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  • Wiley  (46)
  • Oxford University Press  (13)
  • MDPI Publishing
  • MDPI
  • Institute of Electrical and Electronics Engineers (IEEE)
  • Springer Science + Business Media
  • 2015-2019  (41)
  • 2010-2014  (25)
  • 1
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    Algorithms, Vol. 9, Pages 53: Faster Force-Directed Graph Drawing with the Well-Separated Pair Decomposition (2016)
    MDPI Publishing
    Details
    Publication Date: 2016-08-05
    Description: The force-directed paradigm is one of the few generic approaches to drawing graphs. Since force-directed algorithms can be extended easily, they are used frequently. Most of these algorithms are, however, quite slow on large graphs, as they compute a quadratic number of forces in each iteration. We give a new algorithm that takes only O ( m + n log n ) time per iteration when laying out a graph with n vertices and m edges. Our algorithm approximates the true forces using the so-called well-separated pair decomposition. We perform experiments on a large number of graphs and show that we can strongly reduce the runtime, even on graphs with less than a hundred vertices, without a significant influence on the quality of the drawings (in terms of the number of crossings and deviation in edge lengths).
    Electronic ISSN: 1999-4893
    Topics: Computer Science
    Published by MDPI Publishing
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  • 2
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    On the potentially dramatic history of the super-Earth {rho} 55 Cancri e (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-24
    Description: We demonstrate that tidal evolution of the inner planet (‘e’) of the system orbiting the star 55 Cancri could have led to passage through two secular resonances with other planets in the system. The consequence of this evolution is excitation of both the planetary eccentricity and inclination relative to the original orbital plane. The large mass ratio between the innermost planet and the others means that these excitations can be of substantial amplitude and can have dramatic consequences for the system organization. Such evolution can potentially explain the large observed mutual inclination between the innermost and outermost planets in the system, and implies that tidal heating could have substantially modified the structure of planet e, and possibly reduced its mass by Roche lobe overflow. Similar inner secular resonances may be found in many multiple planet systems and suggest that many of the innermost planets in these systems could have suffered similar evolutions.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Excited state mixed valence in a dual-bridged three-chromophore system (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: The optical and resonance Raman spectra of the 2,2′: 6′,2″:6″,6-trioxytriphenyl-amine cation are measured and interpreted. This molecule contains two simultaneous types of coupling between three chromophores and two types of bridging atoms. The first and conventional coupling involves a single nitrogen bridge that couples all three aryl groups. The second is provided by the three oxygen atoms, each of which bridges two adjacent aryl groups. There are two bands in the visible region of the optical absorption spectrum; their assignment and the interpretation of the contributing orbitals and electronic states are described in terms of the neighboring orbital model that explains the effects of the two types of coupling. The bonding changes that take place in the excited electronic states are probed by resonance Raman spectroscopy intensities and analyzed using the time-dependent theory of resonance Raman spectroscopy. The optical absorption spectrum was fit using the measured vibrational frequencies and excited state distortions. The distortions correlate well with the bonding changes predicted by the neighboring orbital model. The resonance Raman data and neighboring orbital model analysis reveal that the two optical absorption bands correspond to charge transfers from aryl groups with different nodal structures in their pi orbitals. Copyright © 2012 John Wiley & Sons, Ltd. The three-chromophore cation (left) has a symmetric charge distribution in its ground state and three equivalent charge-bearing units in its lowest excited state. Coupling between the three units occurs through the central nitrogen and pair-wise through the oxygen. The effects of the coupling on the electronic and resonance Raman spectra are interpreted using the neighboring orbital model.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley
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  • 4
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    Perinuclear positioning of the inactive human cystic fibrosis gene depends on CTCF, A-type lamins and an active histone deacetylase (2012)
    Wiley
    Details
    Publication Date: 2012-04-16
    Description: The nuclear positioning of mammalian genes often correlates with their functional state. For instance, the human cystic fibrosis transmembrane conductance regulator (CFTR) gene associates with the nuclear periphery in its inactive state, but occupies interior positions when active. It is not understood how nuclear gene positioning is determined. Here, we investigated trichostatin A (TSA)-induced repositioning of CFTR in order to address molecular mechanisms controlling gene positioning. Treatment with the histone deacetylase (HDAC) inhibitor TSA induced increased histone acetylation and CFTR repositioning towards the interior within 20 minutes. When CFTR localized in the nuclear interior (either after TSA treatment or when the gene was active) consistent histone H3 hyperacetylation was observed at a CTCF site close to the CFTR promoter. Knockdown experiments revealed that CTCF was essential for perinuclear CFTR positioning and both, CTCF knockdown as well as TSA treatment had similar and CFTR-specific effects on radial positioning. Furthermore, knockdown experiments revealed that also A-type lamins were required for the perinuclear positioning of CFTR. Together, the results showed that CTCF, A-type lamins and an active HDAC were essential for perinuclear positioning of CFTR and these components acted on a CTCF site adjacent to the CFTR promoter. The results are consistent with the idea that CTCF bound close to the CFTR promoter, A-type lamins and an active HDAC form a complex at the nuclear periphery, which becomes disrupted upon inhibition of the HDAC, leading to the observed release of CFTR. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 5
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    Excited state mixed valence in a dual-bridged three-chromophore system (2012)
    Wiley
    Details
    Publication Date: 2012-01-27
    Description: The optical and resonance Raman spectra of the 2,2′: 6′,2″:6″,6-trioxytriphenyl-amine cation are measured and interpreted. This molecule contains two simultaneous types of coupling between three chromophores and two types of bridging atoms. The first and conventional coupling involves a single nitrogen bridge that couples all three aryl groups. The second is provided by the three oxygen atoms, each of which bridges two adjacent aryl groups. There are two bands in the visible region of the optical absorption spectrum; their assignment and the interpretation of the contributing orbitals and electronic states are described in terms of the neighboring orbital model that explains the effects of the two types of coupling. The bonding changes that take place in the excited electronic states are probed by resonance Raman spectroscopy intensities and analyzed using the time-dependent theory of resonance Raman spectroscopy. The optical absorption spectrum was fit using the measured vibrational frequencies and excited state distortions. The distortions correlate well with the bonding changes predicted by the neighboring orbital model. The resonance Raman data and neighboring orbital model analysis reveal that the two optical absorption bands correspond to charge transfers from aryl groups with different nodal structures in their pi orbitals. Copyright © 2012 John Wiley & Sons, Ltd. The three-chromophore cation (left) has a symmetric charge distribution in its ground state and three equivalent charge-bearing units in its lowest excited state. Coupling between the three units occurs through the central nitrogen and pair-wise through the oxygen. The effects of the coupling on the electronic and resonance Raman spectra are interpreted using the neighboring orbital model.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley
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  • 6
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    Stochastic temporal disaggregation of monthly precipitation for regional gridded data sets (2014)
    Wiley
    Details
    Publication Date: 2014-10-10
    Description: Weather generators are used for spatio-temporal downscaling of climate model outputs (e.g., precipitation and temperature) to investigate the impact of climate change on the hydrological cycle. In this study, a multiplicative random cascade model is proposed for the stochastic temporal disaggregation of monthly to daily precipitation fields, which is designed to be applicable to grids of any spatial resolution and extent. The proposed method uses stationary distribution functions that describe the partitioning of precipitation throughout multiple temporal scales (e.g., weekly and bi-weekly scale). Moreover, it explicitly considers the intensity and spatial covariance of precipitation in the disaggregation procedure, but requires no assumption about the temporal relationship and spatial isotropy of precipitation fields. A split sampling test is conducted on a high-resolution (i.e., 4×4 km 2 grid) daily precipitation data set over Germany (≈ 357 000 km 2 ) to assess the performance of the proposed method during future periods. The proposed method has proven to consistently reproduce distinctive location dependent precipitation distribution functions with biases less than 5% during both a calibration and evaluation period. Furthermore, extreme precipitation amounts and the spatial and temporal covariance of the generated fields are comparable to those of the observations. Consequently, the proposed temporal disaggregation approach satisfies the minimum conditions for a precipitation generator aiming at the assessment of hydrological response to climate change at regional and continental scales or for generating seamless predictions of hydrological variables.
    Print ISSN: 0043-1397
    Electronic ISSN: 1944-7973
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    Material Recycling and the Myth of Landfill Diversion (2018)
    Wiley
    Details
    Publication Date: 2018
    Description: Summary Proponents of material recycling typically point to two environmental benefits: disposal (landfill/incinerator) reduction and primary production displacement. However, in this paper we mathematically demonstrate that, without displacement, recycling can delay but not prevent any existing end‐of‐life material from reaching final disposal. The only way to reduce the amount of material ultimately landfilled or incinerated is to produce less in the first place; material that is not made needs not be disposed. Recycling has the potential to reduce the amount of material reaching end of life solely by reducing primary production. Therefore, the “dual benefits” of recycling are in fact one, and the environmental benefit of material recycling rests in its potential to displace primary production. However, displacement of primary production from increased recycling is driven by market forces and is not guaranteed. Improperly assuming all recycled material avoids disposal underestimates the environmental impacts of the product system. We show that the potential magnitude of this error is substantial, though for inert recyclables it is lower than the error introduced by improperly assuming all recycled material displaces primary material production. We argue that life cycle assessment end‐of‐life models need to be updated so as not to overstate the benefits of recycling. Furthermore, scholars and policy makers should focus on finding and implementing ways to increase the displacement potential of recyclable materials rather than focusing on disposal diversion targets.
    Print ISSN: 1088-1980
    Electronic ISSN: 1530-9290
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Wiley
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  • 8
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    Water, Vol. 8, Pages 161: Development of Ecogeomorphological (EGM) Stream Design and Assessment Tools for the Piedmont of Alabama, USA (2016)
    MDPI Publishing
    In: Water
    Details
    Publication Date: 2016-04-21
    Description: Regional data needed for effective stream restoration include hydraulic geometry relationships (i.e., regional curves) and reference channel morphology parameters. Increasingly ecological conditions are being considered when designing, implementing, and assessing restoration efforts. We provide morphology relationships and associated ecological endpoint curves for reference streams in the Alabama piedmont. Twenty-one reference stream reaches were identified in the Tallapoosa drainage of Alabama, ranging from 0.2 to 242 km2 drainage area. Geomorphic surveys were conducted in each stream to measure riffle cross-sections and longitudinal profiles and related to drainage area to develop regional curves. Fish, crayfish, and benthic macroinvertebrates were collected from each surveyed reach and related to drainage area and geomorphic data to provide associated biological community endpoints. Bankfull channel cross-section area, width, mean depth, and estimated discharge were strongly correlated to watershed drainage area, similar to efforts in other areas of the Piedmont ecoregion. Multiple measures of fish assemblages and crayfish size were strongly predicted by drainage area and geomorphic dimensions. Macroinvertebrates showed no taxonomic and limited functional relationships with drainage area and geomorphic dimension. These tools, which integrate geomorphological and ecological conditions, can result in improved stream evaluations and designs increasing the effectiveness of stream restoration projects.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 9
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    Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-16
    Description: Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 x 10 –6 ]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat- Alu (SINE-VNTR- Alu ), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] ( r 2 = 0.999), which showed associations with both the splicing anomalies ( P = 6.5 x 10 –32 ) and with protection against prostate cancer (OR = 0.91, P = 3.8 x 10 –7 ).
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    The runaway instability in general relativistic accretion discs (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-03
    Description: When an accretion disc falls prey to the runaway instability, a large portion of its mass is devoured by the black hole within a few dynamical times. Despite decades of effort, it is still unclear under what conditions such an instability can occur. The technically most advanced relativistic simulations to date were unable to find a clear sign for the onset of the instability. In this work, we present three-dimensional relativistic hydrodynamics simulations of accretion discs around black holes in dynamical space–time. We focus on the configurations that are expected to be particularly prone to the development of this instability. We demonstrate, for the first time, that the fully self-consistent general relativistic evolution does indeed produce a runaway instability.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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