scientific literature in meticulous detail, utilizing the full expressivity of natural language. Often it is particularly these detailed observations (facts) that are of interest, and thus specific to the research questions that motivated observing and reporting them. However, research aiming to synthesize or integrate phenotype data across many studies or even fields is often faced with the need to abstract from detailed observations so as to construct phenotypic concepts that are common across many datasets rather than specific to a few. Yet, observations or facts that would fall under such abstracted concepts are typically not directly asserted by the original authors, usually because they are "obvious" according to common domain knowledge, and thus asserting them would be deemed redundant by anyone with sufficient domain knowledge. For example, a phenotype describing the length of a manual digit for an organism implicitly means that the organism must have had a hand, and thus a forelimb; the presence or absence of a forelimb may have supporting data across a far wider range of taxa than the length of a particular manual digit. Here we describe how within the Phenoscape project we use a pipeline of OWL axiom generation and reasoning steps to infer taxon-specific presence/absence of anatomical entities from anatomical phenotypes. Although presence/absence is all but one, and a seemingly simple way to abstract phenotypes across data sources, it can nonetheless be powerful for linking genotype to phenotype, and it is particularly relevant for constructing synthetic morphological supermatrices for comparative analysis; in fact presence/absence is one of the prevailing character observation types in published character matrices.
description: 4 pages. Peer-reviewed submission presented to the Bio-ontologies SIG Phenotype Day at ISMB 2014, Boston, Mass. http://phenoday2014.bio-lark.org/pdf/11.pdf
Temperature evolution of structural and magnetic properties of stoichiometric LiCu2O2: correlation of thermal expansion coefficient and magnetic order
Creators: name: Ivanov, S. A.
name: Kumar, P. Anil
name: Mathieu, R.
name: Bush, A. A.
name: Ottosson, M.
name: Nordblad, P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Temperature-dependent crystallographic and magnetic studies on stoichiometric single crystals of LiCu2O2 are reported. The magnetic properties are similar to earlier findings demonstrating antiferromagnetic ordering below 25 K. Evidence of magnetoelastic coupling is observed in the thermal expansion along the c-direction; not only at the low temperature antiferromagnetic transitions, but an anomalous behavior of the thermal expansion indicate magnetoelastic coupling also to the magnetic ordering related to a weak spontaneous magnetic moment appearing at 150 K. Ac-susceptibility measurements at different frequencies and superposed dc- fields are employed to further characterize this magnetic anomaly.
description: 12 pages, 5 figures
Evidence that the Human Cytomegalovirus IE2-86 Protein Binds mdm2 and Facilitates mdm2 Degradation
Creators: name: McCarville, J. F.
name: Evers, D. L.
name: Zhang, Z.
name: Huang, E.-S.
name: Dantonel, J.-C.
name: Huong, S.-M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Levels of the p53 tumor suppressor protein are increased in human cytomegalovirus (HCMV)-infected cells and may be important for HCMV pathogenesis. In normal cells p53 levels are kept low due to an autoregulatory feedback loop where p53 activates the transcription of mdm2 and mdm2 binds and ubiquitinates p53, targeting p53 for proteasomal degradation. Here we report that, in contrast to uninfected cells, mdm2 was undetectable upon treatment of infected fibroblasts with the proteasome inhibitor MG132. Cellular depletion of mdm2 was reproducible in p53-null cells transfected with the HCMV IE2-86 protein, but not with IE172, independently of the endogenous mdm2 promoter. IE2-86 also prevented the emergence of presumably ubiquitinated species of p53. The regions of IE2-86 important for mdm2 depletion were those containing the sequences corresponding to the putative zinc finger and C-terminal acidic motifs. mdm2 and IE2-86 coimmunoprecipitated in transfected and infected cell lysates and in a cell-free system. IE2-86 blocked mdm2's p53-independent transactivation of the cyclin A promoter in transient-transfection experiments. Pulse-chase experiments revealed that IE2-86 but not IE1-72 or several loss-of-function IE2-86 mutants increased the half-life of p53 and reduced the half-life of mdm2. Short interfering RNA-mediated depletion of IE2-86 restored the ability of HCMV-infected cells to accumulate mdm2 in response to proteasome inhibition. Taken together, the data suggest that specific interactions between IE2-86 and mdm2 cause proteasome-independent degradation of mdm2 and that this may be important for the accumulation of p53 in HCMV-infected cells.
Prioritized motion-force control of constrained fully-actuated robots: "Task Space Inverse Dynamics"
Creators: name: Del Prete, Andrea
name: Nori, Francesco
name: Metta, Giorgio
name: Natale, Lorenzo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: We present a new framework for prioritized multi-task motion-force control of fully-actuated robots. This work is established on a careful review and comparison of the state of the art. Some control frameworks are not optimal, that is they do not find the optimal solution for the secondary tasks. Other frameworks are optimal, but they tackle the control problem at kinematic level, hence they neglect the robot dynamics and they do not allow for force control. Still other frameworks are optimal and consider force control, but they are computationally less efficient than ours. Our final claim is that, for fully-actuated robots, computing the operational-space inverse dynamics is equivalent to computing the inverse kinematics (at acceleration level) and then the joint-space inverse dynamics. Thanks to this fact, our control framework can efficiently compute the optimal solution by decoupling kinematics and dynamics of the robot. We take into account: motion and force control, soft and rigid contacts, free and constrained robots. Tests in simulation validate our control framework, comparing it with other state-of-the-art equivalent frameworks and showing remarkable improvements in optimality and efficiency.
description: Pre-print submitted to "Robotics and Autonomous Systems"
Fusion-Induced Apoptosis Contributes to Thymocyte Depletion by a Pathogenic Human Immunodeficiency Virus Type 1 Envelope in the Human Thymus
Creators: name: Meissner, E. G.
name: Zhang, L.
name: Jiang, S.
name: Su, L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The mechanisms of CD4+ T-cell depletion during human immunodeficiency virus type 1 (HIV-1) infection remain incompletely characterized. Of particular importance is how CD4+ T cells are depleted within the lymphoid organs, including the lymph nodes and thymus. Herein we characterize the pathogenic mechanisms of an envelope from a rapid progressor (R3A Env) in the NL4-3 backbone (NL4-R3A) which is able to efficiently replicate and deplete CD4+ thymocytes in the human fetal-thymus organ culture (HF-TOC). We demonstrate that uninterrupted replication is required for continual thymocyte depletion. During depletion, NL4-R3A induces an increase in thymocytes which uptake 7AAD, a marker of cell death, and which express active caspase-3, a marker of apoptosis. While 7AAD uptake is observed predominantly in uninfected thymocytes (p24−), active caspase-3 is expressed in both infected (p24+) and uninfected thymocytes (p24−). When added to HF-TOC with ongoing infection, the protease inhibitor saquinavir efficiently suppresses NL4-R3A replication. In contrast, the fusion inhibitors T20 and C34 allow for sustained HIV-1 production. Interestingly, T20 and C34 effectively prevent thymocyte depletion in spite of this sustained replication. Apoptosis of both p24− and p24+ thymocytes appears to be envelope fusion dependent, as T20, but not saquinavir, is capable of reducing thymocyte apoptosis. Together, our data support a model whereby pathogenic envelope-dependent fusion contributes to thymocyte depletion in HIV-1-infected thymus, correlated with induction of apoptosis in both p24+ and p24− thymocytes.
Parametric generation of high frequency coherent light in negative index materials and materials with strong anomalous dispersion
Creators: name: Svidzinsky, Anatoly A.
name: Zhang, Xiwen
name: Wang, Luojia
name: Wang, Jizhou
name: Scully, Marlan O.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate the possibility of generation of coherent radiation with tunable frequencies higher than the frequency of the driving field $ν_{d}$ in a nonlinear medium utilizing the difference combination resonance that occurs when $ν_{d}$ matches the difference of the frequencies of the two generated fields $ω_{1}$ and $ω_{2}$. We find that such a resonance can appear in materials which have opposite signs of refractive index at $ω_{1}$ and $ω_{2}$. It can also occur in positive refractive index materials with strong anomalous dispersion if at one of the generated frequencies the group and phase velocities are opposite to each other. We show that the light amplification mechanism is equivalent to a combination resonance in a system of two coupled parametric oscillators with the opposite sign of masses. Such a mechanism holds promise for a new kind of light source that emits coherent radiation of tunable wavelengths by an optical parametric amplification process with the frequency higher than $ν_{d}$.
Herpes Simplex Virus Type 1 ICP27-Dependent Activation of NF- B
Creators: name: Hargett, D.
name: Rice, S.
name: Bachenheimer, S. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The ability of herpes simplex virus type 1 (HSV-1) to activate NF-κB has been well documented. Beginning at 3 to 5 h postinfection, HSV-1 induces a robust and persistent nuclear translocation of an NF-κB-dependent (p50/p65 heterodimer) DNA binding activity, as measured by electrophoretic mobility shift assay. Activation requires virus binding and entry, as well as de novo infected-cell protein synthesis, and is accompanied by loss of both IκBα and IκBβ. In this study, we identified loss of IκBα as a marker of NF-κB activation, and infection with mutants with individual immediate-early (IE) regulatory proteins deleted indicated that ICP27 was necessary for IκBα loss. Analysis of both N-terminal and C-terminal mutants of ICP27 identified the region from amino acids 21 to 63 as being necessary for IκBα loss. Additional experiments with mutant viruses with combinations of IE genes deleted revealed that the ICP27-dependent mechanism of NF-κB activation may be augmented by functional ICP4. We also analyzed two additional markers for NF-κB activation, phosphorylation of the p65 subunit on Ser276 and Ser536. Phosphorylation of both serines was induced upon HSV infection and required functional ICP4 and ICP27. Pharmacological inhibitor studies revealed that both IκBα and Ser276 phosphorylation were dependent on Jun N-terminal protein kinase activity, while Ser536 phosphorylation was not affected during inhibitor treatment. These results demonstrate that there are several layers of regulation of NF-κB activation during HSV infection, highlighting the important role that NF-κB may play in infection.
Boletín Sociedad Española de Bizantinística (SEB) – nº 47
Creators: name: Estangüi Gómez, Raúl
name: Pérez Moro, David
Publisher: name: Zenodo
Year: 2025

description: Publicación no académica de la Sociedad Española de Bizantinística. Nº 47, abril de 2025.

Non-academic journal of the Spanish Society of Byzantine Studies. Issue 47, April 2025.