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See detailMultiscale Integration of High-Resolution Spaceborne and Drone-Based Imagery for a High-Accuracy Digital Elevation Model Over Tristan da Cunha
Backes, Dietmar UL; Teferle, Felix Norman UL

in Frontiers in Earth Science (2020)

Very high-resolution (VHR) optical Earth observation (EO) satellites as well as low-altitude and easy-to-use unmanned aerial systems (UAS/drones) provide ever-improving data sources for the generation of ... [more ▼]

Very high-resolution (VHR) optical Earth observation (EO) satellites as well as low-altitude and easy-to-use unmanned aerial systems (UAS/drones) provide ever-improving data sources for the generation of detailed 3-dimensional (3D) data using digital photogrammetric methods with dense image matching. Today both data sources represent cost-effective alternatives to dedicated airborne sensors, especially for remote regions. The latest generation of EO satellites can collect VHR imagery up to 0.30 m ground sample distance (GSD) of even the most remote location from different viewing angles many times per year. Consequently, well-chosen scenes from growing image archives enable the generation of high-resolution digital elevation models (DEMs). Furthermore, low-cost and easy to use drones can be quickly deployed in remote regions to capture blocks of images of local areas. Dense point clouds derived from these methods provide an invaluable data source to fill the gap between globally available low-resolution DEMs and highly accurate terrestrial surveys. Here we investigate the use of archived VHR satellite imagery with approx. 0.5 m GSD as well as low-altitude drone-based imagery with average GSD of better than 0.03 m to generate high-quality DEMs using photogrammetric tools over Tristan da Cunha, a remote island in the South Atlantic Ocean which lies beyond the reach of current commercial manned airborne mapping platforms. This study explores the potentials and limitations to combine this heterogeneous data sources to generate improved DEMs in terms of accuracy and resolution. A cross-validation between low-altitude airborne and spaceborne data sets describes the fit between both optical data sets. No co-registration error, scale difference or distortions were detected, and a quantitative cloud-to-cloud comparison showed an average distance of 0.26 m between both point clouds. Both point clouds were merged applying a conventional georeferenced approach. The merged DEM preserves the rich detail from the drone-based survey and provides an accurate 3D representation of the entire study area. It provides the most detailed model of the island to date, suitable to support practical and scientific applications. This study demonstrates that combination archived VHR satellite and low-altitude drone-based imagery provide inexpensive alternatives to generate high-quality DEMs. [less ▲]

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See detailMultiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology.
Makadia, Hirenkumar K.; Anderson, Warren D.; Fey, Dirk et al

in Biophysical journal (2015), 108(1), 211-23

We developed a multiscale model to bridge neuropeptide receptor-activated signaling pathway activity with membrane electrophysiology. Typically, the neuromodulation of biochemical signaling and biophysics ... [more ▼]

We developed a multiscale model to bridge neuropeptide receptor-activated signaling pathway activity with membrane electrophysiology. Typically, the neuromodulation of biochemical signaling and biophysics have been investigated separately in modeling studies. We studied the effects of Angiotensin II (AngII) on neuronal excitability changes mediated by signaling dynamics and downstream phosphorylation of ion channels. Experiments have shown that AngII binding to the AngII receptor type-1 elicits baseline-dependent regulation of cytosolic Ca(2+) signaling. Our model simulations revealed a baseline Ca(2+)-dependent response to AngII receptor type-1 activation by AngII. Consistent with experimental observations, AngII evoked a rise in Ca(2+) when starting at a low baseline Ca(2+) level, and a decrease in Ca(2+) when starting at a higher baseline. Our analysis predicted that the kinetics of Ca(2+) transport into the endoplasmic reticulum play a critical role in shaping the Ca(2+) response. The Ca(2+) baseline also influenced the AngII-induced excitability changes such that lower Ca(2+) levels were associated with a larger firing rate increase. We examined the relative contributions of signaling kinases protein kinase C and Ca(2+)/Calmodulin-dependent protein kinase II to AngII-mediated excitability changes by simulating activity blockade individually and in combination. We found that protein kinase C selectively controlled firing rate adaptation whereas Ca(2+)/Calmodulin-dependent protein kinase II induced a delayed effect on the firing rate increase. We tested whether signaling kinetics were necessary for the dynamic effects of AngII on excitability by simulating three scenarios of AngII-mediated KDR channel phosphorylation: (1), an increased steady state; (2), a step-change increase; and (3), dynamic modulation. Our results revealed that the kinetics emerging from neuromodulatory activation of the signaling network were required to account for the dynamical changes in excitability. In summary, our integrated multiscale model provides, to our knowledge, a new approach for quantitative investigation of neuromodulatory effects on signaling and electrophysiology. [less ▲]

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See detailMultiscale model of sintering: diffusion and plastic flow
Kabore, Brice Wendlassida UL; Peters, Bernhard UL

Scientific Conference (2017, September 27)

Impacting particles or static aggregated particles at high temperature may undergo a permanent change of shape modifying the microstructure. Two particles in contact can develop some bonds within sub ... [more ▼]

Impacting particles or static aggregated particles at high temperature may undergo a permanent change of shape modifying the microstructure. Two particles in contact can develop some bonds within sub-second time. This fast sintering force in the particular case of the snow contribute to the rheological behavior and grain rearrangement [1]. Understanding the kinetics of sintering in granular material is of great importance in some engineering applications. For decades, diffusional processes have received more attention in investigations related to the mechanisms behind sintering [2]. Some works have suggested that the plastic flow might be neglected in sintering process for stresses are not high enough to cause dislocation. However, some studies have showed that stresses experienced in fine particles necks can be high enough and even lead to plasticity driven sintering. The importance of each mechanism in the sintering process may lie in the temporal and spatial scale of interest. Increasing importance is being accorded to the role of plastic flow in sintering. however, several investigations have proved that the conventional plasticity theory may fail to predict plastic activity at micro-scale, The objective of this work is to develop adequate computational model that includes instantaneous and time-dependent plastic flow at micro-scale. We aim at extending existing models of sintering and plasticity to cope with multiple spatial and temporal scales simulations using Extended Discrete Element Method. The numerical results are compare to experimental data on snow. [less ▲]

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See detailMultiscale Modeling of Discrete Mesomodels for Dry-Woven Fabrics
Magliulo, Marco UL; Beex, Lars UL; Zilian, Andreas UL

Scientific Conference (2018, March)

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See detailMultiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
Thiele, Ines UL; Fleming, Ronan MT UL; Que, Richard et al

in PLoS ONE (2012), 7(9), 45635

Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive ... [more ▼]

Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli's metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors. [less ▲]

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See detailMultiscale modeling of mitochondria
Garcia, Guadalupe Clara UL

Doctoral thesis (2019)

Life is based on energy conversion by which cells and organisms can adapt to the environment. The involved biological processes are intrinsically multiscale phenomena since they are based on molecular ... [more ▼]

Life is based on energy conversion by which cells and organisms can adapt to the environment. The involved biological processes are intrinsically multiscale phenomena since they are based on molecular interactions on a small scale leading to the emerging behavior of cells, organs and organisms. To understand the underlying regulation and to dissect the mechanisms that control system behavior, appropriate mathematical multiscale models are needed. Such models do not only offer the opportunity to test different hypothesized mechanisms but can also address current experimental technology gaps by zooming in and out of the dynamics, changing scales, coarse-graining the dynamics and giving us distinct views of the phenomena. In this dissertation substantial efforts were done to combine different computational modeling strategies based on different assumptions and implications to model an essential system of eukaryotic life -- the energy providing mitochondria -- where the spatiotemporal domain is suspected to have a substantial influence on its function. Mitochondria are highly dynamic organelles that fuse, divide, and are transported along the cytoskeleton to ensure cellular energy homeostasis. These processes cover different scales, in space and time, where on the more global scale mitochondria exhibit changes in their molecular content in response to their physiological context including circadian modulation. On the smaller scales, mitochondria show also faster adaptation by changing their morphology within minutes. For both processes, the relation between the underlying structure of either their regulating network or the spatial morphology and the functional consequences are essential to understand principles of energy homeostasis and their link to health and disease conditions. This thesis focuses on different scales of mitochondrial adaptation. On the small scales, fission and fusion of mitochondria are rather well established but substantial evidence indicates that the internal structure is also highly variable in dependence on metabolic condition. However, a quantitative mechanistic understanding how mitochondrial morphology affects energetic states is still elusive. In the first part of this dissertation I address this question by developing an agent-based dynamic model based on three-dimensional morphologies from electron microscopy tomography, which considers the molecular dynamics of the main ATP production components. This multiscale approach allows for investigating the emergent behavior of the energy generating mechanism in dependence on spatial properties and molecular orchestration. Interestingly, comparing spatiotemporal simulations with a corresponding space-independent approach, I found only minor space dependence in equilibrium conditions but qualitative difference in fluctuating environments and in particular indicate that the morphology provides a mechanism to buffer energy at synapses. On the more global scale of the regulation of mitochondrial protein composition, I applied a data driven approach to explore how mitochondrial activity is changing during the day and how food intake restrictions can effect the structure of the underlying adaptation process. To address the question if at different times of the day, the mitochondrial composition might adapt and have potential implications for function, I analyzed temporal patterns of hepatic transcripts of mice that had either unlimited access to food or were hold under temporal food restrictions. My analysis showed that mitochondrial activity exhibits a temporal activity modulation where different subgroups of elements are active at different time points and that food restriction increases temporal regulation. Overall, this thesis provides new insights into mitochondrial biology at different scales by providing an innovative computational modeling framework to investigate the relation between morphology and energy production as well as by characterizing temporal modulation of the regulatory network structure under different conditions. [less ▲]

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See detailMultiscale Modelling of Damage and Fracture in Discrete Materials Using a Variational Quasicontinuum Method
Rokos, Ondrej; Peerlings, Ron; Beex, Lars UL et al

Scientific Conference (2017, September 05)

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See detailA multiscale partitioned reduced order model applied to damage simulation
Goury, Olivier; Kerfriden, Pierre; Bordas, Stéphane UL

Scientific Conference (2013, July)

Simulating fracture in realistic engineering components is computationally expensive. In the context of early-stage design, or reverse engineering, such simulations might need to be performed for a large ... [more ▼]

Simulating fracture in realistic engineering components is computationally expensive. In the context of early-stage design, or reverse engineering, such simulations might need to be performed for a large range of material and geometric parameters, which makes the solution to the parametric problem of fracture unaffordable. Model order reduction, such as the proper orthogonal decomposition (POD), is one way to reduce significantly the computational time by reducing the number of spatial unknowns. The solution is searched for in a reduced space spanned by a few well-chosen basis vectors only. In the context of solid mechanics involving structural softening, the strong topological changes in the zone where damage localises are extremely sensitive to variations of the parameters, which requires reduced spaces of prohibitively large dimensions in order to approximate the solution with a sufficiently high degree of accuracy. Introduced in [1], partitioned model order reduction is an alternative to global model order reduction that essentially divides up the problem into smaller regions. Each region can then be tackled using a reduced model of appropriate size, if at all, depending on the local material non-linearities in the region. In the context of multiscale homogenization, simulations of representative volume elements (RVE) have to be performed to obtain the material properties in the different elements of a coarse mesh. When considering a nonlinear material, those multiple RVE simulations can be com- putationally very expensive. They however only differ by the history of boundary conditions applied. This contribution proposes to apply partitioned model order reduction to those RVEs with reduced bases parametrized by the boundary conditions. REFERENCES [1] P. Kerfriden, O. Goury, T. Rabczuk, S. Bordas, A partitioned model order reduction approach to rationalise computational expenses in nonlinear fracture mechanics, Computer Methods in Applied Mechanics and Engineering, 256:169–188, 2013. [less ▲]

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See detailMultiscale quasicontinuum approaches for beam lattices
Beex, Lars UL; Peerlings, Ron; Geers, Marc et al

Scientific Conference (2014, July)

The quasicontinuum (QC) method was originally developed to reduce the computational efforts of large-scale atomistic (conservative) lattice computations. QC approaches have an intrinsically multiscale ... [more ▼]

The quasicontinuum (QC) method was originally developed to reduce the computational efforts of large-scale atomistic (conservative) lattice computations. QC approaches have an intrinsically multiscale character, as they combine fully resolved regions in which discrete lattice events can occur, with coarse-grained regions in which the lattice model is interpolated and integrated (summed in QC terminology). In previous works, virtual-power-based QC approaches were developed for dissipative (i.e. non-conservative) lattice computations which can for instance be used for fibrous materials. The virtual-power-based QC approaches have focused on dissipative spring/truss networks, but numerous fibrous materials can more accurately be described by (planar) beam networks. In this presentation, different QC approaches for planar beam lattices are introduced. In contrast to spring/truss lattices, beam networks include not only displacements but also rotations which need to be incorporated in the QC method, resulting in a mixed formulation. Furthermore, the presentation will show that QC approaches for planar beam lattices require higher-order interpolations to obtain accurate results, which also influences the numerical integration (summation in QC terminology). Results using different interpolations and types of integration will be shown for multiscale examples. [less ▲]

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See detailMULTISCALE QUASICONTINUUM APPROACHES FOR DISCRETE MODELS OF FIBROUS MATERIALS SUCH AS ELECTRONIC TEXTILE AND PAPER MATERIALS
Beex, Lars UL; Peerlings, Ron; Geers, Marc et al

Scientific Conference (2014, July 20)

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See detailMultiscale Quasicontinuum Approaches for Planar Beam Lattices
Beex, Lars UL; Kerfriden, Pierre; Bordas, Stéphane UL

Scientific Conference (2014, July)

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See detailA multiscale quasicontinuum method for dissipative lattice models and discrete networks
Beex, Lars UL; Peerlings, Ron; Geers, Marc

in Journal of the Mechanics and Physics of Solids (2014), 64

Lattice models and discrete networks naturally describe mechanical phenomena at the mesoscale of fibrous materials. A disadvantage of lattice models is their computational cost. The quasicontinuum (QC ... [more ▼]

Lattice models and discrete networks naturally describe mechanical phenomena at the mesoscale of fibrous materials. A disadvantage of lattice models is their computational cost. The quasicontinuum (QC) method is a suitable multiscale approach that reduces the computational cost of lattice models and allows the incorporation of local lattice defects in large-scale problems. So far, all QC methods are formulated for conservative (mostly atomistic) lattice models. Lattice models of fibrous materials however, often require non-conservative interactions. In this paper, a QC formulation is derived based on the virtual-power of a non-conservative lattice model. By using the virtual-power statement instead of force-equilibrium, errors in the governing equations of the force-based QC formulations are avoided. Nevertheless, the non-conservative interaction forces can still be directly inserted in the virtual-power QC framework. The summation rules for energy-based QC methods can still be used in the proposed framework as shown by two multiscale examples. [less ▲]

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See detailA multiscale quasicontinuum method for lattice models with bond failure and fiber sliding
Beex, Lars UL; Peerlings, Ron; Geers, Marc

in Computer Methods in Applied Mechanics and Engineering (2014), 269

Structural lattice models incorporating trusses and beams are frequently used to mechanically model fibrous materials, because they can capture (local) mesoscale phenomena. Physically relevant lattice ... [more ▼]

Structural lattice models incorporating trusses and beams are frequently used to mechanically model fibrous materials, because they can capture (local) mesoscale phenomena. Physically relevant lattice computations are however computationally expensive. A suitable multiscale approach to reduce the computational cost of large-scale lattice computations is the quasicontinuum (QC) method. This method resolves local mesoscale phenomena in regions of interest and coarse grains elsewhere, using only the lattice model. In previous work, a virtual-power-based QC framework is proposed for lattice models that include local dissipative mechanisms. In this paper, the virtual-power-based QC method is adopted for lattice models in which bond failure and subsequent frictional fiber sliding are incorporated – which are of significant importance for fibrous materials such as paper, cardboard, textile and electronic textile. Bond failure and fiber sliding are nonlocal dissipative mechanisms and to deal with this nonlocality, the virtual-power-based QC method is equipped with a mixed formulation in which the kinematic variables as well as the internal history variables are interpolated. Previously defined summation rules can still be used to sample the governing equations in this QC framework. Illustrative examples are presented. [less ▲]

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See detailMultiscale Quasicontinuum Methods for Dissipative Truss Models and Beam Networks
Beex, Lars UL; Peerlings, Ron; Geers, Marc et al

Presentation (2014, November 05)

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See detailMultiscale quasicontinuum methods for fibrous materials
Beex, Lars UL; Peerlings, Ron; Geers, Marc et al

Scientific Conference (2014, July)

The QC method was originally proposed for (conservative) atomistic lattice models and is based on energy-minimization. Lattice models for fibrous materials however, are often non-conservative and energy ... [more ▼]

The QC method was originally proposed for (conservative) atomistic lattice models and is based on energy-minimization. Lattice models for fibrous materials however, are often non-conservative and energy-based QC methods can thus not straightforwardly be used. Examples presented here are a lattice model proposed for woven fabrics and a lattice model to describe interfiber bond failure and subsequent frictional fiber slidings. A QC framework is proposed that is based on the virtual-power statement of a non-conservative lattice model. Using the virtual-power statement, dissipative mechanisms can be included in the QC framework while the same summation rules suffice. Its validity is shown for a lattice model with elastoplastic trusses. The virtual-power-based QC method is also adopted to deal with the lattice model for bond failure and subsequent fiber sliding presented. In contrast to elastoplastic interactions that are intrinsically local dissipative mechanisms, bond failure and subsequent fiber sliding entail nonlocal dissipative mechanisms. Therefore, the virtual-power-based QC method is also equipped with a mixed formulation in which not only the displacements are interpolated, but also the internal variables associated with dissipation. [less ▲]

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See detailMultiscale simulations of fracture, mesh burden reduction with applications to surgical simulation
Bordas, Stéphane UL

Presentation (2014, April 10)

ABSTRACT We present recent results aiming at affording faster and error-controlled simulations of multi scale phenomena including fracture of heterogeneous materials and cutting of biological tissue. In a ... [more ▼]

ABSTRACT We present recent results aiming at affording faster and error-controlled simulations of multi scale phenomena including fracture of heterogeneous materials and cutting of biological tissue. In a second part, we describe methodologies to isolate the user from the burden of mesh generation and regeneration as moving boundaries evolve. Results include advances in implicit boundary finite elements, (enriched) isogeometric extended boundary elements/finite element methods for multi-crack propagation and an asynchronous GPU/CPU method for contact and cutting of heterogeneous materials in real-time with applications to surgical simulation. ABOUT THE PRESENTER In 1999, Stéphane Bordas joined a joint graduate programme of the French Institute of Technology (Ecole Spéciale des Travaux Publics) and the American Northwestern University. In 2003, he graduated in Theoretical and Applied Mechanics with a PhD from Northwestern University. Between 2003 and 2006, he was at the Laboratory of Structural and Continuum Mechanics at the Swiss Federal Institute of Technology in Lausanne, Switzerland. In 2006, he became permanent lecturer at Glasgow University’s Civil Engineering Department. Stéphane joined the Computational Mechanics team at Cardiff University in September 2009, as a Professor in Computational Mechanics and directed the institute of Mechanics and Advanced Materials from October 2010 to November 2013. He is the Editor of the book series “Advances in Applied Mechanics” since July 2013. In November 2013, he joined the University of Luxembourg as a Professor in Computational Mechanics. The main axes of his research team include (1) free boundary problems and problems involving complex geometries, in particular moving boundaries and (2) ‘a posteriori’ discretisation and model error control, rationalisation of the computational expense. Stéphane’s keen interest is to actively participate in innovation, technological transfer as well as software tool generation. This has been done through a number of joint ventures with various industrial partners (Bosch GmbH, Cenaero, inuTech GmbH, Siemens-LMS, Soitec SA) and the release of open-source software. In 2012, Stéphane was awarded an ERC Starting Independent Research Grant (RealTcut), to address the need for surgical simulators with a computational mechanics angle with a focus on the multi-scale simulation of cutting of heterogeneous materials in real-time. [less ▲]

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See detailMultiscale-multiphysics approaches for engineering applications
Pozzetti, Gabriele UL; Peters, Bernhard UL

in AIP Conference Proceedings (2017), 1863(1), 180001

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See detailLa multisensorialité dans les oeuvres de science-fiction
Derian, Maxime UL

in Hermès: Cognition, Communication, Politique (2016), 74(1), 209-2013

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See detailMultiset Collision Attacks on Reduced-Round SNOW 3G and SNOW 3G (+)
Biryukov, Alex UL; Priemuth-Schmid, Deike UL; Zhang, Bin UL

in ACNS 2010 (2010)

The stream cipher SNOW 3G designed in 2006 by ETSI/SA-GE is a base algorithm for the second set of 3GPP confidentiality and integrity algorithms. In this paper we study the resynchronization mechanism of ... [more ▼]

The stream cipher SNOW 3G designed in 2006 by ETSI/SA-GE is a base algorithm for the second set of 3GPP confidentiality and integrity algorithms. In this paper we study the resynchronization mechanism of SNOW 3G and of a similar cipher SNOW 3G ⊕  using multiset collision attacks. For SNOW 3G we show a simple 13-round multiset distinguisher with complexity of 28 steps. We show full key recovery chosen IV resynchronization attacks for up to 18 out of 33 initialization rounds of SNOW3G ⊕  with a complexity of 257 to generate the data and 253 steps of analysis. [less ▲]

Detailed reference viewed: 164 (3 UL)