cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Disordered Solids Without Well-Defined Transverse Phonons: The Nature of Hard Sphere Glasses
Creators: name: Wang, Xipeng
name: Zheng, Wen
name: Wang, Lijin
name: Xu, Ning
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We probe the Ioffe-Regel limits of glasses with repulsions near the zero-temperature jamming transition by measuring the dynamical structure factors. At zero temperature, the transverse Ioffe-Regel frequency vanishes at the jamming transition with a diverging length, but the longitudinal one does not, which excludes the existence of a diverging length associated with the longitudinal excitations. At low temperatures, the transverse and longitudinal Ioffe-Regel frequencies approach zero at the jamming-like transition and glass transition, respectively. As a consequence, glasses between the glass transition and jamming-like transition, which are hard sphere glasses in the low temperature limit, can only carry well-defined longitudinal phonons and have an opposite pressure dependence of the ratio of the shear modulus to the bulk modulus from glasses beyond the jamming-like transition.
description: 5 pages, 4 figures
Hydrology IV HYLO4P1
Creators: name: Ikudayisi, Akinola
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Civil engineering not elsewhere classified

description: Subject : Hydrology IV Subject code : HYLO4P1 Course : B.Tech Engineering: Civil Examiner : DR AM Ikudayisi Moderator : Mr M Mambwe Date : November 2019
On the formation of the Kepler-10 planetary system
Creators: name: Terquem, Caroline
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: In this paper, we investigate the conditions required for the 3 and 17 Earth mass solid planets in the Kepler-10 system to have formed through collisions and mergers within an initial population of embryos. By performing a large number of N-body simulations, we show that the total mass of the initial population had to be significantly larger than the masses of the two planets, and that the two planets must have built-up farther away than their present location, at a distance of at least a few au from the central star. The planets had to grow fast enough so that they would detach themselves from the population of remaining, less massive, cores and migrate in to their present location. By the time the other cores migrated in, the disc's inner edge would have moved out so that these cores cannot be detected today. We also compute the critical core mass beyond which a massive gaseous envelope would be accreted and show that it is larger than 17 Earth masses if the planetesimal accretion rate onto the core is larger than 10^{-6} Earth mass per year. For a planetesimal accretion rate between 10^{-6} and 10^{-5} Earth mass per year, the 17 Earth mass core would not be expected to have accreted more than about 1 Earth mass of gas. The results presented in this paper suggest that a planetary system like Kepler-10 may not be unusual, although it has probably formed in a rather massive disc.
description: 12 pages, accepted for publication in MNRAS
Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes
Creators: name: Wolfenden, R.
name: Lewis, C. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The magnitude of an enzyme's affinity for the altered substrate in the transition state exceeds its affinity for the substrate in the ground state by a factor matching the rate enhancement that the enzyme produces. Particularly remarkable are those enzymes that act as simple protein catalysts, without the assistance of metals or other cofactors. To determine the extent to which one such enzyme, human uroporphyrinogen decarboxylase, enhances the rate of substrate decarboxylation, we examined the rate of spontaneous decarboxylation of pyrrolyl-3-acetate. Extrapolation of first-order rate constants measured at elevated temperatures indicates that this reaction proceeds with a half-life of 2.3 × 109 years at 25 °C in the absence of enzyme. This enzyme shows no significant homology with orotidine 5′-monophosphate decarboxylase (ODCase), another cofactorless enzyme that catalyzes a very slow reaction. It is proposed that, in both cases, a protonated basic residue (Arg-37 in the case of human UroD; Lys-93 in the case of yeast ODCase) furnishes a counterion that helps the scissile carboxylate group of the substrate leave water and enter a relatively nonpolar environment, stabilizes the incipient carbanion generated by the departure of CO2, and supplies the proton that takes its place.
Pavement Technology IV PATE4P2
Creators: name: Abejide, Samuel
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Civil engineering not elsewhere classified

description: Subject : Pavement Technology IV Subject code : PATE4P2 Course : B.Tech Engineering: Civil Examiner : Mr Samuel Abejide Moderator : Mr Cladious Nhawu Date : November 2019
Neutrinos and dark energy after Planck and BICEP2: data consistency tests and cosmological parameter constraints
Creators: name: Zhang, Jing-Fei
name: Geng, Jia-Jia
name: Zhang, Xin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The detection of the B-mode polarization of the cosmic microwave background (CMB) by the BICEP2 experiment implies that the tensor-to-scalar ratio $r$ should be involved in the base standard cosmology. In this paper, we extend the $Λ$CDM+$r$+neutrino/dark radiation models by replacing the cosmological constant with the dynamical dark energy with constant $w$. Four neutrino plus dark energy models are considered, i.e., the $w$CDM+$r+\sum m_ν$, $w$CDM+r + $N_{\rm eff}$, $w$CDM+r + $\sum m_ν$ + $N_{\rm eff}$, and $w$CDM+r + $N_{\rm eff}$ + $m_{ν,{\rm sterile}}^{\rm eff}$ models. The current observational data considered in this paper include the Planck temperature data, the WMAP 9-year polarization data, the baryon acoustic oscillation data, the Hubble constant direct measurement data, the Planck Sunyaev-Zeldovich cluster counts data, the Planck CMB lensing data, the cosmic shear data, and the BICEP2 polarization data. We test the data consistency in the four cosmological models, and then combine the consistent data sets to perform joint constraints on the models. We focus on the constraints on the parameters $w$, $\sum m_ν$, $N_{\rm eff}$, and $m_{ν,{\rm sterile}}^{\rm eff}$.
description: 22 pages, 8 figures, 5 tables
Interferometric measurement of the biphoton wave function
Creators: name: Beduini, Federica A.
name: Zielińska, Joanna A.
name: Lucivero, Vito G.
name: Astiz, Yannick A. de Icaza
name: Mitchell, Morgan W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Interference between an unknown two-photon state (a "biphoton") and the two-photon component of a reference state gives a phase-sensitive arrival-time distribution containing full information about the biphoton temporal wave function. Using a coherent state as a reference, we observe this interference and reconstruct the wave function of single-mode biphotons from a low-intensity narrowband squeezed vacuum state.
description: 4 pages, 3 figures
Behavioural Studies BFS11P1
Creators: name: Wilkinson, Jeanne
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Food sciences not elsewhere classified

description: Subject : Behavioural Studies Subject code : BFS11P1 Course : ND Consumer Sciences: Food & Nutrition Examiner : Mrs J Wilkinson Moderator : Ms NA Kruger Date : June 2019
Accretion onto a black hole in a string cloud background
Creators: name: Ganguly, Apratim
name: Ghosh, Sushant G.
name: Maharaj, Sunil D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We examine the accretion process onto the black hole with a string cloud background, where the horizon of the black hole has an enlarged radius $r_H=2 M/(1-α)$, due to the string cloud parameter $α\; (0 \leq α< 1)$. The problem of stationary, spherically symmetric accretion of a polytropic fluid is analysed to obtain an analytic solution for such a perturbation. Generalised expressions for the accretion rate $\dot{M}$, critical radius $r_s$, and other flow parameters are found. The accretion rate $\dot{M}$ is an explicit function of the black hole mass $M$, as well as the gas boundary conditions and the string cloud parameter $α$. We also find the gas compression ratios and temperature profiles below the accretion radius and at the event horizon. It is shown that the mass accretion rate, for both the relativistic and the non-relativistic fluid by a black hole in the string cloud model, increases with increase in $α$.
description: 9 pages, To appear in Phys. Rev. D
A chemical-genetic approach to study G protein regulation of   cell function in vivo
Creators: name: Roth, B. L.
name: Rosemond, E.
name: Lu, H.
name: Ma, X.
name: Li, J. H.
name: Scarselli, M.
name: Guettier, J.-M.
name: Gonzalez, F. J.
name: Gautam, D.
name: de Azua, I. R.
name: Armbruster, B. N.
name: Wess, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Impaired functioning of pancreatic β cells is a key hallmark of type 2 diabetes. β cell function is modulated by the actions of different classes of heterotrimeric G proteins. The functional consequences of activating specific β cell G protein signaling pathways in vivo are not well understood at present, primarily due to the fact that β cell G protein-coupled receptors (GPCRs) are also expressed by many other tissues. To circumvent these difficulties, we developed a chemical-genetic approach that allows for the conditional and selective activation of specific β cell G proteins in intact animals. Specifically, we created two lines of transgenic mice each of which expressed a specific designer GPCR in β cells only. Importantly, the two designer receptors differed in their G protein-coupling properties (Gq/11 versus Gs). They were unable to bind endogenous ligand(s), but could be efficiently activated by an otherwise pharmacologically inert compound (clozapine-N-oxide), leading to the conditional activation of either β cell Gq/11 or Gs G proteins. Here we report the findings that conditional and selective activation of β cell Gq/11 signaling in vivo leads to striking increases in both first- and second-phase insulin release, greatly improved glucose tolerance in obese, insulin-resistant mice, and elevated β cell mass, associated with pathway-specific alterations in islet gene expression levels. Selective stimulation of β cell Gs triggered qualitatively similar in vivo metabolic effects. Thus, this developed chemical-genetic strategy represents a powerful approach to study G protein regulation of β cell function in vivo.
A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection
Creators: name: Hu, X.
name: Yang, L.
name: Pu, D.
name: Xiao, X.
name: Chen, C.
name: Wang, D.-Z.
name: Qiao, C.
name: Jiang, J.
name: Agbandje-Mckenna, M.
name: Drouin, L. M.
name: Li, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: To engineer gene vectors that target striated muscles after systemic delivery, we constructed a random library of adeno-associated virus (AAV) by shuffling the capsid genes of AAV serotypes 1 to 9, and screened for muscle-targeting capsids by direct in vivo panning after tail vein injection in mice. After 2 rounds of in vivo selection, a capsid gene named M41 was retrieved mainly based on its high frequency in the muscle and low frequency in the liver. Structural analyses revealed that the AAVM41 capsid is a recombinant of AAV1, 6, 7, and 8 with a mosaic capsid surface and a conserved capsid interior. AAVM41 was then subjected to a side-by-side comparison to AAV9, the most robust AAV for systemic heart and muscle gene delivery; to AAV6, a parental AAV with strong muscle tropism. After i.v. delivery of reporter genes, AAVM41 was found more efficient than AAV6 in the heart and muscle, and was similar to AAV9 in the heart but weaker in the muscle. In fact, the myocardium showed the highest gene expression among all tissues tested in mice and hamsters after systemic AAVM41 delivery. However, gene transfer in non-muscle tissues, mainly the liver, was dramatically reduced. AAVM41 was further tested in a genetic cardiomyopathy hamster model and achieved efficient long-term δ-sarcoglycan gene expression and rescue of cardiac functions. Thus, direct in vivo panning of capsid libraries is a simple tool for the de-targeting and retargeting of viral vector tissue tropisms facilitated by acquisition of desirable sequences and properties.
Food & Food science III FFS31P1
Creators: name: Xamlashe, Nomahlubi
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Food sciences not elsewhere classified

description: Subject : Food & Food Science III Subject code : FFS31P1 Course : ND Consumer Sciences: Food & Nutrition Examiner : Ms N Xamlashe Moderator : Ms L Mothepu Date : June 2019
Application of the fractional stable distributions for approximation of gene expression profiles
Creators: name: Saenko, Viacheslav
name: Saenko, Yurij
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistics Theory (math.ST)
subject: Genomics (q-bio.GN)
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 62H12, 62P10, 92B15

description: At the present time reliably established that probability density functions of gene expression of microarray experiments possess a number of universal properties. First of all these distributions have power asymptotic and secondly the shape of these distributions are inherent for all organisms and tissues. This fact led to appearance of a number works where authors are investigating various probability distributions for approximation of empirical distributions of gene expression. Nevertheless all these distributions aren't limit distribution and aren't solution of any equations. These facts by our opinion are essential shortcoming of these probability laws. Besides, expression of individual gene aren't accidental event and it depends from expression other genes. This allows to talk about existence of genic regulatory net in the cell. In the work the class of fractional stable distributions (FSD) are described. This class of distributions is limit distribution of sum independent identical distributed random variables. These distributions have power-law asymptotic and this fact allow us to apply their for approximation of experimental densities gene expression of microarray experiments. The parameters of FSDs are statistically estimated by experimental dates and empirical density is compared whit theoretical density. In the work the algorithms of parameters estimation and simulating of FSD variables are presented. The results of such comparison allow to make conclusion that empirical densities of gene expression can be approximate by FSD.
How cholesterol could be drawn to the cytoplasmic leaf of the plasma membrane by phosphatidylethanolamine
Creators: name: Giang, Ha
name: Schick, Michael
Publisher: name: arXiv
Year: 2014
Subjects: subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: In the mammalian plasma membrane, cholesterol can translocate rapidly between the exoplasmic and cytoplasmic leaves, so that its distribution between them should be given by the equality of its chemical potential in the leaves. Due to its favorable interaction with sphingomyelin, which is almost entirely in the outer leaf, one expects the great majority of cholesterol to be there also. Experimental results do not support this, implying that there is some mechanism which attracts cholesterol to the inner leaf. We hypothesize that it is drawn there to reduce the bending free energy of the membrane caused by the presence of phosphatidylethanolamine (PE). It does this in two ways: first by simply diluting the amount of PE in the inner leaf, and second by ordering the tails of the PE so as to reduce its spontaneous curvature. Incorporating this mechanism into a model free energy for the bilayer, we find that between 50 and 60% of the total cholesterol should be in the inner leaf of human erythrocytes.
A quantitative model for age-dependent expression of the p16INK4a tumor suppressor
Creators: name: Tsygankov, D.
name: Elston, T. C.
name: Sanoff, H. K.
name: Liu, Y.
name: Sharpless, N. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Recent work has shown that expression of the p16INK4a tumor suppressor increases with chronological age. Expression is accelerated by gerontogenic behaviors such as tobacco use and physical inactivity, and is also influenced by allelic genotype of a polymorphic single nucleotide polymorphism (SNP) rs10757278 that is physically linked with the p16INK4a ORF. To understand the relationship between p16INK4a expression, chronologic age, subject characteristics and host genetics, we sought to develop a mathematical model that links p16INK4a expression with aging. Using an annotated dataset of 170 healthy adults for whom p16INK4a expression and subject genotypes were known, we developed two alternative stochastic models that relate p16INK4a expression to age, smoking, exercise and rs10757278 genotype. Levels of p16INK4a increased exponentially and then saturated at later chronologic ages. The model, which best fit the data, suggests saturation occurs because of p16INK4a-dependent attrition of subjects at older chronologic ages, presumably due to death or chronic illness. An important feature of our model is that factors that contribute to death in a non p16INK4a-dependent manner do not affect our analysis. Interestingly, tobacco-related increases in p16INK4a expression are predicted to arise from a decrease in the rate of p16INK4a-dependent death. This analysis is most consistent with the model that p16INK4a expression monotonically increases with age, and higher expression is associated with increased subject attrition.
SHAPEMOL: a 3-D code for calculating CO line emission in planetary and protoplanetary nebulae. Detailed model fitting of the complex nebula NGC 6302
Creators: name: Santander-Garcia, M.
name: Bujarrabal, V.
name: Koning, N.
name: Steffen, W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA has reached unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window for probing molecular warm gas (~50-1000 K). On the other hand, the software SHAPE has emerged in the past few years as a standard tool for determining the morphology and velocity field of different kinds of gaseous emission nebulae via spatio-kinematical modelling. SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for simplifying the analyses of molecular data, we introduce shapemol, a complement to SHAPE, with which we intend to fill the so-far under-developed molecular niche. shapemol enables user-friendly, spatio-kinematic modelling with accurate non-LTE calculations of excitation and radiative transfer in CO lines. It allows radiative transfer solving in the 12CO and 13CO J=1-0 to J=17-16 lines, but its implementation permits easily extending the code to different molecular species. shapemol allows easily generating synthetic maps and line profiles to match against interferometric or single-dish observations. We fully describe shapemol and discuss its limitations and the sources of uncertainty to be expected in the final synthetic profiles or maps. As an example of the power and versatility of shapemol, we build a model of the molecular envelope of the planetary nebula NGC 6302 and compare it with 12CO and 13CO J=2-1 interferometric maps from SMA and high-J transitions from Herschel/HIFI. We find the molecular envelope to have a complex, broken ring-like structure with an inner, hotter region and several 'fingers' and high-velocity blobs, emerging outwards from the plane of the ring. We derive a mass of 0.11 Msun for the molecular envelope.
description: 19 pages, 15 figures. Accepted for publication in Astronomy & Astrophysics
Accurate SHAPE-directed RNA structure determination
Creators: name: Li, T. W.
name: Deigan, K. E.
name: Weeks, K. M.
name: Mathews, D. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis.
Antitumorigenesis of antioxidants in a transgenic Rac1 model of Kaposi's sarcoma
Creators: name: Mesri, E. A.
name: Cavallin, L. E.
name: Yan, B.
name: Hale, L. P.
name: Dong, C.
name: Ma, Q.
name: Cesarman, E.
name: Zhu, S.
name: Wang, H.
name: Duran, E. M.
name: Goldschmidt-Clermont, P. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Kaposi's sarcoma (KS) is the major AIDS-associated malignancy. It is characterized by the proliferation of spindle cells, inflammatory infiltrate, and aberrant angiogenesis caused by Kaposi's sarcoma herpesvirus (KSHV) infection. Small GTPase Rac1, an inflammatory signaling mediator triggering reactive oxygen species (ROS) production by NADPH-oxidases, is implicated in carcinogenesis and tumor angiogenesis. Here, we show that expression of a constitutively active Rac1 (RacCA) driven by the α-smooth muscle actin promoter in transgenic mice is sufficient to cause KS-like tumors through mechanisms involving ROS-driven proliferation, up-regulation of AKT signaling, and hypoxia-inducible factor 1-α–related angiogenesis. RacCA-induced tumors expressed KS phenotypic markers; displayed remarkable transcriptome overlap with KS lesions; and were, like KS, associated with male gender. The ROS scavenging agent N-acetyl-cysteine inhibited angiogenesis and completely abrogated transgenic RacCA tumor formation, indicating a causal role of ROS in tumorigenesis. Consistent with a pathogenic role in KS, immunohistochemical analysis revealed that Rac1 is overexpressed in KSHV+ spindle cells of AIDS-KS biopsies. Our results demonstrate the direct oncogenicity of Rac1 and ROS and their contribution to a KS-like malignant phenotype, further underscoring the carcinogenic potential of oxidative stress in the context of chronic infection and inflammation. They define the RacCA transgenic mouse as a model suitable for studying the role of oxidative stress in the pathogenesis and therapy of KS, with relevance to other inflammation-related malignancies. Our findings suggest host and viral genes triggering Rac1 or ROS production as key determinants of KS onset and potential KS chemopreventive or therapeutic targets.
Basal cells as stem cells of the mouse trachea and human airway epithelium
Creators: name: Lu, Y.
name: Rawlins, E. L.
name: Hogan, B. L. M.
name: Clark, C. P.
name: Randell, S. H.
name: Xue, Y.
name: Onaitis, M. W.
name: Rock, J. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The pseudostratified epithelium of the mouse trachea and human airways contains a population of basal cells expressing Trp-63 (p63) and cytokeratins 5 (Krt5) and Krt14. Using a KRT5-CreERT2 transgenic mouse line for lineage tracing, we show that basal cells generate differentiated cells during postnatal growth and in the adult during both steady state and epithelial repair. We have fractionated mouse basal cells by FACS and identified 627 genes preferentially expressed in a basal subpopulation vs. non-BCs. Analysis reveals potential mechanisms regulating basal cells and allows comparison with other epithelial stem cells. To study basal cell behaviors, we describe a simple in vitro clonal sphere-forming assay in which mouse basal cells self-renew and generate luminal cells, including differentiated ciliated cells, in the absence of stroma. The transcriptional profile identified 2 cell-surface markers, ITGA6 and NGFR, which can be used in combination to purify human lung basal cells by FACS. Like those from the mouse trachea, human airway basal cells both self-renew and generate luminal daughters in the sphere-forming assay.
BRG1 requirement for long-range interaction of a locus control region with a downstream promoter
Creators: name: Dean, A.
name: Kim, S.-I.
name: Bresnick, E. H.
name: Bultman, S. J.
name: Kiefer, C. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The dynamic packaging of DNA into chromatin is a fundamental step in the control of diverse nuclear processes. Whereas certain transcription factors and chromosomal components promote the formation of higher-order chromatin loops, the co-regulator machinery mediating loop assembly and disassembly is unknown. Using mice bearing a hypomorphic allele of the BRG1 chromatin remodeler, we demonstrate that the Brg1 mutation abrogated a cell type-specific loop between the β-globin locus control region and the downstream βmajor promoter, despite trans-acting factor occupancy at both sites. By contrast, distinct loops were insensitive to the Brg1 mutation. Molecular analysis with a conditional allele of GATA-1, a key regulator of hematopoiesis, in a novel cell-based system provided additional evidence that BRG1 functions early in chromatin domain activation to mediate looping. Although the paradigm in which chromatin remodelers induce nucleosome structural transitions is well established, our results demonstrating an essential role of BRG1 in the genesis of specific chromatin loops expands the repertoire of their functions.
Maximum Multipath Routing Throughput in Multirate Wireless Mesh Networks
Creators: name: Qureshi, Jalaluddin
name: Foh, Chuan Heng
name: Cai, Jianfei
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: In this paper, we consider the problem of finding the maximum routing throughput between any pair of nodes in an arbitrary multirate wireless mesh network (WMN) using multiple paths. Multipath routing is an efficient technique to maximize routing throughput in WMN, however maximizing multipath routing throughput is a NP-complete problem due to the shared medium for electromagnetic wave transmission in wireless channel, inducing collision-free scheduling as part of the optimization problem. In this work, we first provide problem formulation that incorporates collision-free schedule, and then based on this formulation we design an algorithm with search pruning that jointly optimizes paths and transmission schedule. Though suboptimal, compared to the known optimal single path flow, we demonstrate that an efficient multipath routing scheme can increase the routing throughput by up to 100% for simple WMNs.
description: This paper has been accepted for publication in IEEE 80th Vehicular Technology Conference, VTC-Fall 2014
Nutrition III NUT31P1
Creators: name: Mafu, Thobekile
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Food sciences not elsewhere classified

description: Subject : Nutrition III Subject code : NUT31P1 Course : ND Consumer Sciences: Food & Nutrition Examiner : Ms T Mafu Moderator : Ms P Kheswa Date : June 2019
Cloud of strings for radiating black holes in Lovelock gravity
Creators: name: Ghosh, Sushant G.
name: Maharaj, Sunil D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We present exact spherically symmetric null dust solutions in the third order Lovelock gravity with a string cloud background in arbitrary $N$ dimensions,. This represents radiating black holes and generalizes the well known Vaidya solution to Lovelock gravity with a string cloud in the background. We also discuss the energy conditions and horizon structures, and explicitly bring out the effect of the string clouds on the horizon structure of black hole solutions for the higher dimensional general relativity and Einstein-Gauss-Bonnet theories. It turns out that the presence of the coupling constant of the Gauss-Bonnet terms and/or background string clouds completely changes the structure of the horizon and this may lead to a naked singularity. We recover known spherically symmetric radiating models as well as static black holes in the appropriate limits.
description: 9 pages, To appear in Phys. Rev. D
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain
Creators: name: Weeks, K. M.
name: Mortimer, S. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: A striking and widespread observation is that higher-order folding for many RNAs is very slow, often requiring minutes. In some cases, slow folding reflects the need to disrupt stable, but incorrect, interactions. However, a molecular explanation for slow folding in most RNAs is unknown. The specificity domain of the Bacillus subtilis RNase P ribozyme undergoes a rate-limiting folding step on the minute time-scale. This RNA also contains a C2′-endo nucleotide at A130 that exhibits extremely slow local conformational dynamics. This nucleotide is evolutionarily conserved and essential for tRNA recognition by RNase P. Here we show that deleting this single nucleotide accelerates folding by an order of magnitude even though this mutation does not change the global fold of the RNA. These results demonstrate that formation of a single stacking interaction at a C2′-endo nucleotide comprises the rate-determining step for folding an entire 154 nucleotide RNA. C2′-endo nucleotides exhibit slow local dynamics in structures spanning isolated helices to complex tertiary interactions. Because the motif is both simple and ubiquitous, C2′-endo nucleotides may function as molecular timers in many RNA folding and ligand recognition reactions.
Caveolae are required for protease-selective signaling by protease-activated receptor-1
Creators: name: Arora, P.
name: Russo, A.
name: Trejo, J.
name: Soh, U. J. K.
name: Paing, M. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Protease-activated receptor-1 (PAR1) is a G-protein–coupled receptor uniquely activated by proteolysis. Thrombin, a coagulant protease, induces inflammatory responses and endothelial barrier permeability through the activation of PAR1. Activated protein C (APC), an anti-coagulant protease, also activates PAR1. However, unlike thrombin, APC elicits anti-inflammatory responses and protects against endothelial barrier dysfunction induced by thrombin. We found that thrombin and APC signaling were lost in PAR1-deficient endothelial cells, indicating that PAR1 is the major effector of protease signaling. To delineate the mechanism responsible for protease-selective signaling by PAR1, we examined the effect of APC and thrombin on the activation of RhoA and Rac1, small GTPases that differentially regulate endothelial barrier permeability. Thrombin caused robust RhoA signaling but not Rac1 activation, whereas APC stimulated a marked increase in Rac1 activation but not RhoA signaling, consistent with the opposing functions of these proteases on endothelial barrier integrity. Strikingly, APC signaling and endothelial barrier protection effects were abolished in cells lacking caveolin-1, whereas thrombin signaling remained intact. These findings suggest that compartmentalization of PAR1 in caveolae is critical for APC selective signaling to Rac1 activation and endothelial barrier protection. We further report that APC induces PAR1 phosphorylation and desensitizes endothelial cells to thrombin signaling but promotes limited receptor cleavage and negligible internalization and degradation even after prolonged APC exposure. Thus, APC selective signaling and endothelial barrier protective effects are mediated through compartmentalization of PAR1 in caveolae and a novel mechanism of PAR1 signal regulation.
Digital Systems I DSYS1B1 ; DSYS1P1
Creators: name: Clark, Juan
name: Gcadinja, Lungile
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Electrical engineering not elsewhere classified

description: Subject : Digital Systems I Subject code : DSYS1B1; DSYS1P1 Course : ND Engineering: Electrical Examiner : Mr JA Clark & Mr LC Gcadinja Moderator : Mr N Pakathi Date : June 2019
Cellular immune response to cryptic epitopes during therapeutic gene transfer
Creators: name: Hirsch, M.
name: Alexander, J.
name: Samulski, R. J.
name: Tisch, R.
name: Seiber, D.
name: Asokan, A.
name: Sette, A.
name: Fan, Y.
name: Frelinger, J.
name: Sidney, J.
name: Goudy, K.
name: Monahan, P.
name: Li, C.
name: Sun, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The immune response has been implicated as a critical factor in determining the success or failure of clinical gene therapy trials. Generally, such a response is elicited by the desired transgene product or, in some cases, the delivery system. In the current study, we report the previously uncharacterized finding that a therapeutic cassette currently being used for human investigation displays alternative reading frames (ARFs) that generate unwanted protein products to induce a cytotoxic T lymphocyte (CTL) response. In particular, we tested the hypothesis that antigenic epitopes derived from an ARF in coagulation factor IX (F9) cDNA can induce CTL reactivity, subsequently killing F9-expressing hepatocytes. One peptide (p18) of 3 candidates from an ARF of the F9 transgene induced CD8+ T cell reactivity in mice expressing the human MHC class I molecule B0702. Subsequently, upon systemic administration of adeno-associated virus (AAV) serotype 2 vectors packaged with the F9 transgene (AAV2/F9), a robust CD8+ CTL response was elicited against peptide p18. Of particular importance is that the ARF epitope-specific CTLs eliminated AAV2/F9-transduced hepatocytes but not AAV2/F9 codon-optimized (AAV2/F9-opt)-transduced liver cells in which p18 epitope was deleted. These results demonstrate a previously undiscovered mechanism by which CTL responses can be elicited by cryptic epitopes generated from a therapeutic transgene and have significant implications for all gene therapy modalities. Such unforeseen epitope generation warrants careful analysis of transgene sequences for ARFs to reduce the potential for adverse events arising from immune responses during clinical gene therapy protocols.
CHIP regulates leucine-rich repeat kinase-2 ubiquitination, degradation, and toxicity
Creators: name: Lee, Yun-Il
name: Ross, Christopher A.
name: Jiang, Haibing
name: Petrucelli, Leonard
name: Patterson, Cam
name: Bailey, Rachel
name: Liu, Zhaohui
name: Smith, Wanli W.
name: Dawson, Ted M.
name: Zhang, Yong-Jie
name: Moore, Darren J.
name: Ko, Han Seok
name: Shin, Joo-Ho
name: Dawson, Valina L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Mutation in leucine-rich repeat kinase-2 (LRRK2) is the most common cause of late-onset Parkinson's disease (PD). Although most cases of PD are sporadic, some are inherited, including those caused by LRRK2 mutations. Because these mutations may be associated with a toxic gain of function, controlling the expression of LRRK2 may decrease its cytotoxicity. Here we show that the carboxyl terminus of HSP70-interacting protein (CHIP) binds, ubiquitinates, and promotes the ubiquitin proteasomal degradation of LRRK2. Overexpression of CHIP protects against and knockdown of CHIP exacerbates toxicity mediated by mutant LRRK2. Moreover, HSP90 forms a complex with LRRK2, and inhibition of HSP90 chaperone activity by 17AAG leads to proteasomal degradation of LRRK2, resulting in increased cell viability. Thus, increasing CHIP E3 ligase activity and blocking HSP90 chaperone activity can prevent the deleterious effects of LRRK2. These findings point to potential treatment options for LRRK2-associated PD.
Coexisting chaotic and multi-periodic dynamics in a model of cardiac alternans
Creators: name: Skardal, Per Sebastian
name: Restrepo, Juan G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Dynamical Systems (math.DS)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The spatiotemporal dynamics of cardiac tissue is an active area of research for biologists, physicists, and mathematicians. Of particular interest is the study of period-doubling bifurcations and chaos due to their link with cardiac arrhythmogenesis. In this paper we study the spatiotemporal dynamics of a recently developed model for calcium-driven alternans in a one dimensional cable of tissue. In particular, we observe in the cable coexistence of regions with chaotic and multi-periodic dynamics over wide ranges of parameters. We study these dynamics using global and local Lyapunov exponents and spatial trajectory correlations. Interestingly, near nodes -- or phase reversals -- low-periodic dynamics prevail, while away from the nodes the dynamics tend to be higher-periodic and eventually chaotic. Finally, we show that similar coexisting multi-periodic and chaotic dynamics can also be observed in a detailed ionic model.
Randomness Requirement on CHSH Bell Test in the Multiple Run Scenario
Creators: name: Yuan, Xiao
name: Cao, Zhu
name: Ma, Xiongfeng
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The Clauser-Horne-Shimony-Holt inequality test is widely used as a mean of invalidating the local deterministic theories and a tool of device independent quantum cryptographic tasks. There exists a randomness (freewill) loophole in the test, which is widely believed impossible to be closed perfectly. That is, certain random inputs are required for the test. Following a randomness quantification method used in literature, we investigate the randomness required in the test under various assumptions. By comparing the results, one can conclude that the key to make the test result reliable is to rule out correlations between multiple runs.
description: 15 pages, 3 figures, comments are welcome
Embedding topological fractals in universal spaces
Creators: name: Banakh, Taras
name: Strobin, Filip
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Topology (math.GN)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: 28A80, 37C25, 37C70, 54H20

description: Let $X$ be a universal (Urysohn) space. We prove that every topological fractal is homeomorphic (isometric) to the attractor $A_{\mathcal F}$ of a function system ${\mathcal F}$ on $X$ consisting of Rakotch contractions.
description: 5 pages
title: Migrantischer Feminismus: „Wir schreiben uns in die Geschichte“
Creators: name: Zamani, Dschihan
Publisher: name: DuEPublico
Year: 2023

description: Auf der Suche nach Kämpfen der Frauen*bewegung(en) in Deutschland in den 1980er- und 1990er-Jahren, lassen sich nur wenige Einträge zu migrantisch feministischer Selbstorganisation in der feministischen Literatur finden. War diese Zeit im Vergleich zu den 1960er- und 1970er-Jahren also eine eher „stille Zeit“ (vgl. dazu Tuzcu 2017: 38ff.)
Ganz und gar nicht! Deshalb sind Encarnación Gutiérrez Rodriguez, Professorin fü Soziologie an der Goethe-Universität und Pinar Tuzcu, Professorin an der Universität Kassel auf Spurensuche gegangen und haben mit Migrant*innen, Schwarzen Frauen*, Sinti*zze und Romn*ja, exilierten und jüdischen Frauen* gesprochen. Sie alle haben die Geschichte des „Migrantischen Feminismus“, der sich in den 1980er- und 1990er-Jahren politisch selbstorgansiert hat, maßgeblich geprägt. Welche Kämpfe wurden hier geführt und wieso sind sie nicht Teil der Erzählung der sogenannten deutschen Frauen*bewegung? Welche Erinnerungen bleiben uns und welche müssen wir neu erzählen?
description: blog interdisziplinäre geschlechterforschung
Circadian oscillation of nucleotide excision repair in mammalian brain
Creators: name: Kang, Tae-Hong
name: Kemp, Michael
name: Sancar, Aziz
name: Reardon, Joyce T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The circadian clock regulates the daily rhythms in the physiology and behavior of many organisms, including mice and humans. These cyclical changes at molecular and macroscopic levels affect the organism's response to environmental stimuli such as light and food intake and the toxicity and efficacy of chemo- and radiotherapeutic agents. In this work, we investigated the circadian behavior of the nucleotide excision repair capacity in the mouse cerebrum to gain some insight into the optimal circadian time for favorable therapeutic response with minimal side effects in cancer treatment with chemotherapeutic drugs that produce bulky adducts in DNA. We find that nucleotide excision repair activity in the mouse cortex is highest in the afternoon/evening hours and is at its lowest in the night/early morning hours. The circadian oscillation of the repair capacity is caused at least in part by the circadian oscillation of the xeroderma pigmentosum A DNA damage recognition protein.
Consumers indirectly increase infection risk in grassland food webs
Creators: name: Power, A. G.
name: Mitchell, C. E.
name: Borer, E. T.
name: Seabloom, E. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Most pathogens exist within complicated food webs of interacting hosts, vectors, competitors, and predators. Although theory has demonstrated a variety of mechanisms by which predation and competition in food webs can indirectly control infection risk in hosts, there have until now been no experimental tests of this theory. We sampled the effect of long-term exclusion of large vertebrate herbivores on the prevalence of infection by a group of aphid-vectored viruses that infect grasses (barley and cereal yellow dwarf viruses) in an oak savannah in central California. We found that pathogen prevalence was ≈4-fold higher in the presence of consumers than in areas where they were excluded. Vertebrate consumers did not directly alter infection rates by this aphid-vectored pathogen group, but rather increased infection risk by increasing the relative abundance of highly-competent hosts in the grassland community. This large-scale experiment, measuring changes in host abundance and infection risk in response to altered consumption rates, confirms theoretical predictions that consumers can indirectly increase infection risk by altering the composition of whole communities. Most importantly, these results demonstrate that, even in complex natural communities, alterations to food web composition such as consumer invasion or extinction can lead to significant impacts that cascade throughout entire communities, including changes in infection risk.
Sex-Associated Differences in Cytomegalovirus Prevention: Prophylactic Strategy is Potentially Associated With a Strong Kidney Function Impairment in Female Renal Transplant Patients
Creators: name: Blazquez-Navarro, Arturo
name: Dang-Heine, Chantip
name: Bauer, Chris
name: Wittenbrink, Nicole
name: Wolk, Kerstin
name: Sabat, Robert
name: Witzke, Oliver
name: Westhoff, Timm H.
name: Sawitzki, Birgit
name: Reinke, Petra
name: Thomusch, Oliver
name: Hugo, Christian
name: Babel, Nina
name: Or-Guil, Michal
Publisher: name: Humboldt-Universität zu Berlin
Year: 2020
Subjects: subject: prevention
subject: valganciclovir
subject: gender
subject: graft function
subject: cytomegalovirus
subject: 610 Medizin und Gesundheit

description: Post-transplantation cytomegalovirus (CMV) syndrome can be prevented using the antiviral drug (val)ganciclovir. (Val)ganciclovir is typically administered following a prophylactic or a pre-emptive strategy. The prophylactic strategy entails early universal administration, the pre-emptive strategy, early treatment in case of infection. However, it is not clear which strategy is superior with respect to transplantation outcome; sex-specific effects of these prevention strategies are not known. We have retrospectively analyzed 540 patients from the multi-centre Harmony study along eight pre-defined visits: 308 were treated according to a prophylactic, 232 according to a pre-emptive strategy. As expected, we observed an association of prophylactic strategy with lower incidence of CMV syndrome, delayed onset and lower viral loads compared to the pre-emptive strategy. However, in female patients, the prophylactic strategy was associated with a strong impairment of glomerular filtration rate one year post-transplant (difference: −11.8 ± 4.3 ml min−1·1.73 m−2, p = 0.006). Additionally, we observed a tendency of higher incidence of acute rejection and severe BK virus reactivation in the prophylactic strategy group. While the prophylactic strategy was more effective for preventing CMV syndrome, our results suggest for the first time that the prophylactic strategy might lead to inferior transplantation outcomes in female patients, providing evidence for a strong association with sex. Further randomized controlled studies are necessary to confirm this potential negative effect.
Electronics I ETRO1B1 ; ETRO1P1
Creators: name: Dwaza, Khaya
name: Ndondo, Ovid
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Electrical engineering not elsewhere classified

description: Subject : Electronics I Subject code : ETRO1B1 ; ETRO1P1 Course : ND Engineering: Electrical Examiner : Mr KN Dwaza & OVT Ndondo Moderator : Mr M Sibanda Date : June 2019