cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Spin-electron acoustic waves: The Landau damping and ion contribution in the spectrum
Creators: name: Andreev, Pavel A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Separated spin-up and spin-down quantum kinetics is derived for more detailed research of the spin-electron acoustic waves. Kinetic theory allows to obtain spectrum of the spin-electron acoustic waves including effects of occupation of quantum states more accurately than quantum hydrodynamics. We apply quantum kinetic to calculate the Landau damping of the spin-electron acoustic waves. We have considered contribution of ions dynamics in the spin-electron acoustic wave spectrum. We obtain contribution of ions in the Landau damping in temperature regime of classic ions. Kinetic analysis for ion-acoustic, zero sound, and Langmuir waves at separated spin-up and spin-down electron dynamics is presented as well.
description: 14 pages
Monitoring processes with changing variances
Creators: name: Ord, J. Keith
name: Hyndman, Rob J.
name: Koehler, Anne B.
name: Snyder, Ralph D.
Publisher: name: Monash University
Year: 2017
Subjects: Uncategorized

description: Statistical process control (SPC) has evolved beyond its classical applications in manufacturing to monitoring economic and social phenomena. This extension requires consideration of autocorrelated and possibly non-stationary time series. Less attention has been paid to the possibility that the variance of the process may also change over time. In this paper we use the innovations state space modeling framework to develop conditionally heteroscedastic models. We provide examples to show that the incorrect use of homoscedastic models may lead to erroneous decisions about the nature of the process. The framework is extended to include counts data, when we also introduce a new type of chart, the P-value chart, to accommodate the changes in distributional form from one period to the next.
Synergy between pathogen release and resource availability in plant invasion
Creators: name: Mitchell, C. E.
name: Jarosik, V.
name: Blumenthal, D.
name: Pysek, P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Why do some exotic plant species become invasive? Two common hypotheses, increased resource availability and enemy release, may more effectively explain invasion if they favor the same species, and therefore act in concert. This would be expected if plant species adapted to high levels of available resources in their native range are particularly susceptible to enemies, and therefore benefit most from a paucity of enemies in their new range. We tested this possibility by examining how resource adaptations influence pathogen richness and release among 243 European plant species naturalized in the United States. Plant species adapted to higher resource availability hosted more pathogen species in their native range. Plants from mesic environments hosted more fungi than plants from xeric environments, and plants from nitrogen-rich environments hosted more viruses than plants from nitrogen-poor environments. Furthermore, plants classified as competitors hosted more than 4 times as many fungi and viruses as did stress tolerators. Patterns of enemy release mirrored those of pathogen richness: competitors and species from mesic and nitrogen-rich environments were released from many pathogen species, while stress tolerators and species from xeric and nitrogen-poor environments were released from relatively few pathogen species. These results suggest that enemy release contributes most to invasion by fast-growing species adapted to resource-rich environments. Consequently, enemy release and increases in resource availability may act synergistically to favor exotic over native species.
The isomorphism conjecture for groups with generalized free product structure
Creators: name: Roushon, S. K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Geometric Topology (math.GT)
subject: Algebraic Topology (math.AT)
subject: K-Theory and Homology (math.KT)
subject: FOS: Mathematics
subject: Primary: 19J05, 19J10, 19J25, 19D35, Secondary: 57N37

description: In this article we study the K- and L-theory of groups acting on trees. We consider the problem in the context of the fibered isomorphism conjecture of Farrell and Jones. We show that in the class of residually finite groups it is enough to prove the conjecture for finitely presented groups with one end. Also, we deduce that the conjecture is true for the fundamental groups of graphs of finite groups and of trees of virtually cyclic groups. To motivate the reader we include a survey on some classical works on this subject.
description: 43 pages, Section 3 contains parts of arXiv:math/0510297. (to appear in the Handbook of Group Actions, Vol II.)
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies
Creators: name: Warburton, D.
name: Lange, K.
name: Carpenter, N. J.
name: Erdman, C.
name: Rao, K. W.
name: Barlow, G. M.
name: Lott, I. T.
name: Tirosh-Wagner, T.
name: Snyder, M.
name: Doran, E.
name: Kasowski, M.
name: Korbel, J. O.
name: Chen, X.-N.
name: Grubert, F.
name: Gao, M. C.
name: Cohen, M. Y.
name: Van Riper, A. J.
name: Sobel, E. M.
name: Pettenati, M. J.
name: Gerstein, M. B.
name: Lewin, S. O.
name: Urban, A. E.
name: Shaffer, L. G.
name: Shohat, M.
name: Pueschel, S. M.
name: Moeschler, J. B.
name: Falik-Zaccai, T.
name: Dai, L.
name: Weissman, S.
name: McGillivray, B. C.
name: Aylsworth, A. S.
name: Clark, R. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular gene loci on chromosome 21 (HSA21) are sufficient to cause DS and its associated features. Here we present a high-resolution genetic map of DS phenotypes based on an analysis of 30 subjects carrying rare segmental trisomies of various regions of HSA21. By using state-of-the-art genomics technologies we mapped segmental trisomies at exon-level resolution and identified discrete regions of 1.8–16.3 Mb likely to be involved in the development of 8 DS phenotypes, 4 of which are congenital malformations, including acute megakaryocytic leukemia, transient myeloproliferative disorder, Hirschsprung disease, duodenal stenosis, imperforate anus, severe mental retardation, DS-Alzheimer Disease, and DS-specific congenital heart disease (DSCHD). Our DS-phenotypic maps located DSCHD to a <2-Mb interval. Furthermore, the map enabled us to present evidence against the necessary involvement of other loci as well as specific hypotheses that have been put forward in relation to the etiology of DS—i.e., the presence of a single DS consensus region and the sufficiency of DSCR1 and DYRK1A, or APP, in causing several severe DS phenotypes. Our study demonstrates the value of combining advanced genomics with cohorts of rare patients for studying DS, a prototype for the role of copy-number variation in complex disease.
The ratio of NR2A/B NMDA receptor subunits determines the qualities of ocular dominance plasticity in visual cortex
Creators: name: Philpot, B. D.
name: Cho, K. K. A.
name: Khibnik, L.
name: Bear, M. F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Bidirectional synaptic plasticity during development ensures that appropriate synapses in the brain are strengthened and maintained while inappropriate connections are weakened and eliminated. This plasticity is well illustrated in mouse visual cortex, where monocular deprivation during early postnatal development leads to a rapid depression of inputs from the deprived eye and a delayed strengthening of inputs from the non-deprived eye. The mechanisms that control these bidirectional synaptic modifications remain controversial. Here we demonstrate, both in vitro and in vivo, that genetic deletion or reduction of the NR2A NMDA receptor subunit impairs activity-dependent weakening of synapses and enhances the strengthening of synapses. Although brief monocular deprivation in juvenile WT mice normally causes a profound depression of the deprived-eye response without a change in the non-deprived eye response, NR2A-knockout mice fail to exhibit deprivation-induced depression and instead exhibit precocious potentiation of the non-deprived eye inputs. These data support the hypothesis that a reduction in the NR2A/B ratio during monocular deprivation is permissive for the compensatory potentiation of non-deprived inputs.
The Evolving Model of EBLIP in Research and Practice
Creators: LaFitte, Denise
Brettle, Alison
Publisher: name: University of Alberta Library
Year: 2023

In our 2016 book, Being Evidence Based in Library and Information Practice, we outlined a revised model for evidence-based library and information practice (EBLIP) across different types of libraries. This model focused on flexible aspects that could guide library and information professionals toward being evidence based. The model was grounded in research and further informed by specific examples arising in practice. We posited that being evidence based is a mindset in which librarians actively reflect on their practice. The model involves questioning our practice, gathering or creating evidence where needed,

and continually striving to improve practice by thoughtfully and critically incorporating evidence into decision-making.
Toll-like receptor signaling controls reactivation of KSHV from latency
Creators: name: Gregory, Sean M.
name: Damania, Blossom
name: Dittmer, Dirk P.
name: Dillon, Patrick J.
name: West, John A.
name: Hilscher, Chelsey
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease. Like other herpesviruses, KSHV establishes life-long latency in the human host with intermittent periods of reactivation. Physiological triggers of herpesviral reactivation are poorly defined. Toll-like receptors (TLRs) recognize pathogens and are vital for the host innate immune response. We screened multiple TLR agonists for their ability to initiate KSHV replication in latently infected PEL. Agonists specific for TLR7/8 reactivated latent KSHV and induced viral lytic gene transcription and replication. Furthermore, vesicular stomatitis virus (VSV), a bonafide physiological activator of TLR7/8, also reactivated KSHV from latency. This demonstrates that secondary pathogen infection of latently infected cells can reactivate KSHV. Human herpesviruses establish life-long latency in the host, and it is plausible that a latently infected cell will encounter multiple pathogens during its lifetime and that these encounters lead to episodic reactivation. Our findings have broad implications for physiological triggers of latent viral infections, such as herpesviral reactivation and persistence in the host.
Electroweak sphalerons in the reduced minimal 3-3-1 model
Creators: name: Phong, Vo Quoc
name: Long, Hoang Ngoc
name: Van, Vo Thanh
name: Thanh, Nguyen Chi
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We calculate the electroweak sphaleron rates in the reduced minimal 3-3-1 (RM331) model. In the context of the early Universe, this model undergoes a sequence of two first-order phase transitions, $SU(3) \rightarrow SU(2)$ at the TeV scale and $SU(2)\rightarrow U(1)$ at the $10^2$ GeV scale, as the Universe cools down from the hot big bang. By a thin-wall approximation, we show that for each phase transition in this sequence, the sphaleron rate is larger than the cosmological expansion rate at temperatures higher than the critical temperature, and after the phase transition, the sphaleron process is decoupled. This may provide baryon-number violation (B violation) necessary for baryogenesis in the relationship with nonequilibrium physics in the early Universe.
description: 13 pages, 3 figures
A semiclassical approach for the Higgs boson
Creators: name: Fariborz, Amir H.
name: Jora, Renata
name: Schechter, Joseph
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Starting from the equations of motion of the fields involved in a theory with spontaneous symmetry breaking and by making simple assumptions regarding their behavior we derive simple tree level relations between the mass of the Higgs boson in the theory and the masses of the gauge bosons corresponding to the broken generators. We show that these mass relations have a clear meaning if both the scalars and the gauge bosons are composite states made of two fermions.
description: 6 pages
Validation-based insertional mutagenesis identifies lysine demethylase FBXL11 as a negative regulator of NF B
Creators: name: Jackson, M. W.
name: Zhang, Y.
name: Gudkov, A. V.
name: Kandel, E. S.
name: Lu, T.
name: Stark, G. R.
name: Singhi, A. D.
name: Yang, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: We describe a highly efficient use of lentiviral validation-based insertional mutagenesis (VBIM) to generate large populations of mammalian cells in which a strong promoter is inserted into many different genomic loci, causing greatly increased expression of downstream sequences. Many different selections or screens can follow, to isolate dominant mutant clones with a desired phenotypic change. The inserted promoter can be excised or silenced at will, to prove that the insertion caused the mutation. Cloning DNA flanking the insertion site identifies the locus precisely. VBIM virus particles are pseudotyped with VSV G protein, allowing efficient infection of most mammalian cell types, including non-dividing cells, and features are included that give high yields of stable virus stocks. In several different selections, useful mutants have been obtained at frequencies of approximately 10−6 or higher. We used the VBIM technique to isolate mutant human cells in which the F-box leucine-rich protein 11 (FBXL11), a histone H3K36 demethylase, is shown to be a negative regulator of NFκB. High levels of FBXL11 block the ability of NFκB to bind to DNA or activate gene expression, and siRNA-mediated reduction of FBXL11 expression has the opposite effects. The H212A mutation of FBXL11 abolishes both its histone H3K36 demethylase activity and its ability to inhibit NFκB. Thus, we have used a powerful tool for mutagenesis of mammalian cells to reveal an aspect of the complex regulation of NFκB-dependent signaling.
Safety Evaluation of Transit Signal Priority with Bus Speed Volatility as a Surrogate Measure: Case Study in Minnesota
Creators: name: Song, Yu
name: Tse, Hoki
name: Lind, Eric M.
name: Chitturi, Madhav V.
name: Noyce, David A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: Previous studies have found correlations between the implementation of transit signal priority (TSP) and the reduction in number of crashes. To further understand how TSP affects traffic safety, a more in-depth evaluation was carried out using detailed bus automatic vehicle location (AVL) data. The data was from Minneapolis-Saint Paul Metro Transit Bus Route 5, where TSP was implemented at 30 signalized intersections in early 2019. A surrogate safety measure, bus speed volatility (BSV), was used to estimate the safety effects of TSP, with a higher BSV indicating more safety risks. A regression analysis was carried out on 23,123 event-level observations, with event defined as a bus traversal of a TSP-equipped intersection. Results indicate that with a TSP request, BSV was significantly lower than without a TSP request, confirming the effectiveness of TSP in smoothing bus trips through intersections, thus reducing risks of bus collisions and passenger fall-overs.
Absorption at the dust sublimation radius and the dichotomy between X-ray and optical classification in the Seyfert galaxy H0557-385
Creators: name: Coffey, Damien
name: Longinotti, Anna Lia
name: Rodriguez-Ardila, Alberto
name: Guainazzi, Matteo
name: Miniutti, Giovanni
name: Bianchi, Stefano
name: de la Calle, Ignacio
name: Piconcelli, Enrico
name: Ballo, Lucia
name: Linares, Manuel
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: In this work, the analysis of multi-epoch (1995-2010) X-ray observations of the Seyfert 1 galaxy H0557-385 is presented. The wealth of data presented in this analysis show that the source exhibits dramatic spectral variability, from a typical unabsorbed Seyfert 1 type spectrum to a Compton-thin absorbed state, on time scales of ~5 years. This extreme change in spectral shape can be attributed to variations in the column density and covering fraction of a neutral absorbing medium attenuating the emission from the central continuum source. Evidence for Compton reflection of the intrinsic nuclear emission is present in each of the spectra, though this feature is most prominent in the low-state spectra, where the associated Fe emission line complex is clearly visible. In addition to the variable absorbing medium, a warm absorber component has been detected in each spectral state. Optical spectroscopy concurrent with the 2010 XMM-Newton observation campaign have detected the presence of broad optical emission lines during an X-ray absorption event.From the analysis of both X-ray and optical spectroscopic data, it has been inferred that the X-ray spectral variability is a result of obscuration of the central emission region by a clumpy absorber covering >80 per cent of the source with an average column density of NH ~7x10^{23} cm^{-2}, and which is located outside the broad line region at a distance from the central source consistent with the dust sublimation radius of the AGN.
description: Accepted for publication on MNRAS, 15 pages, 7 figures
Auguin_et_al_Behavioural_Heterogeneity_KillerWhales_data_for_review
Creators: name: Tixier, Paul
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 310301
subject: Behavioural ecology

description: Data associated with Auguin et al. “Behavioural heterogeneity across killer whale social units in their response to feeding opportunities from fisheries”
UnShadowNet: Illumination critic guided contrastive learning for shadow removal
Creators: name: Dasgupta, Subhrajyoti
name: Das, Arindam
name: Yogamani, Senthil
name: Das, Sudip
name: EISING, CIARAN
name: Bursuc, Andrei
name: Bhattacharya, Ujjwal
Publisher: name: University of Limerick
Year: 2023
Subjects: classificationCode: 40
subject: Engineering

description: Shadows are frequently encountered natural phenomena that significantly hinder the performance of computer vision perception systems in practical settings, e.g., autonomous driving. A solution to this would be to eliminate shadow regions from the images before the processing of the perception system. Yet, training such a solution requires pairs of aligned shadowed and non-shadowed images which are difficult to obtain. We introduce a novel weakly supervised shadow removal framework UnShadowNet trained using contrastive learning. It is composed of a DeShadower network responsible for the removal of the extracted shadow under the guidance of an Illumination network which is trained adversarially by the illumination critic and a Refinement network to further remove artefacts. We show that UnShadowNet can be easily extended to a fully-supervised set-up to exploit the ground-truth when available. UnShadowNet outperforms existing state-of-the-art approaches on three publicly available shadow datasets (ISTD, adjusted ISTD, SRD) in both the weakly and fully supervised setups.
The Impact of Perceptions of Social Media Advertisements on Advertising Value, Brand Awareness and Brand Associations: Research on Generation Y Instagram Users
Creators: name: Efendioglu, Ibrahim Halil
name: Durmaz, Yakup
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Economics (econ.GN)
subject: FOS: Economics and business

description: The aim of this paper is to examine how consumer perceptions of social media advertisements affect advertising value and brand awareness. With a rapid increase in the number of social media users over the last ten years, a new advertising domain has become available for companies. Brands that manage social media well in their advertising strategies can quickly influence consumer decision-making and create awareness. However, in social media advertising, which is different from traditional advertising, creating content should be produced and this content should be perceived in a short time by consumers. To achieve this, it is necessary to build rapport with consumers and to present correctly what they wish to see in advertisements by creating awareness. In view of the increasing importance of social media advertising, the study examines how consumer perceptions of Instagram advertisements affect advertising value and brand awareness. This study was conducted with Generation Y consumers on the basis of their Instagram habits, a popular social media app. For this purpose, surveys were held with 665 participants who use Instagram. The collected data were analyzed using structural equation modeling. According to the analysis results, Y generations perceptions of Instagram advertisements have both a positive and negative impact on advertising value and brand awareness and brand associations.
A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-  nuclear translocation
Creators: name: Garg, N.
name: Green, C. B.
name: Rosen, C. J.
name: Kawai, M.
name: Ackert-Bicknell, C.
name: Adamo, M. L.
name: Horowitz, M. C.
name: Kojima, S.
name: Clemmons, D. R.
name: Lecka-Czernik, B.
name: Douris, N.
name: Gilbert, M. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Nocturnin (NOC) is a circadian-regulated protein related to the yeast family of transcription factors involved in the cellular response to nutrient status. In mammals, NOC functions as a deadenylase but lacks a transcriptional activation domain. It is highly expressed in bone-marrow stromal cells (BMSCs), hepatocytes, and adipocytes. In BMSCs exposed to the PPAR-γ (peroxisome proliferator-activated receptor-γ) agonist rosiglitazone, Noc expression was enhanced 30-fold. Previously, we reported that Noc−/− mice had low body temperature, were protected from diet-induced obesity, and most importantly exhibited absence of Pparg circadian rhythmicity on a high-fat diet. Consistent with its role in influencing BMSCs allocation, Noc−/− mice have reduced bone marrow adiposity and high bone mass. In that same vein, NOC overexpression enhances adipogenesis in 3T3-L1 cells but negatively regulates osteogenesis in MC3T3-E1 cells. NOC and a mutated form, which lacks deadenylase activity, bind to PPAR-γ and markedly enhance PPAR-γ transcriptional activity. Both WT and mutant NOC facilitate nuclear translocation of PPAR-γ. Importantly, NOC-mediated nuclear translocation of PPAR-γ is blocked by a short peptide fragment of NOC that inhibits its physical interaction with PPAR-γ. The inhibitory effect of this NOC-peptide was partially reversed by rosiglitazone, suggesting that effect of NOC on PPAR-γ nuclear translocation may be independent of ligand-mediated PPAR-γ activation. In sum, Noc plays a unique role in the regulation of mesenchymal stem-cell lineage allocation by modulating PPAR-γ activity through nuclear translocation. These data illustrate a unique mechanism whereby a nutrient-responsive gene influences BMSCs differentiation, adipogenesis, and ultimately body composition.
XMM-Newton and Canadian Galactic Plane Survey Observations of the Supernova Remnant G107.5-1.5
Creators: name: Jackson, M. S.
name: Safi-Harb, S.
name: Kothes, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present an XMM-Newton observation of the highly polarized low-surface brightness supernova remnant G107.5-1.5, discovered with the Canadian Galactic Plane Survey (CGPS). We do not detect diffuse X-ray emission from the SNR and set an upper limit on the surface brightness of ~2 x 10^30 erg arcmin^-2 s^-1, at an assumed distance of 1.1 kpc. We found eight bright point sources in the field, including the ROSAT source 1RXS J225203.8+574249 near the centre of the radio shell. Spectroscopic analysis of some of the embedded point sources, including the ROSAT source, has been performed, and all eight sources are most likely ruled out as the associated neutron star, primarily due to counterpart bright stars in optical and infrared bands. Timing analysis of the bright point sources yielded no significant evidence for pulsations, but, due to the timing resolution, only a small part of the frequency space could be searched. An additional ten fainter point sources were identified in the vicinity of the SNR. Further X-ray observation of these and the region in the vicinity of the radio shell may be warranted.
description: 9 pages, 4 figures
Absence of a local rest frame in far from equilibrium quantum matter
Creators: name: Arnold, Peter
name: Romatschke, Paul
name: van der Schee, Wilke
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Nuclear Theory (nucl-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In a collision of strongly coupled quantum matter we find that the dynamics of the collision produces regions where a local rest frame cannot be defined because the energy-momentum tensor does not have a real time-like eigenvector. This effect is purely quantum mechanical, since for classical systems, a local rest frame can always be defined. We study the relation with the null and weak energy condition, which are violated in even larger regions, and compare with previously known examples. While no pathologies or instabilities arise, it is interesting that regions without a rest frame are possibly present in heavy ion collisions.
description: 5 pages, 4 figures; v2: fixed typo, v3: added references, matches published version
Adaptive Piecewise Poly-Sinc Methods for Ordinary Differential Equations
Creators: name: Khalil, Omar
name: El-Sharkawy, Hany
name: Youssef, Maha
name: Baumann, Gerd
Publisher: name: arXiv
Year: 2022
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: We propose a new method of adaptive piecewise approximation based on Sinc points for ordinary differential equations. The adaptive method is a piecewise collocation method which utilizes Poly-Sinc interpolation to reach a preset level of accuracy for the approximation. Our work extends the adaptive piecewise Poly-Sinc method to function approximation, for which we derived an a priori error estimate for our adaptive method and showed its exponential convergence in the number of iterations. In this work, we show the exponential convergence in the number of iterations of the a priori error estimate obtained from the piecewise collocation method, provided that a good estimate of the exact solution of the ordinary differential equation at the Sinc points exists. We use a statistical approach for partition refinement. The adaptive greedy piecewise Poly-Sinc algorithm is validated on regular and stiff ordinary differential equations.
description: 26 pages, 19 figures
Allele-specific copy number analysis of tumors
Creators: name: Naume, B.
name: Sun, W.
name: Lingjaerde, O. C.
name: Weigman, V. J.
name: Kristensen, V. N.
name: Marynen, P.
name: Perou, C. M.
name: Nordgard, S. H.
name: Russnes, H. G.
name: Rye, I. H.
name: Zetterberg, A.
name: Van Loo, P.
name: Borresen-Dale, A.-L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: We present an allele-specific copy number analysis of the in vivo breast cancer genome. We describe a unique bioinformatics approach, ASCAT (allele-specific copy number analysis of tumors), to accurately dissect the allele-specific copy number of solid tumors, simultaneously estimating and adjusting for both tumor ploidy and nonaberrant cell admixture. This allows calculation of “ASCAT profiles” (genome-wide allele-specific copy-number profiles) from which gains, losses, copy number-neutral events, and loss of heterozygosity (LOH) can accurately be determined. In an early-stage breast carcinoma series, we observe aneuploidy (>2.7n) in 45% of the cases and an average nonaberrant cell admixture of 49%. By aggregation of ASCAT profiles across our series, we obtain genomic frequency distributions of gains and losses, as well as genome-wide views of LOH and copy number-neutral events in breast cancer. In addition, the ASCAT profiles reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events between the five previously identified molecular breast cancer subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared with other subtypes, and their ASCAT profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. Finally, from the ASCAT profiles, we construct a genome-wide map of allelic skewness in breast cancer, indicating loci where one allele is preferentially lost, whereas the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development.
Biomimetic cilia arrays generate simultaneous pumping and mixing regimes
Creators: name: Washburn, S.
name: Shields, A. R.
name: Evans, B. A.
name: Falvo, M. R.
name: Superfine, R.
name: Fiser, B. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Living systems employ cilia to control and to sense the flow of fluids for many purposes, such as pumping, locomotion, feeding, and tissue morphogenesis. Beyond their use in biology, functional arrays of artificial cilia have been envisaged as a potential biomimetic strategy for inducing fluid flow and mixing in lab-on-a-chip devices. Here we report on fluid transport produced by magnetically actuated arrays of biomimetic cilia whose size approaches that of their biological counterparts, a scale at which advection and diffusion compete to determine mass transport. Our biomimetic cilia recreate the beat shape of embryonic nodal cilia, simultaneously generating two sharply segregated regimes of fluid flow: Above the cilia tips their motion causes directed, long-range fluid transport, whereas below the tips we show that the cilia beat generates an enhanced diffusivity capable of producing increased mixing rates. These two distinct types of flow occur simultaneously and are separated in space by less than 5 μm, approximately 20% of the biomimetic cilium length. While this suggests that our system may have applications as a versatile microfluidics device, we also focus on the biological implications of our findings. Our statistical analysis of particle transport identifying an enhanced diffusion regime provides novel evidence for the existence of mixing in ciliated systems, and we demonstrate that the directed transport regime is Poiseuille–Couette flow, the first analytical model consistent with biological measurements of fluid flow in the embryonic node.
Bird communities in future bioenergy landscapes of the Upper Midwest
Creators: name: Gratton, C.
name: Meehan, T. D.
name: Hurlbert, A. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Mandates for biofuel and renewable electricity are creating incentives for biomass production in agricultural landscapes of the Upper Midwest. Different bioenergy crops are expected to vary in their effects on biodiversity and ecosystem services. Here, we use data from the North American Breeding Bird Survey to forecast the impact of potential bioenergy crops on avian species richness and the number of bird species of conservation concern in Midwestern landscapes. Our analysis suggests that expanded production of annual bioenergy crops (e.g., corn and soybeans) on marginal land will lead to declines in avian richness between 7% and 65% across 20% of the region, and will make managing at-risk species more challenging. In contrast, replacement of annual with diverse perennial bioenergy crops (e.g., mixed grasses and forbs) is expected to bring increases in avian richness between 12% and 207% across 20% of the region, and possibly aid the recovery of several species of conservation concern.
Dissipative phase locking of exciton-polariton condensates
Creators: name: Ohadi, H.
name: Gregory, R. L.
name: Freegarde, T.
name: Rubo, Y. G.
name: Kavokin, A. V.
name: Lagoudakis, P. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We demonstrate, both experimentally and theoretically, a new phenomenon: the presence of dissipative coupling in the system of driven bosons. This is evidenced for a particular case of externally excited spots of exciton-polariton condensates in semiconductor microcavities. We observe that for two spatially separated condensates the dissipative coupling leads to the phase locking, either in-phase or out-of-phase, between the condensates. The effect depends on the distance between the condensates. For several excited spots, we observe the appearance of spontaneous vorticity in the system.
description: 21 pages, 12 figures
Chemically accurate coarse graining of double-stranded DNA
Creators: name: Papoian, G. A.
name: Savelyev, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Coarse-grained (CG) modeling approaches are widely used to simulate many important biological processes involving DNA, including chromatin folding and genomic packaging. The bending propensity of a semiflexible DNA molecule critically influences these processes. However, existing CG DNA models do not retain a sufficient fidelity of the important local chain motions, whose propagation at larger length scales would generate correct DNA persistent lengths, in particular when the solution’s ionic strength is widely varied. Here we report on a development of an accurate CG model for the double-stranded DNA chain, with explicit treatment of mobile ions, derived systematically from all-atom molecular dynamics simulations. Our model generates complex local motions of the DNA chain, similar to fully atomistic dynamics, leading also to a quantitative agreement of our simulation results with the experimental data on the dependence of the DNA persistence length on the solution ionic strength. We also predict a structural transition in a torsionally stressed DNA nanocircle as the buffer ionic strength is increased beyond a threshold value.
Galaxy clusters enveloped by vast volumes of relativistic electrons
Creators: name: Cuciti, V.
name: de Gasperin, F.
name: Brueggen, M.
name: Vazza, F.
name: Brunetti, G.
name: Shimwell, T. W.
name: Edler, H. W.
name: van Weeren, R. J.
name: Botteon, A.
name: Cassano, R.
name: Di Gennaro, G.
name: Gastaldello, F.
name: Drabent, A.
name: Rottgering, H. J. A.
name: Tasse, C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The central regions of galaxy clusters are permeated by magnetic fields and filled with relativistic electrons. When clusters merge, the magnetic fields are amplified and relativistic electrons are re-accelerated by turbulence in the intra cluster medium. These electrons reach energies of 1 -- 10 GeV and, in the presence of magnetic fields, produce diffuse radio halos that typically cover an area of ~1 square Mpc. Here we report observations of four clusters whose radio halos are embedded in much more extended, diffuse radio emission, filling a volume 30 times larger than that of radio halos. The emissivity in these larger features is about 20 times lower than the emissivity in radio halos. We conclude that relativistic electrons and magnetic fields extend far beyond radio halos, and that the physical conditions in the outer regions of the clusters are quite different from those in the radio halos.
description: 21 pages, 8 figures, Nature in press
Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase
Creators: name: Reardon, J. T.
name: Kang, T.-H.
name: Lindsey-Boltz, L. A.
name: Sancar, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Cisplatin is one of the most commonly used anticancer drugs. It kills cancer cells by damaging their DNA, and hence cellular DNA repair capacity is an important determinant of its efficacy. Here, we investigated the repair of cisplatin-induced DNA damage in mouse liver and testis tissue extracts prepared at regular intervals over the course of a day. We find that the XPA protein, which plays an essential role in repair of cisplatin damage by nucleotide excision repair, exhibits circadian oscillation in the liver but not in testis. Consequently, removal of cisplatin adducts in liver extracts, but not in testis extracts, exhibits a circadian pattern with zenith at ∼5 pm and nadir at ∼5 am. Furthermore, we find that the circadian oscillation of XPA is achieved both by regulation of transcription by the core circadian clock proteins including cryptochrome and by regulation at the posttranslational level by the HERC2 ubiquitin ligase. These findings may be used as a guide for timing of cisplatin chemotherapy.
Global Islands
Creators: name: Sayre, Roger
Publisher: name: GEO Knowledge Hub
Year: 2022
Subjects: mapping global islands
island extents
islands GIS data

description: The Global Islands resource, produced by the U.S. Geological Survey, Esri, and The World Conservation Monitoring Center, is a 30 m base resolution, Landsat-derived, island polygons datalayer. The islands were derived from a 30 m global shoreline vector (GSV) that was produced from a semi-automated interpretation of every 2014 Landsat scene that contained a coastline. The islands were classed into three size categories: continental mainlands, big islands (> 1km2), and small islands (<1km2). These island polygons were then merged with an existing Global Islands Database from WCMC. The merged product contains approximately 370,000 islands, of which the approximately 22,500 islands in the big island class are named. In addition to the data, the Global Islands GEO Knowledge Hub also contains other knowledge products (publications, online explorer tools, etc.) related to the Global Islands resource.
How memory generates heterogeneous dynamics in temporal networks
Creators: name: Vestergaard, Christian L.
name: Génois, Mathieu
name: Barrat, Alain
Publisher: name: arXiv
Year: 2014
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Social and Information Networks (cs.SI)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Empirical temporal networks display strong heterogeneities in their dynamics, which profoundly affect processes taking place on these networks, such as rumor and epidemic spreading. Despite the recent wealth of data on temporal networks, little work has been devoted to the understanding of how such heterogeneities can emerge from microscopic mechanisms at the level of nodes and links. Here we show that long-term memory effects are present in the creation and disappearance of links in empirical networks. We thus consider a simple generative modeling framework for temporal networks able to incorporate these memory mechanisms. This allows us to study separately the role of each of these mechanisms in the emergence of heterogeneous network dynamics. In particular, we show analytically and numerically how heterogeneous distributions of contact durations, of inter-contact durations and of numbers of contacts per link emerge. We also study the individual effect of heterogeneities on dynamical processes, such as the paradigmatic Susceptible-Infected epidemic spreading model. Our results confirm in particular the crucial role of the distributions of inter-contact durations and of the numbers of contacts per link.
Concerted O atom-proton transfer in the O--O bond forming step in water oxidation
Creators: name: Hu, X.
name: Concepcion, J. J.
name: Yang, W.
name: Meyer, T. J.
name: Hoertz, P. G.
name: Chen, Z.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: As the terminal step in photosystem II, and a potential half-reaction for artificial photosynthesis, water oxidation (2H2O → O2 + 4e- + 4H+) is key, but it imposes a significant mechanistic challenge with requirements for both 4e-/4H+ loss and O—O bond formation. Significant progress in water oxidation catalysis has been achieved recently by use of single-site Ru metal complex catalysts such as [Ru(Mebimpy)(bpy)(OH2)]2+ [Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine; bpy = 2,2′-bipyridine]. When oxidized from to RuV = O3+, these complexes undergo O—O bond formation by O-atom attack on a H2O molecule, which is often the rate-limiting step. Microscopic details of O—O bond formation have been explored by quantum mechanical/molecular mechanical (QM/MM) simulations the results of which provide detailed insight into mechanism and a strategy for enhancing catalytic rates. It utilizes added bases as proton acceptors and concerted atom–proton transfer (APT) with O-atom transfer to the O atom of a water molecule in concert with proton transfer to the base (B). Base catalyzed APT reactivity in water oxidation is observed both in solution and on the surfaces of oxide electrodes derivatized by attached phosphonated metal complex catalysts. These results have important implications for catalytic, electrocatalytic, and photoelectrocatalytic water oxidation.
A tentative assessment of fMRI data sharing in the journal Plos One: results from the Stockholm BrainHack
Creators: name: Nilsonne, Gustav
name: Wiens, Stefan
Publisher: name: figshare
Year: 2023
Subjects: Other health sciences not elsewhere classified

description: This was originally published 2018-05-04 on Gustav Nilsonne’s blog at www.nilsonne.net
Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility
Creators: name: Johnson, M. D. L.
name: Heiniger, R. W.
name: Sperlazza, J. R.
name: Wolfgang, M. C.
name: Orans, J.
name: Redinbo, M. R.
name: Coggan, K. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Several bacterial pathogens require the “twitching” motility produced by filamentous type IV pili (T4P) to establish and maintain human infections. Two cytoplasmic ATPases function as an oscillatory motor that powers twitching motility via cycles of pilus extension and retraction. The regulation of this motor, however, has remained a mystery. We present the 2.1 Å resolution crystal structure of the Pseudomonas aeruginosa pilus-biogenesis factor PilY1, and identify a single site on this protein required for bacterial translocation. The structure reveals a modified β-propeller fold and a distinct EF-hand-like calcium-binding site conserved in pathogens with retractile T4P. We show that preventing calcium binding by PilY1 using either an exogenous calcium chelator or mutation of a single residue disrupts Pseudomonas twitching motility by eliminating surface pili. In contrast, placing a lysine in this site to mimic the charge of a bound calcium interferes with motility in the opposite manner—by producing an abundance of nonfunctional surface pili. Our data indicate that calcium binding and release by the unique loop identified in the PilY1 crystal structure controls the opposing forces of pilus extension and retraction. Thus, PilY1 is an essential, calcium-dependent regulator of bacterial twitching motility.
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome
Creators: name: Lombo, T.
name: Rein, A.
name: Leonard, C. W.
name: Weeks, K. M.
name: Datta, S. A. K.
name: Bess, J. W.
name: Gorelick, R. J.
name: Gherghe, C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: All retroviral genomic RNAs contain a cis-acting packaging signal by which dimeric genomes are selectively packaged into nascent virions. However, it is not understood how Gag (the viral structural protein) interacts with these signals to package the genome with high selectivity. We probed the structure of murine leukemia virus RNA inside virus particles using SHAPE, a high-throughput RNA structure analysis technology. These experiments showed that NC (the nucleic acid binding domain derived from Gag) binds within the virus to the sequence UCUG-UR-UCUG. Recombinant Gag and NC proteins bound to this same RNA sequence in dimeric RNA in vitro; in all cases, interactions were strongest with the first U and final G in each UCUG element. The RNA structural context is critical: High-affinity binding requires base-paired regions flanking this motif, and two UCUG-UR-UCUG motifs are specifically exposed in the viral RNA dimer. Mutating the guanosine residues in these two motifs—only four nucleotides per genomic RNA—reduced packaging 100-fold, comparable to the level of nonspecific packaging. These results thus explain the selective packaging of dimeric RNA. This paradigm has implications for RNA recognition in general, illustrating how local context and RNA structure can create information-rich recognition signals from simple single-stranded sequence elements in large RNAs.