cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Factors Influencing Adeno-Associated Virus-Mediated Gene Transfer to Human Cystic Fibrosis Airway Epithelial Cells: Comparison with Adenovirus Vectors
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Adeno-associated virus (AAV) vectors appear promising for use in gene therapy in cystic fibrosis (CF) patients, yet many features of AAV-mediated gene transfer to airway epithelial cells are not well understood. We compared the transduction efficiencies of AAV vectors and adenovirus (Ad) vectors in immortalized cell lines from CF patients and in nasal epithelial primary cultures from normal humans and CF patients. Similar dose-dependent relationships between the vector multiplicities of infection and the efficiencies of lacZ gene transfer were observed. However, levels of transduction for both Ad and recombinant AAV (rAAV) were significantly lower in the airway epithelial cell than in the control cell lines HeLa and HEK 293. Transduction efficiencies differed among cultured epithelial cell types, with poorly differentiated cells transducing more efficiently than well-differentiated cells. A time-dependent increase in gene expression was observed after infection for both vectors. For Ad, but not for AAV, this increase was dependent on prolonged incubation of cells with the vector. Furthermore, for rAAV (but not for rAd), the delay in maximal transduction could be abrogated by wild-type Ad helper infection. Thus, although helper virus is not required for maximal transduction, it increases the kinetics by which this is achieved. Expression of Ad E4 open reading frame 6 or addition of either hydroxyurea or camptothecin resulted in increased AAV transduction, as previously demonstrated for nonairway cells (albeit to lower final levels), suggesting that second-strand synthesis may not be the sole cause of inefficient transduction. Finally, the efficiency of AAV-mediated ex vivo gene transfer to lung cells was similar to that previously described for Ad vectors in that transduction was limited to regions of epithelial injury and preferentially targeted basal-like cells. These studies address the primary factors influencing rAAV infection of human airway cells and should impact successful gene delivery in CF patients.
Astronomy of two Indian tribes: Banjaras and Kolams
Creators: name: Vahia, Mayank N
name: Halkare, Ganesh
name: Menon, Kishore
name: Calamur, Harini
Publisher: name: arXiv
Year: 2014
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We report field studies of the astronomical beliefs of two Indian tribes: the Banjaras and the Kolams. The Banjaras are an ancient tribe connected with the gypsies of Europe while the Kolams have been foragers until recently. They share their landscape with each other and also with the Gonds whose astronomy was reported previously (Vahia and Halkare, 2013). The primary profession of the Banjaras was trade, based on the large-scale movement of goods over long distances, but their services were taken over by the railways about one hundred years ago. Since then the Banjaras have begun the long journey to a sedentary lifestyle. Meanwhile, the Kolams were foragers until about fifty years ago when the Government of India began to help them lead a settled life. Here, we compare their astronomical beliefs of the Banjaras and the Kolams, which indicate the strong sense of identity that each community possesses. Our study also highlights their perspective about the sky and its relation to their daily lives. We show that apart from the absolute importance of the data on human perception of the sky, the data also reveal subtle aspects of interactions between physically co-located but otherwise isolated communities as well as their own lifestyles. We also show that there is a strong relationship between profession and perspective of the sky.
description: 20 pages, 5 images and 5 tables
Identification of a Cytotoxic T-Lymphocyte Response to the Novel BARF0 Protein of Epstein-Barr Virus: a Critical Role for Antigen Expression
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: The Epstein-Barr virus (EBV)-encoded BARF0 open reading frame gene products are consistently expressed in EBV-positive Burkitt’s lymphoma (BL) cell lines, nasopharyngeal carcinoma cell lines, and lymphoblastoid cell lines (LCLs). Here we show that the BARF0 sequence includes an HLA A*0201-restricted cytotoxic T-lymphocyte (CTL) epitope. By using theoretically predicted HLA A2 binding motifs and peptide-loaded antigen presentation-deficient T2 cells, polyclonal BARF0-specific CD8+ CTLs were isolated from four different healthy EBV-seropositive donors but not from two seronegative donors. These CTL lines recognized the peptide epitope LLWAARPRL, which was found to be conserved in 33 of 34 virus strains originating from Caucasian, African, and Asian individuals. The BARF0-specific CTL lines could lyse EBV-negative BL cells stably transfected with the BARF0 gene but did not kill HLA A2-matched EBV-positive BL cells and LCLs in a standard 51Cr release assay. Reverse transcriptase PCR analysis demonstrated that these EBV-positive cell lines expressed significantly lower levels of BARF0 mRNA than transfected cells. This data indicated that the BARF0 epitope could be endogenously processed; however, antigen levels in the target cell were a limiting factor for the effective interaction between BARF0-expressing cells and CTLs. The limited expression of BARF0 antigen in EBV-infected BL cells and LCLs might contribute to the escape of immune recognition from virus-specific CTLs present in the host.
Additional file 12 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 12: Table S2. Genome-wide association study results using simulated traits.
Identification of Positive and Negative Regulatory Regions Involved in Regulating Expression of the Human Cytomegalovirus UL94 Late Promoter: Role of IE2-86 and Cellular p53 in Mediating Negative Regulatory Function
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: The human cytomegalovirus (HCMV) UL94 gene product is a herpesvirus-common virion protein that is expressed with true late kinetics. To identify the important cis- and trans-acting factors which contribute to UL94 transcriptional regulation, we have cloned, sequenced, and analyzed UL94 promoter function by transient transfection analysis. Transfection of UL94 promoter-reporter gene constructs into permissive human fibroblasts or U373(MG) cells indicated that promoter activity was detected following infection with HCMV. Point mutations within a TATA-like element located upstream of the RNA start site significantly reduced UL94 promoter activity. Deletion mutagenesis of the promoter indicated that a positive regulatory element (PRE) was likely to exist downstream of the UL94 mRNA start site, while a negative regulatory element (NRE) was present upstream of the TATA box. At late times of infection, the PRE appeared to have a dominant effect over the NRE to stimulate maximum levels of UL94 promoter activity, while at earlier times of infection, no activity associated with the PRE could be detected. The NRE, however, appeared to cause constitutive down-regulation of UL94 promoter activity. Binding sites for the cellular p53 protein located within the NRE appeared to contribute to NRE function, and NRE function could be recapitulated in cotransfection assays by concomitant expression of p53 and HCMV IE2-86 protein. Our results suggest a novel mechanism by which the cellular protein p53, which is involved in both transcriptional regulation and progression of cellular DNA synthesis, plays a central role in the regulation of a viral promoter which is not activated prior the onset of viral DNA replication.
Fast non-thermal switching between macroscopic charge-ordered quantum states induced by charge injection
Creators: name: Vaskivskyi, I.
name: Mihailovic, I. A.
name: Brazovskii, S.
name: Gospodaric, J.
name: Mertelj, T.
name: Svetin, D.
name: Sutar, P.
name: Mihailovic, D.
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: The functionality of logic and memory elements in current electronics is based on multi-stability, driven either by manipulating local concentrations of electrons in transistors, or by switching between equivalent states of a material with a degener- ate ground state in magnetic or ferroelectric materials. Another possibility is offered by phase transitions with switching between metallic and insulating phases, but classical phase transitions are limited in speed by slow nucleation, proliferation of domains and hysteresis. We can in principle avoid these problems by using quantum states for switching, but microscopic systems suffer from decoherence which prohibits their use in everyday devices. Macroscopic quantum states, such as the superconducting ground state have the advantage that on a fundamental level they do not suffer from decoherence plaguing microscopic systems. Here we demonstrate for the first time ultrafast non-thermal switching between different metastable electronically ordered states by pulsed electrical charge injection. The macroscopic nature of the many-body quantum states(1-4) - which are not part of the equilibrium phase diagram - gives rise to unprecedented stability and remarka- bly sharp switching thresholds. Fast sub-50 ps switching, large associated re- sistance changes, 2-terminal operation and demonstrable high fidelity of bi-stability control suggest new opportunities for the use of macroscopic quantum states in electronics, particularly for an ultrafast non-volatile quantum charge-order resistive random access memory (QCOR-RAM).
description: 12 pages, 3 figures
Limited Entry of Adenovirus Vectors into Well-Differentiated Airway Epithelium Is Responsible for Inefficient Gene Transfer
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Investigations of the efficiency and safety of human adenovirus vector (AdV)-mediated gene transfer in the airways of patients with cystic fibrosis (CF) in vivo have demonstrated little success in correcting the CF bioelectrical functional defect, reflecting the inefficiency of AdV-mediated gene transfer to the epithelial cells that line the airway luminal surface. In this study, we demonstrate that low AdV-mediated gene transfer efficiency to well-differentiated (WD) cultured airway epithelial cells is due to three distinct steps in the apical membrane of the airway epithelial cells: (i) the absence of specific adenovirus fiber-knob protein attachment receptors; (ii) the absence of αvβ3/5 integrins, reported to partially mediate the internalization of AdV into the cell cytoplasm; and (iii) the low rate of apical plasma membrane uptake pathways of WD airway epithelial cells. Attempts to increase gene transfer efficiency by increasing nonspecific attachment of AdV were unsuccessful, reflecting the inability of the attached vector to enter (penetrate) WD cells via nonspecific entry paths. Strategies to improve the efficiency of AdV for the treatment of CF lung disease will require methods to increase the attachment of AdV to and promote its internalization into the WD respiratory epithelium.
Additional file 1 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Population structure of the sequenced pigs according to the two first principal components.
Production of High-Titer Recombinant Adeno-Associated Virus Vectors in the Absence of Helper Adenovirus
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Recently, efficient and long-term in vivo gene transfer by recombinant adeno-associated virus type 2 (rAAV) vectors has been demonstrated in a variety of tissues. Further improvement in vector titer and purity will expedite this in vivo exploration and provide preclinical information required for use in human gene therapy. In an effort to obtain higher titers, we constructed a novel AAV helper plasmid which utilizes translational control of AAV Rep genes (J. Li et al., J. Virol. 71:5236–5243, 1997). To address the issue of purity, in this study we report the first rAAV production method which is completely free of adenovirus (Ad) helper virus. The new production system uses a plasmid construct which contains a mini-Ad genome capable of propagating rAAV in the presence of AAV Rep and Cap genes. This construct is missing some of the early and most of the late Ad genes and is incapable of producing infectious Ad. Transfection of 293 cells with the new mini-Ad helper and AAV packaging plasmids results in high-titer rAAV vectors with yields greater than 1,000 transducing units, or 105 viral particles per cell. When rAAV vectors were produced by using this production scheme and compared to traditional heat-inactivated rAAV preparations in vitro and in vivo, we observed transduction equivalent to or better than normal levels. The complete removal of infectious Ad from AAV production should facilitate a better understanding of immune response to AAV vectors in vivo, eliminate the need for developing replication-competent Ad assays, and provide a more defined reagent for clinical use.
Additional file 2 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S2. Prediction accuracy for all traits and lines.
Wave-packet rectification in nonlinear electronic systems: A tunable Aharonov-Bohm diode
Creators: name: Li, Yunyun
name: Zhou, Jun
name: Marchesoni, Fabio
name: Li, Baowen
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Rectification of electron wave-packets propagating along a quasi-one dimensional chain is commonly achieved via the simultaneous action of nonlinearity and longitudinal asymmetry, both confined to a limited portion of the chain termed wave diode. However, it is conceivable that, in the presence of an external magnetic field, spatial asymmetry perpendicular to the direction of propagation suffices to ensure rectification. This is the case of a nonlinear ring-shaped lattice with different upper and lower halves (diode), which is attached to two elastic chains (leads). The resulting device is mirror symmetric with respect to the ring vertical axis, but mirror asymmetric with respect to the chain direction. Wave propagation along the two diode paths can be modeled for simplicity by a discrete Schrödinger equation with cubic nonlinearities. Numerical simulations demonstrate that, thanks to the Aharonov-Bohm effect, such a diode can be operated by tuning the magnetic flux across the ring.
description: 4 figures, accepted by Scientific Reports, in press
Protection against Fatal Sindbis Virus Encephalitis by Beclin, a Novel Bcl-2-Interacting Protein
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: bcl-2, the prototypic cellular antiapoptotic gene, decreases Sindbis virus replication and Sindbis virus-induced apoptosis in mouse brains, resulting in protection against lethal encephalitis. To investigate potential mechanisms by which Bcl-2 protects against central nervous system Sindbis virus infection, we performed a yeast two-hybrid screen to identify Bcl-2-interacting gene products in an adult mouse brain library. We identified a novel 60-kDa coiled-coil protein, Beclin, which we confirmed interacts with Bcl-2 in mammalian cells, using fluorescence resonance energy transfer microscopy. To examine the role of Beclin in Sindbis virus pathogenesis, we constructed recombinant Sindbis virus chimeras that express full-length human Beclin (SIN/beclin), Beclin lacking the putative Bcl-2-binding domain (SIN/beclinΔBcl-2BD), or Beclin containing a premature stop codon near the 5′ terminus (SIN/beclinstop). The survival of mice infected with SIN/beclin was significantly higher (71%) than the survival of mice infected with SIN/beclinΔBcl-2BD (9%) or SIN/beclinstop (7%) (P < 0.001). The brains of mice infected with SIN/beclin had fewer Sindbis virus RNA-positive cells, fewer apoptotic cells, and lower viral titers than the brains of mice infected with SIN/beclinΔBcl-2BD or SIN/beclinstop. These findings demonstrate that Beclin is a novel Bcl-2-interacting cellular protein that may play a role in antiviral host defense.
Wave-vector and polarization dependence of conical refraction
Creators: name: Turpin, A.
name: Loiko, Yu. V.
name: Kalkandjiev, T. K.
name: Tomizawa, H.
name: Mompart, J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We experimentally address the wave-vector and polarization dependence of the internal conical refraction phenomenon by demonstrating that an input light beam of elliptical transverse profile refracts into two beams after passing along one of the optic axes of a biaxial crystal, i.e. it exhibits double refraction instead of refracting conically. Such double refraction is investigated by the independent rotation of a linear polarizer and a cylindrical lens. Expressions to describe the position and the intensity pattern of the refracted beams are presented and applied to predict the intensity pattern for an axicon beam propagating along the optic axis of a biaxial crystal.
On the strongly damped wave equation with constraint
Creators: name: Bonetti, Elena
name: Rocca, Elisabetta
name: Schimperna, Giulio
name: Scala, Riccardo
Publisher: name: Weierstrass Institute
Year: 2015
Subjects: subject: wave equation
subject: strong damping
subject: weak solution
subject: maximal monotone operator
subject: duality.
subject: 35L05
subject: 74D10
subject: 47H05
subject: 46A20

description: A weak formulation for the so-called semilinear strongly damped wave equation with constraint is introduced and a corresponding notion of solution is de?ned. The main idea in this approach consists in the use of duality techniques in Sobolev-Bochner spaces, aimed at providing a suitable "relaxation" of the constraint term. A global in time existence result is proved under the natural condition that the initial data have finite "physical" energy.
The Epstein-Barr Virus (EBV) SM Protein Enhances Pre-mRNA Processing of the EBV DNA Polymerase Transcript
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: The Epstein-Barr virus (EBV) DNA polymerase (pol) mRNA, which contains a noncanonical polyadenylation signal, UAUAAA, is cleaved and polyadenylated inefficiently (S. C. S. Key and J. S. Pagano, Virology 234:147–159, 1997). We postulated that the EBV early proteins SM and M, which appear to act posttranscriptionally and are homologs of herpes simplex virus (HSV) ICP27, might compensate for the inefficient processing of pol pre-mRNA. Here we show that the SM and M proteins interact with each other in vitro. In addition, glutathione S-transferase–SM/M fusion proteins precipitate the heterogeneous ribonucleoprotein (hnRNP) C1 splicing protein. Further, the SM protein is coimmunoprecipitated from SM-expressing cell extracts with an antibody to the hnRNP A1/A2 proteins, which are splicing and nuclear shuttling proteins. Finally, the amount of processed EBV DNA polymerase mRNA was increased three- to fourfold in a HeLa cell line expressing SM; this increase was not due to enhanced transcription. Thus, inefficient processing of EBV pol RNA by cellular cleavage and polyadenylation factors appears to be compensated for and may be regulated by the early EBV protein, SM, perhaps via RNA 3′-end formation.
Copositive matrices with circulant zero pattern
Creators: name: Hildebrand, Roland
Publisher: name: Weierstrass Institute
Year: 2016
Subjects: subject: Copositive matrix
subject: zero pattern
subject: extreme ray
subject: 15B48
subject: 15A21

description: Let n be an integer not smaller than 5 and let u1,...,un be nonnegative real n-vectors such that the indices of their positive elements form the sets 1,2,...,n-2,2,3,...,n-1,...,n,1,...,n-3, respectively. Here each index set is obtained from the previous one by a circular shift. The set of copositive forms which vanish on the vectors u1,...,un is a face of the copositive cone. We give an explicit semi-definite description of this face and of its subface consisting of positive semi-definite matrices, and study their properties. If the vectors u1,...,un and their positive multiples exhaust the zero set of an exceptional copositive form belonging to this face, then we call this form regular, otherwise degenerate. We show that degenerate forms are always extremal, and regular forms can be extremal only if n is odd. We construct explicit examples of extremal degenerate forms for any order n, and examples of extremal regular forms for any odd order n. The set of all degenerate forms, i.e., defined by different collections u1,...,un of zeros, is a submanifold of codimension 2n, the set of all regular forms a submanifold of codimension n.
Additional file 3 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Figure S3. Genomic prediction accuracy obtained with each set of preselected whole-genome sequence (WGS) variants (either Top40k or ChipPlusSign) against that obtained with the marker array (Chip) in each of the five replicates.
Distortion of Infall Regions in Redshift Space-I
Creators: name: Abdullah, Mohamed H.
name: Praton, Elizabeth A.
name: Ali, Gamal B.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We show that spherical infall models (SIMs) can better describe some galaxy clusters in redshift slice space than in traditional axially-convolved projection space. This is because in SIM, the presence of transverse motion between cluster and observer, and/or shear flow about the cluster (such as rotation), causes the infall artifact to tilt, obscuring the characteristic two-trumpet profile; and some clusters resemble such tilted artifacts. We illustrate the disadvantages of applying SIM to convolved data and, as an alternative, introduce a method fitting a tilted 2D envelope to determine a 3D envelope. We also introduce a fitting algorithm and test it on toy SIM simulations as well as three clusters (Virgo, A1459, and A1066). We derive relations useful for using the tilt and width-to-length ratio of the fitted envelopes to analyze peculiar velocities. We apply them to our three clusters as a demonstration. We find that transverse motion between cluster and observer can be ruled out as sole cause of the observed tilts, and that a multi-cluster study could be a feasible way to find our infall toward Virgo cluster.
title: Una lettura critica della grammatica morale di Marc D. Hauser
Creators: name: Severini , Eleonora
Publisher: name: Roma Tre-Press
Year: 2012

description: In questo intervento verrà proposta una lettura critica del paradigma morale elaborato da Marc D. Hauser a partire dall'analisi del modello linguistico di Francesco Ferretti. Si tratterà, in sostanza, di muovere ad Hauser le obiezioni che Ferretti solleva nei confronti di Noam Chomsky. Questo rappresenterà l'occasione anche per individuare e discutere le condizioni di possibilità con cui una teoria linguistica – così come un'etica – deve fare i conti: la plausibilità evoluzionistica e la plausibilità cognitiva. Obiettivo del saggio è mostrare come talvolta le convinzioni teoriche vincolino a tal punto l'indagine speculativa da rappresentare un ostacolo alla corretta impostazione di un problema. In particolare ciò verrà messo in luce discutendo una criticità metodologica alla base della grammatica universale tanto in rapporto al linguaggio quanto alla morale.

description: B@belonline vol. 13 Chaos/Kosmos
Nonlocal phase transitions in homogeneous and periodic media
Creators: name: Cozzi, Matteo
name: Dipierro, Serena
name: Valdinoci, Enrico
Publisher: name: Weierstrass Institute
Year: 2016
Subjects: subject: nonlocal Ginzburg-Landau-Allen-Cahn equation
subject: De Giorgi conjecture
subject: planelike minimizers
subject: chaotic orbits
subject: 35R11
subject: 82B26

description: We discuss some results related to a phase transition model in which the potential energy induced by a double-well function is balanced by a fractional elastic energy. In particular, we present asymptotic results (such as Gamma-convergence, energy bounds and density estimates for level sets), flatness and rigidity results, and the construction of planelike minimizers in periodic media.
 Finally, we consider a nonlocal equation with a multiwell potential, motivated by models arising in crystal dislocations, and we construct orbits exhibiting symbolic dynamics, inspired by some classical results by Paul Rabinowitz.
Neckpinch singularities in fractional mean curvature flows
Creators: name: Cinti, Eleonora
name: Sinestrari, Carlo
name: Valdinoci, Enrico
Publisher: name: Weierstrass Institute
Year: 2016
Subjects: subject: fractional perimeter
subject: fractional mean curvature flow
subject: 53C44
subject: 35R11

description: In this paper we consider the evolution of boundaries of sets by a fractional mean curvature flow. We show that, for any dimension n ≥ 2, there exist embedded hypersurfaces in Rn which develop a singularity without shrinking to a point. Such examples are well known for the classical mean curvature flow for n ≥ 3. Interestingly, when n=2, our result provides instead a counterexample in the nonlocal framework to the well known Grayson's Theorem [17], which states that any smooth embedded curve in the plane evolving by (classical) MCF shrinks to a point. The essential step in our construction is an estimate which ensures that a suitably small perturbation of a thin strip has positive fractional curvature at every boundary point.
Additional file 4 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Table S1. Comparison of the results obtained with a single replicate or with five replicates.
Advances in Macromolecular Data Storage
Creators: name: Mansuripur, Masud
Publisher: name: arXiv
Year: 2014
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Emerging Technologies (cs.ET)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: We propose to develop a new method of information storage to replace magnetic hard disk drives and other instruments of secondary/backup data storage. The proposed method stores petabytes of user-data in a sugar cube (1 cm3), and can read/write that information at hundreds of megabits/sec. Digital information is recorded and stored in the form of a long macromolecule consisting of at least two bases, A and B. (This would be similar to DNA strands constructed from the four nucleic acids G,C,A,T.) The macromolecules initially enter the system as blank slates. A macromolecule with, say, 10,000 identical bases in the form of AAAAA....AAA may be used to record a kilobyte block of user-data (including modulation and error-correction coding), although, in this blank state, it can only represent the null sequence 00000....000. Suppose this blank string of A's is dragged before an atomically-sharp needle of a scanning tunneling microscope (STM). When electric pulses are applied to the needle in accordance with the sequence of 0s and 1s of a 1 kB block of user-data, selected A molecules will be transformed into B molecules (e.g., a fraction of A will be broken off and discarded). The resulting string now encodes the user-data in the form of AABABBA...BAB. The same STM needle can subsequently read the recorded information, as A and B would produce different electric signals when the strand passes under the needle. The macromolecule now represents a data block to be stored in a "parking lot" within the sugar cube, and later brought to a read station on demand. Millions of parking spots and thousands of Read/Write stations may be integrated within the micro-fabricated sugar cube, thus providing access to petabytes of user-data in a scheme that benefits from the massive parallelism of thousands of Read/Write stations within the same three-dimensionally micro-structured device.
description: 6 pages, 6 figures, 21 references
Additional file 5 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Figure S4. Genomic prediction accuracy by density of preselected whole-genome sequence variants in the prediction model.
Neural mechanisms of language control in bilingual speech production
Creators: name: Zhu, Di
Publisher: name: Macquarie University
Year: 2023
Subjects: Other education not elsewhere classified

description: Bilinguals have a remarkable ability to coordinate their languages during speech production; they can switch language with ease, but can also stay in a single language if required. What are the neural mechanisms underlying such language control? It has been proposed that bilingual control is supported by a range of cognitive processes (e.g. inhibition), with recent neuroimaging evidence pointing towards the engagement of executive-control brain regions during language switching. Building on these existing knowledge, the present thesis aimed to further investigate the exact manner in which language control takes place in the bilingual brain, focussing on three particular aspects: scope, timing, and demands for control under different circumstances. Chapter 2 examined the scope of language control, by looking at whole-language and item-specific control side by side in a modified language-switching paradigm. The role of the pre-supplementary motor area (a key brain region for domain-general inhibitory control) was then probed using transcranial magnetic stimulation (TMS). An overall performance decrement following the disruption of this brain region revealed its essential role in general speech execution, while no reliable evidence was found for its specific involvement in either whole-language or item-specific control. Chapter 3 investigated the timing of language control, by dividing the language-switching process into two separate stages (preparation and production). Brain activities were recorded using magnetoencephalography (MEG), and reconstructed into source activities in pre-selected regions of interest. The findings suggested that different control processes took place during the preparation stage and production stage, supported by the left and right inferior frontal gyrus, respectively. Chapter 4 examined how the demands for language control differed between natural and forced switching. The effects of language switching and mixing were compared across three different contexts, with varying levels of external constraint on language selection. The behavioural and MEG results indicated that freedom of language selection and consistent language choice for each given concept were both factors that contributed to making natural switching easier than forced switching. Taken together, the findings in this thesis expand our current knowledge on the neural mechanisms of language control in bilingual speech production, particularly regarding whole-language and item-specific control, preparation and execution of a language switch, and reduction of control demands in natural switching. These new findings deepen our understanding of bilinguals’ skilful language coordination in daily life.
The Epstein-Barr Virus Immediate-Early Gene Product, BRLF1, Interacts with the Retinoblastoma Protein during the Viral Lytic Cycle
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Retinoblastoma protein (Rb) is a key regulator of cellular proliferation, controlling entry into G1/S in the cell cycle, largely through its action in binding the cellular transcription factor E2F, which activates genes important in DNA synthesis. Small DNA tumor viruses encode gene products which can functionally inactivate Rb, promoting cellular proliferation and viral DNA synthesis. In this study, the Epstein-Barr virus (EBV) immediate-early lytic gene product, BRLF1 (R), is shown to bind Rb in vivo, shortly after induction of the viral lytic cycle in EBV-infected Akata cells. Furthermore, the temporal kinetics of R-Rb interaction correlate with displacement of E2F1 from Rb. Mapping of the domains required for the interaction of R and Rb proteins reveals that R binds specifically to the N terminus of Rb, outside the Rb pocket, and that the first 200 amino acids of R are required for this interaction. The interaction of R and Rb may initiate cell cycle progression and facilitate viral DNA synthesis during lytic replication.
Modeling structural change in spatial system dynamics: A Daisyworld example
Creators: name: Neuwirth, Christian
name: Peck, Angela
name: Simonovic, Slobodan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Computer and information sciences

description: System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.
A Phylogenetically Conserved Stem-Loop Structure at the 5′ Border of the Internal Ribosome Entry Site of Hepatitis C Virus Is Required for Cap-Independent Viral Translation
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: Hepatitis C virus (HCV) initiates translation of its polyprotein under the control of an internal ribosome entry site (IRES) that comprises most of the 341-nucleotide (nt) 5′ nontranslated RNA (5′NTR). A comparative analysis of related flaviviral sequences suggested that an RNA segment for which secondary structure was previously ill defined (domain II, nt 44 to 118) forms a conserved stem-loop that is located at the 5′ border of the HCV IRES and thus may function in viral translation. This prediction was tested by a mutational analysis of putative helical structures that examined the impact of both covariant and noncovariant nucleotide substitutions on IRES activity in vivo and in vitro. Results of these experiments provide support for predicted base pair interactions between nt 44 to 52 and 111 to 118 and between nt 65 to 70 and 97 to 102 of the HCV 5′NTR. Substitutions at either nt 45 and 46 or nt 116 and 117 resulted in reciprocal changes in V1 nuclease cleavage patterns within the opposing strand of the putative helix, consistent with the predicted base pair interactions. IRES activity was highly dependent on maintenance of the stem-loop II structure but relatively tolerant of covariant nucleotide substitutions within predicted helical segments. Sequence alignments suggested that the deduced domain II structure is conserved within the IRESs of pestiviruses as well as the novel flavivirus GB virus B. Despite marked differences in primary nucleotide sequence within conserved helical segments, the sequences of the intervening single-stranded loop segments are highly conserved in these different viruses. This suggests that these segments of the viral RNA may interact with elements of the host translational machinery that are broadly conserved among different mammalian species.
Additional file 6 of Genomic prediction with whole-genome sequence data in intensely selected pig lines
Creators: name: Ros-Freixedes, Roger
name: Johnsson, Martin
name: Whalen, Andrew
name: Chen, Ching-Yi
name: Valente, Bruno D.
name: Herring, William O.
name: Gorjanc, Gregor
name: Hickey, John M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Figure S5. Genomic prediction accuracy of whole-genome sequence data in multi-line scenarios compared to the marker arrays in within-line scenarios.
Activation of cJUN N-Terminal Kinase by Herpes Simplex Virus Type 1 Enhances Viral Replication
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: Signal transduction pathways convey signals generated at the cell surface into the cell nucleus in order to initiate a program of gene expression that is characteristic for particular stimuli. Here we present evidence that infection by herpes simplex virus type 1 activated the two terminal kinases, cJUN N-terminal kinase (JNK) and p38, of stress-activated signal transduction kinase cascades. By using a solid-phase kinase assay, a phospho-specific antibody, and extracts prepared from a variety of infected cell types, we determined that activation of both kinases began 3 to 4 h postinfection (p.i.) and remained elevated out to 14 h p.i. Through the use of UV-irradiated or antibody-neutralized wild-type virus and the temperature-sensitive mutant tsB7, the high level of JNK activation was shown to be dependent on viral gene expression. Activation of JNK following infection by vi13, an ICP4 mutant virus that does not express early or late genes, suggested that only virus entry and immediate-early gene expression were necessary for JNK activation. The activation of JNK and p38 correlated with increased chloramphenicol acetyltransferase (CAT) activity in reporter assays dependent upon the activity of cJUN and ATF2 trans-activation domains. Increased CAT activity dependent on TRE and CRE promoter sites was also observed in response to herpes simplex virus infection. The activities of ERK and ERK-dependent transcription factors were unchanged or depressed following infection, showing that activation of JNK and p38 was a specific event. Finally, the activation of JNK was important for the efficiency of viral replication. The yield of virus in NIH 3T3 cells stably expressing JIP-1, an inhibitor of JNK translocation to the nucleus, was reduced 70% compared to that of control cells, in single-step growth experiments.
The World Trade Web: A Multiple-Network Perspective
Creators: name: Sgrignoli, Paolo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: General Economics (econ.GN)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Economics and business

description: International Trade (IT) plays a fundamental role in today's economy: by connecting world countries production and consumption processes, it radically contributes in shaping their economy and development path. Although its evolving structure and determinants have been widely analyzed in the literature, much less has been done to understand its interplay with other complex phenomena. The aim of this work is, precisely in this direction, to study the relations of IT with International Migration (IM) and Foreign Direct Investments (FDI). In both cases the procedure used is to first approach the problem in a multiple-networks perspective and than deepen the analysis by using ad hoc econometrics techniques. With respect to IM, a general positive correlation with IT is highlighted and product categories for which this effect is stronger are identified and cross-checked with previous classifications. Next, employing spatial econometric techniques and proposing a new way to define country neighbors based on the most intense IM flows, direct/indirect network effects are studied and a stronger competitive effect of third country migrants is identified for a specific product class. In the case of FDI, first correlations between the two networks are identified, highlighting how they can be mostly explained by countries economic/demographic size and geographical distance. Then, using the Heckman selection model with a gravity equation, (non-linear) components arising from distance, position in the Global Supply Chain and presence of Regional Trade Agreements are studied. Finally, it is shown how IT and FDI correlation changes with sectors: they are complements in manufacturing, but substitutes in services.
description: PhD thesis at IMT Institute for Advanced Studies Lucca. 114 pages, 12 figures, 18 tables
Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitutions. This observation is in contrast to that for subtype B HIV-1, where sequence variability is associated with such substitutions, and these substitutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated with the CD4 level in the infected person, while such a correlation was found with subtype B V3 sequences. Viruses were isolated from a subset of the subjects; all isolates used CCR5 and not CXCR4 as a coreceptor, and none was able to grow in MT-2 cells, a hallmark of the syncytium-inducing phenotype that is correlated with CXCR4 usage. The overall sequence variability of the subtype C V3 region was no greater than that of the conserved regions of gp120. This limited sequence variability was also a feature of subtype B V3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered coreceptor usage is rare in subtype C HIV-1 isolates in sub-Saharan Africa and that sequence variability is not a feature of the V3 region of env in the absence of altered coreceptor usage.
Warped DGP model in warm intermediate inflation with a general dissipative coefficient in light of BICEP2 and Planck results
Creators: name: Herrera, Ramon
name: Videla, Nelson
name: Olivares, Marco
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A warm inflationary universe scenario on a warped Dvali-Gabadadze-Porrati brane during intermediate inflation is studied. We consider a general form for the dissipative coefficient $Γ(T,ϕ)\propto T^{m}/ϕ^{m-1}$, and also study this model in the weak and strong dissipative regimes. We analyze the evolution of the universe in the slow-roll approximation, and find the exact solutions to the equations of motion. In both regimes, we utilize recent data from the BICEP2 experiment and also from the Planck satellite to constrain the parameters in our model in accordance with the theory of cosmological perturbations.
description: 27 pages and 4 figures. Accepted for publication in Phys. Rev. D