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See detailLes manuels d'introduction au droit: de Capitant à la période contemporaine
Ancel, Pascal UL

in Les manuels de droit (2014)

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See detailLes manuels français d’introduction au droit de Capitant à aujourd’hui
Ancel, Pascal UL

in Les manuels de droit (2014)

Detailed reference viewed: 57 (1 UL)
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See detailManuscriptorium – Bibliothèque nationale tchèque
Vomacka, Eloïse UL

in Revue de l’IFHA (2011)

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See detailMany Independent Objective (MIO) Algorithm for Test Suite Generation
Arcuri, Andrea UL

in Symposium on Search-Based Software Engineering (SSBSE) (2017)

Automatically generating test suites is intrinsically a multi- objective problem, as any of the testing targets (e.g, statements to exe- cute or mutants to kill) is an objective on its own. Test suite ... [more ▼]

Automatically generating test suites is intrinsically a multi- objective problem, as any of the testing targets (e.g, statements to exe- cute or mutants to kill) is an objective on its own. Test suite generation has peculiarities that are quite di erent from other more regular optimi- sation problems. For example, given an existing test suite, one can add more tests to cover the remaining objectives. One would like the smallest number of small tests to cover as many objectives as possible, but that is a secondary goal compared to covering those targets in the rst place. Furthermore, the amount of objectives in software testing can quickly become unmanageable, in the order of (tens/hundreds of) thousands, es- pecially for system testing of industrial size systems. Traditional multi- objective optimisation algorithms can already start to struggle with just four or ve objectives to optimize. To overcome these issues, di erent techniques have been proposed, like for example the Whole Test Suite (WTS) approach and the Many-Objective Sorting Algorithm (MOSA). However, those techniques might not scale well to very large numbers of objectives and limited search budgets (a typical case in system test- ing). In this paper, we propose a novel algorithm, called Many Indepen- dent Objective (MIO) algorithm. This algorithm is designed and tailored based on the speci c properties of test suite generation. An empirical study, on a set of arti cial and actual software, shows that the MIO al- gorithm can achieve higher coverage compared to WTS and MOSA, as it can better exploit the peculiarities of test suite generation. [less ▲]

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See detailMany ways to resistance: How melanoma cells evade targeted therapies
Kozar, Ines UL; Margue, Christiane UL; Rothengatter, Sonja et al

in Biochimica et Biophysica Acta - Reviews on Cancer (2019), 1871(2), 313-322

Melanoma is an aggressive malignancy originating from pigment-producing melanocytes. The development of targeted therapies (MAPK pathway inhibitors) and immunotherapies (immune checkpoint inhibitors) led ... [more ▼]

Melanoma is an aggressive malignancy originating from pigment-producing melanocytes. The development of targeted therapies (MAPK pathway inhibitors) and immunotherapies (immune checkpoint inhibitors) led to a substantial improvement in overall survival of patients. However, the long-term efficacy of such treatments is limited by side effects, lack of clinical effects and the rapidly emerging resistance to treatment. A number of molecular mechanisms underlying this resistant phenotype have already been elucidated. In this review, we summarise currently available treatment options for metastatic melanoma and the known resistance mechanisms to targeted therapies. A focus will be placed on “phenotype switching” as a mechanism and driver of drug resistance, together with an overview of novel approaches to circumvent resistance. A large body of recent data and literature suggests that tumour progression and phenotype switching could be better controlled and development of resistance prevented or at least delayed, by combining drugs targeting fast- and slow-proliferating cells. [less ▲]

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See detailMany-Body Descriptors for Predicting Molecular Properties with Machine Learning: Analysis of Pairwise and Three-Body Interactions in Molecules
Pronobis, Wiktor; Tkatchenko, Alexandre UL; Müller, Klaus-Robert

in Journal of Chemical Theory and Computation (2018), 14

Machine learning (ML) based prediction of molecular properties across chemical compound space is an important and alternative approach to efficiently estimate the solutions of highly complex many-electron ... [more ▼]

Machine learning (ML) based prediction of molecular properties across chemical compound space is an important and alternative approach to efficiently estimate the solutions of highly complex many-electron problems in chemistry and physics. Statistical methods represent molecules as descriptors that should encode molecular symmetries and interactions between atoms. Many such descriptors have been proposed; all of them have advantages and limitations. Here, we propose a set of general two-body and three-body interaction descriptors which are invariant to translation, rotation, and atomic indexing. By adapting the successfully used kernel ridge regression methods of machine learning, we evaluate our descriptors on predicting several properties of small organic molecules calculated using density-functional theory. We use two data sets. The GDB-7 set contains 6868 molecules with up to 7 heavy atoms of type CNO. The GDB-9 set is composed of 131722 molecules with up to 9 heavy atoms containing CNO. When trained on 5000 random molecules, our best model achieves an accuracy of 0.8 kcal/mol (on the remaining 1868 molecules of GDB-7) and 1.5 kcal/mol (on the remaining 126722 molecules of GDB-9) respectively. Applying a linear regression model on our novel many-body descriptors performs almost equal to a nonlinear kernelized model. Linear models are readily interpretable: a feature importance ranking measure helps to obtain qualitative and quantitative insights on the importance of two- and three-body molecular interactions for predicting molecular properties computed with quantum-mechanical methods. [less ▲]

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See detailMany-body dispersion effects in the binding of adsorbates on metal surfaces
Maurer, Reinhard J.; Ruiz, Victor G.; Tkatchenko, Alexandre UL

in JOURNAL OF CHEMICAL PHYSICS (2015), 143(10),

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we ... [more ▼]

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic-inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate-surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches. (C) 2015 AIP Publishing LLC. [less ▲]

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See detailMany-Body Dispersion Interactions in Molecular Crystal Polymorphism
Marom, Noa; DiStasio, Jr; Atalla, Viktor et al

in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013), 52(26), 6629-6632

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See detailMany-Body Perturbation Theory Approach to Raman Spectroscopy and Its Application to 2D Materials
Reichardt, Sven UL

Doctoral thesis (2018)

Raman spectroscopy has become one of the most important techniques for the characterization of materials, as it allows the simultaneous probing of several properties, such as electronic and vibrational ... [more ▼]

Raman spectroscopy has become one of the most important techniques for the characterization of materials, as it allows the simultaneous probing of several properties, such as electronic and vibrational excitations, at once. This versatility, however, makes its theoretical description very challenging and, up to now, no fully satisfactory and general way for the calculation of Raman spectra from first principles exists. In this thesis, we aim to fill this gap and present a coherent theory of Raman scattering within the framework of many-body perturbation theory. We develop a novel and general, correlation function-based approach for the calculation of Raman scattering rates that can potentially also be applied to ultra-fast Raman spectroscopy out of equilibrium. Besides these theoretical developments, we present concrete computational recipes for the calculation of Raman intensities that allow the inclusion of both excitonic effects and non-adiabatic effects of lattice vibrations. The latter has so far not been possible with state-of-the-art methods, which can only take into account one of the two effects. As a first test case, we apply our theory to graphene, for which we use it to study the laser frequency and Fermi energy dependence of the Raman G-peak intensity. The flexibility of our approach also allows us to demonstrate that non-resonant processes and quantum mechanical interference effects play a significant role in Raman scattering. This applies not only to graphene but also to other two-dimensional materials of current interest, such as MoTe2 and MoS2. In addition to the development of a consistent and comprehensive description of Raman scattering, we derive a novel approach for the calculation of phonon frequencies and the screened electron-phonon coupling. It can be applied also to strongly correlated systems, for which the currently used methods are not entirely satisfactory or insufficient. Our new method goes beyond the limitations of the methods currently in use and will permit the computation of phonon-related quantities also in systems with strong correlation effects such as Kohn anomalies (e.g., graphene) or Peierls instabilities. Lastly, we present work on the application of (magneto-)Raman spectroscopy as a probe for many-body effects in graphene. Here we focus on the description of the phenomenon of magneto-phonon resonances and how it can be used to probe electronic excitation energies and to extract electron and phonon lifetimes. [less ▲]

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See detailMany-body van der Waals interactions in molecules and condensed matter
Distasio, R. A.; Gobre, V. V.; Tkatchenko, Alexandre UL

in Journal of Physics Condensed Matter (2014), 26(21),

This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology ... [more ▼]

This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions - both captured at the MBD level of theory - play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored. © 2014 IOP Publishing Ltd. [less ▲]

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See detailMaori lexical items in the mainstream television news in New Zealand
De Bres, Julia UL

in New Zealand English Journal (2006), 20

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See detailmapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
Jonsson, Hakon; Ginolhac, Aurélien UL; Schubert, Mikkel et al

in Bioinformatics (Oxford, England) (2013), 29(13), 1682-4

MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary ... [more ▼]

MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples. RESULTS: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (lambda), nick frequency (nu) and cytosine deamination rates in both double-stranded regions ( ) and overhangs ( ). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. AVAILABILITY: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. [less ▲]

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See detailmapDamage: testing for damage patterns in ancient DNA sequences.
Ginolhac, Aurélien UL; Rasmussen, Morten; Gilbert, M. Thomas P. et al

in Bioinformatics (Oxford, England) (2011), 27(15), 2153-5

SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage ... [more ▼]

SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. AVAILABILITY AND IMPLEMENTATION: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems. [less ▲]

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See detailMapping a Space of Biography: Karl Triebold and the Waldschule of Senne I-Bielefeld (c. 1923-1939)
Thyssen, Geert UL

in History of Education (2012), 41(4), 457-467

Detailed reference viewed: 202 (2 UL)
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See detailMapping and load balancing on distributed memory systems
Bouvry, Pascal UL; Chassin, J.; Dobrucky, M. et al

in µP'94, Eight Symposium on Computer and Microprocessor Applications (1994)

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See detailMapping antipsychiatry. Elemente für die Geschichte einer transnationalen Bewegung
Majerus, Benoît UL

in Themenportal Europäische Geschichte (2010)

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See detailMapping Combinational Circuits to Homogenous Trellis-Constrained Codes
Franck, Christian UL

Poster (2017, July)

Detailed reference viewed: 145 (20 UL)